Starting phenix.real_space_refine
on Sat Aug 23 08:51:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5x0m_6698/08_2025/5x0m_6698.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5x0m_6698/08_2025/5x0m_6698.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/5x0m_6698/08_2025/5x0m_6698.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5x0m_6698/08_2025/5x0m_6698.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/5x0m_6698/08_2025/5x0m_6698.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5x0m_6698/08_2025/5x0m_6698.map"
  }
  resolution = 3.8
  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=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      62      5.16       5
     C    7031      2.51       5
     N    1683      2.21       5
     O    1878      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10654
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 10395
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1323, 10395
          Classifications: {'peptide': 1323}
          Incomplete info: {'truncation_to_alanine': 122}
          Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 45, 'TRANS': 1274}
          Chain breaks: 2
          Unresolved chain link angles: 10
          Unresolved non-hydrogen bonds: 445
          Unresolved non-hydrogen angles: 566
          Unresolved non-hydrogen dihedrals: 376
          Unresolved non-hydrogen chiralities: 34
          Planarities with less than four sites: {'ASP:plan': 11, 'ARG:plan': 12, 'ASN:plan1': 5, 'HIS:plan': 1, 'GLN:plan1': 7, 'GLU:plan': 6, 'PHE:plan': 8, 'TYR:plan': 1, 'TRP:plan': 3}
          Unresolved non-hydrogen planarities: 247
    Chain: "B"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 3, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "D"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "E"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "F"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "G"
      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: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.89, per 1000 atoms: 0.27
  Number of scatterers: 10654
  At special positions: 0
  Unit cell: (131.58, 130.29, 125.13, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      62     16.00
     O    1878      8.00
     N    1683      7.00
     C    7031      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 288 " - pdb=" SG  CYS A 337 " distance=2.24
    Simple disulfide: pdb=" SG  CYS A 328 " - pdb=" SG  CYS A 343 " distance=1.72
    Simple disulfide: pdb=" SG  CYS A 709 " - pdb=" SG  CYS A 717 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A1011 " - pdb=" SG  CYS A1030 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A1368 " - pdb=" SG  CYS A1381 " distance=1.83

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-3
      " BMA B   3 " - " BMA B   4 "
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG B   2 " - " BMA B   3 "
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " BMA F   3 "
      " NAG G   1 " - " NAG G   2 "
    BETA1-6
      " BMA B   3 " - " BMA B   5 "
    NAG-ASN
      " NAG A1606 " - " ASN A1028 "
      " NAG B   1 " - " ASN A 330 "
      " NAG C   1 " - " ASN A1034 "
      " NAG D   1 " - " ASN A1015 "
      " NAG E   1 " - " ASN A 312 "
      " NAG F   1 " - " ASN A 308 "
      " NAG G   1 " - " ASN A 300 "
  Time building additional restraints: 1.12
  Conformation dependent library (CDL) restraints added in 489.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2514

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 4 sheets defined
      69.2% alpha, 1.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...
    Processing helix  chain 'A' and resid 47 through 59
    Processing helix  chain 'A' and resid 94 through 110
    Processing helix  chain 'A' and resid 128 through 139
    Processing helix  chain 'A' and resid 139 through 159
      removed outlier: 4.053A  pdb=" N   SER A 143 " --> pdb=" O   GLN A 139 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   MET A 147 " --> pdb=" O   SER A 143 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   MET A 159 " --> pdb=" O   ILE A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 187
      removed outlier: 3.764A  pdb=" N   PHE A 172 " --> pdb=" O   LEU A 168 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   LEU A 173 " --> pdb=" O   GLU A 169 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   SER A 174 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   VAL A 181 " --> pdb=" O   THR A 177 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   LYS A 183 " --> pdb=" O   GLU A 179 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   VAL A 184 " --> pdb=" O   VAL A 180 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   ARG A 187 " --> pdb=" O   LYS A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 197
    Processing helix  chain 'A' and resid 202 through 215
      removed outlier: 3.647A  pdb=" N   THR A 209 " --> pdb=" O   ASP A 205 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ILE A 211 " --> pdb=" O   LEU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 241
      removed outlier: 3.565A  pdb=" N   ARG A 230 " --> pdb=" O   ARG A 227 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   VAL A 231 " --> pdb=" O   ALA A 228 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   LEU A 232 " --> pdb=" O   PHE A 229 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   VAL A 238 " --> pdb=" O   TRP A 235 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ILE A 240 " --> pdb=" O   THR A 237 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   VAL A 241 " --> pdb=" O   VAL A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 256
      removed outlier: 3.670A  pdb=" N   THR A 256 " --> pdb=" O   SER A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 281
      removed outlier: 4.123A  pdb=" N   LEU A 261 " --> pdb=" O   SER A 257 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   LEU A 264 " --> pdb=" O   ASP A 260 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   PHE A 267 " --> pdb=" O   LEU A 263 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   PHE A 270 " --> pdb=" O   LEU A 266 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   PHE A 272 " --> pdb=" O   SER A 268 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   VAL A 274 " --> pdb=" O   PHE A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 310
    Processing helix  chain 'A' and resid 360 through 374
      removed outlier: 3.703A  pdb=" N   ALA A 364 " --> pdb=" O   THR A 360 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   LEU A 366 " --> pdb=" O   GLY A 362 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   VAL A 368 " --> pdb=" O   ALA A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 388
      removed outlier: 4.065A  pdb=" N   LEU A 380 " --> pdb=" O   TYR A 376 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   ALA A 384 " --> pdb=" O   LEU A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 403
      removed outlier: 3.543A  pdb=" N   ILE A 398 " --> pdb=" O   LEU A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 435
      removed outlier: 3.581A  pdb=" N   LEU A 412 " --> pdb=" O   LEU A 408 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   MET A 422 " --> pdb=" O   SER A 418 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   GLU A 428 " --> pdb=" O   LYS A 424 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   GLU A 429 " --> pdb=" O   ARG A 425 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   ARG A 434 " --> pdb=" O   LYS A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 518
    Processing helix  chain 'A' and resid 520 through 537
      removed outlier: 3.861A  pdb=" N   THR A 534 " --> pdb=" O   VAL A 530 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 573
      removed outlier: 3.803A  pdb=" N   ASN A 555 " --> pdb=" O   LEU A 551 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   TYR A 556 " --> pdb=" O   ARG A 552 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   SER A 560 " --> pdb=" O   TYR A 556 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ILE A 561 " --> pdb=" O   ILE A 557 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ILE A 571 " --> pdb=" O   VAL A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 574 through 579
    Processing helix  chain 'A' and resid 581 through 604
      removed outlier: 3.989A  pdb=" N   VAL A 591 " --> pdb=" O   ASP A 587 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   PHE A 593 " --> pdb=" O   ILE A 589 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   GLY A 599 " --> pdb=" O   ILE A 595 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   GLU A 601 " --> pdb=" O   GLU A 597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 606 through 618
      removed outlier: 3.617A  pdb=" N   PHE A 609 " --> pdb=" O   LEU A 606 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   PHE A 612 " --> pdb=" O   PHE A 609 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 624
      removed outlier: 4.112A  pdb=" N   PHE A 623 " --> pdb=" O   ARG A 619 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 625 through 635
      removed outlier: 3.515A  pdb=" N   VAL A 633 " --> pdb=" O   ASN A 629 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   MET A 634 " --> pdb=" O   PHE A 630 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   THR A 635 " --> pdb=" O   MET A 631 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 639 through 663
      removed outlier: 3.613A  pdb=" N   ILE A 658 " --> pdb=" O   ILE A 654 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 666 through 671
      removed outlier: 3.742A  pdb=" N   MET A 671 " --> pdb=" O   TYR A 667 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 700
      removed outlier: 4.047A  pdb=" N   VAL A 694 " --> pdb=" O   SER A 690 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ALA A 697 " --> pdb=" O   ILE A 693 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 702 through 714
      removed outlier: 3.550A  pdb=" N   MET A 706 " --> pdb=" O   TRP A 702 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   MET A 710 " --> pdb=" O   MET A 706 " (cutoff:3.500A)
      removed outlier: 4.561A  pdb=" N   VAL A 712 " --> pdb=" O   ASP A 708 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ASP A 714 " --> pdb=" O   MET A 710 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 717 through 724
    Processing helix  chain 'A' and resid 728 through 733
    Processing helix  chain 'A' and resid 734 through 744
      removed outlier: 3.582A  pdb=" N   LEU A 740 " --> pdb=" O   LEU A 736 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 834 through 855
      removed outlier: 4.307A  pdb=" N   GLN A 839 " --> pdb=" O   ASP A 835 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   LYS A 854 " --> pdb=" O   PHE A 850 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   ASN A 855 " --> pdb=" O   LEU A 851 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 855 through 875
      removed outlier: 3.940A  pdb=" N   PHE A 861 " --> pdb=" O   TYR A 857 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   VAL A 865 " --> pdb=" O   PHE A 861 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   LEU A 875 " --> pdb=" O   VAL A 871 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 884 through 912
      removed outlier: 3.973A  pdb=" N   LEU A 891 " --> pdb=" O   VAL A 887 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   THR A 898 " --> pdb=" O   ASP A 894 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   ILE A 903 " --> pdb=" O   ALA A 899 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   VAL A 912 " --> pdb=" O   MET A 908 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 913 through 918
      removed outlier: 3.511A  pdb=" N   PHE A 918 " --> pdb=" O   PHE A 914 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 920 through 938
      removed outlier: 3.821A  pdb=" N   ASP A 926 " --> pdb=" O   TRP A 922 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   VAL A 929 " --> pdb=" O   LEU A 925 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ASN A 936 " --> pdb=" O   ALA A 932 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   PHE A 937 " --> pdb=" O   TYR A 933 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 949 through 953
    Processing helix  chain 'A' and resid 954 through 957
      removed outlier: 3.556A  pdb=" N   ARG A 957 " --> pdb=" O   ARG A 954 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 954 through 957'
    Processing helix  chain 'A' and resid 958 through 963
      removed outlier: 3.791A  pdb=" N   LEU A 962 " --> pdb=" O   LEU A 958 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 968 through 1002
      removed outlier: 3.503A  pdb=" N   GLU A 977 " --> pdb=" O   SER A 973 " (cutoff:3.500A)
      Proline residue:  A 980  - end of helix
      removed outlier: 3.710A  pdb=" N   LEU A 987 " --> pdb=" O   PHE A 983 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   VAL A 988 " --> pdb=" O   ASN A 984 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   PHE A 991 " --> pdb=" O   LEU A 987 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   TRP A 993 " --> pdb=" O   GLY A 989 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ILE A 998 " --> pdb=" O   LEU A 994 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1026 through 1032
      removed outlier: 3.817A  pdb=" N   CYS A1030 " --> pdb=" O   ASP A1026 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1047 through 1059
      removed outlier: 4.148A  pdb=" N   VAL A1057 " --> pdb=" O   SER A1053 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1062 through 1073
      removed outlier: 4.044A  pdb=" N   ASP A1069 " --> pdb=" O   GLN A1065 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1086 through 1089
    Processing helix  chain 'A' and resid 1090 through 1101
      removed outlier: 3.518A  pdb=" N   PHE A1094 " --> pdb=" O   LEU A1090 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   PHE A1098 " --> pdb=" O   PHE A1094 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1107 through 1124
      removed outlier: 4.416A  pdb=" N   ASP A1113 " --> pdb=" O   CYS A1109 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   GLN A1117 " --> pdb=" O   ASP A1113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1132 through 1146
      removed outlier: 4.066A  pdb=" N   ALA A1146 " --> pdb=" O   ARG A1142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1159 through 1168
      removed outlier: 3.851A  pdb=" N   MET A1163 " --> pdb=" O   PRO A1159 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   TYR A1164 " --> pdb=" O   GLN A1160 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   VAL A1168 " --> pdb=" O   TYR A1164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1171 through 1188
      removed outlier: 3.784A  pdb=" N   MET A1187 " --> pdb=" O   ASN A1183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1194 through 1225
      removed outlier: 4.275A  pdb=" N   PHE A1198 " --> pdb=" O   GLN A1194 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   SER A1199 " --> pdb=" O   SER A1195 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   VAL A1201 " --> pdb=" O   GLU A1197 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ILE A1210 " --> pdb=" O   ASN A1206 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ILE A1211 " --> pdb=" O   LEU A1207 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   VAL A1218 " --> pdb=" O   PHE A1214 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   GLY A1223 " --> pdb=" O   ILE A1219 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   LEU A1224 " --> pdb=" O   LYS A1220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1231 through 1249
      removed outlier: 3.821A  pdb=" N   VAL A1241 " --> pdb=" O   ASP A1237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1260 through 1271
      removed outlier: 4.057A  pdb=" N   LEU A1264 " --> pdb=" O   SER A1260 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ARG A1265 " --> pdb=" O   PRO A1261 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ARG A1268 " --> pdb=" O   LEU A1264 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ARG A1271 " --> pdb=" O   LEU A1267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1272 through 1278
      removed outlier: 3.662A  pdb=" N   LEU A1275 " --> pdb=" O   VAL A1272 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   LEU A1276 " --> pdb=" O   GLY A1273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1288 through 1319
      removed outlier: 3.580A  pdb=" N   ARG A1293 " --> pdb=" O   LEU A1289 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   ARG A1297 " --> pdb=" O   ARG A1293 " (cutoff:3.500A)
      removed outlier: 5.599A  pdb=" N   THR A1298 " --> pdb=" O   LYS A1294 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LEU A1305 " --> pdb=" O   ASN A1301 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   VAL A1315 " --> pdb=" O   PHE A1311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1340 through 1351
      removed outlier: 3.818A  pdb=" N   LEU A1346 " --> pdb=" O   SER A1342 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   GLN A1348 " --> pdb=" O   ILE A1344 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   THR A1351 " --> pdb=" O   PHE A1347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1354 through 1363
      removed outlier: 3.605A  pdb=" N   VAL A1358 " --> pdb=" O   GLY A1354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1384 through 1396
      removed outlier: 3.593A  pdb=" N   ALA A1389 " --> pdb=" O   ALA A1385 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   TYR A1390 " --> pdb=" O   LEU A1386 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   SER A1393 " --> pdb=" O   ALA A1389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1401 through 1424
      removed outlier: 3.916A  pdb=" N   ALA A1407 " --> pdb=" O   ILE A1403 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   ILE A1410 " --> pdb=" O   TYR A1406 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   TYR A1418 " --> pdb=" O   VAL A1414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1426 through 1441
      removed outlier: 4.052A  pdb=" N   TYR A1430 " --> pdb=" O   THR A1426 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1452 through 1459
    Processing helix  chain 'A' and resid 1470 through 1475
    Processing helix  chain 'A' and resid 1489 through 1505
    Processing helix  chain 'A' and resid 1508 through 1521
      removed outlier: 3.582A  pdb=" N   ASP A1512 " --> pdb=" O   VAL A1508 " (cutoff:3.500A)
      Proline residue:  A1516  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 67
    Processing sheet with id=AA2, first strand: chain 'A' and resid 287 through 290
      removed outlier: 3.569A  pdb=" N   LYS A 287 " --> pdb=" O   LEU A 344 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LEU A 344 " --> pdb=" O   LYS A 287 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1012 through 1013
      removed outlier: 3.510A  pdb=" N   ASP A1013 " --> pdb=" O   THR A1017 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   THR A1017 " --> pdb=" O   ASP A1013 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1447 through 1449

    549 hydrogen bonds defined for protein.
    1584 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: 1.69

  Time building geometry restraints manager: 1.45 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1794
        1.32 -     1.45: 3059
        1.45 -     1.57: 5966
        1.57 -     1.69: 3
        1.69 -     1.82: 105
  Bond restraints: 10927
  Sorted by residual:
  bond pdb=" C   ASP A1072 "
       pdb=" N   SER A1073 "
    ideal  model  delta    sigma   weight residual
    1.330  1.574 -0.243 1.42e-02 4.96e+03 2.94e+02
  bond pdb=" C   LEU A 935 "
       pdb=" N   ASN A 936 "
    ideal  model  delta    sigma   weight residual
    1.334  1.485 -0.151 1.33e-02 5.65e+03 1.29e+02
  bond pdb=" C   VAL A1047 "
       pdb=" N   GLY A1048 "
    ideal  model  delta    sigma   weight residual
    1.335  1.231  0.104 1.26e-02 6.30e+03 6.77e+01
  bond pdb=" C   PHE A 674 "
       pdb=" N   PRO A 675 "
    ideal  model  delta    sigma   weight residual
    1.334  1.493 -0.160 2.34e-02 1.83e+03 4.65e+01
  bond pdb=" C   SER A 574 "
       pdb=" N   PRO A 575 "
    ideal  model  delta    sigma   weight residual
    1.335  1.421 -0.086 1.30e-02 5.92e+03 4.36e+01
  ... (remaining 10922 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.53: 14546
        3.53 -     7.05: 250
        7.05 -    10.58: 54
       10.58 -    14.11: 7
       14.11 -    17.63: 17
  Bond angle restraints: 14874
  Sorted by residual:
  angle pdb=" CA  VAL A 503 "
        pdb=" C   VAL A 503 "
        pdb=" N   PRO A 504 "
      ideal   model   delta    sigma   weight residual
     120.83  114.03    6.80 6.10e-01 2.69e+00 1.24e+02
  angle pdb=" CA  ASP A1072 "
        pdb=" C   ASP A1072 "
        pdb=" N   SER A1073 "
      ideal   model   delta    sigma   weight residual
     118.36  104.60   13.76 1.33e+00 5.65e-01 1.07e+02
  angle pdb=" CA  PRO A 519 "
        pdb=" N   PRO A 519 "
        pdb=" CD  PRO A 519 "
      ideal   model   delta    sigma   weight residual
     112.00   99.57   12.43 1.40e+00 5.10e-01 7.88e+01
  angle pdb=" CA  VAL A1047 "
        pdb=" C   VAL A1047 "
        pdb=" N   GLY A1048 "
      ideal   model   delta    sigma   weight residual
     117.27  130.68  -13.41 1.51e+00 4.39e-01 7.88e+01
  angle pdb=" O   ASP A1072 "
        pdb=" C   ASP A1072 "
        pdb=" N   SER A1073 "
      ideal   model   delta    sigma   weight residual
     122.41  134.39  -11.98 1.42e+00 4.96e-01 7.12e+01
  ... (remaining 14869 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.78: 5871
       26.78 -    53.57: 509
       53.57 -    80.35: 135
       80.35 -   107.13: 58
      107.13 -   133.91: 14
  Dihedral angle restraints: 6587
    sinusoidal: 2692
      harmonic: 3895
  Sorted by residual:
  dihedral pdb=" CA  TRP A 121 "
           pdb=" C   TRP A 121 "
           pdb=" N   MET A 122 "
           pdb=" CA  MET A 122 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -46.09 -133.91     0      5.00e+00 4.00e-02 7.17e+02
  dihedral pdb=" CA  GLY A 605 "
           pdb=" C   GLY A 605 "
           pdb=" N   LEU A 606 "
           pdb=" CA  LEU A 606 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   58.11  121.89     0      5.00e+00 4.00e-02 5.94e+02
  dihedral pdb=" CA  CYS A1157 "
           pdb=" C   CYS A1157 "
           pdb=" N   HIS A1158 "
           pdb=" CA  HIS A1158 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   75.27  104.73     0      5.00e+00 4.00e-02 4.39e+02
  ... (remaining 6584 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.131: 1707
       0.131 -    0.261: 47
       0.261 -    0.392: 8
       0.392 -    0.522: 2
       0.522 -    0.653: 1
  Chirality restraints: 1765
  Sorted by residual:
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN A1015 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.75   -0.65 2.00e-01 2.50e+01 1.07e+01
  chirality pdb=" CA  PRO A 719 "
            pdb=" N   PRO A 719 "
            pdb=" C   PRO A 719 "
            pdb=" CB  PRO A 719 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.28    0.44 2.00e-01 2.50e+01 4.80e+00
  chirality pdb=" CA  PRO A 575 "
            pdb=" N   PRO A 575 "
            pdb=" C   PRO A 575 "
            pdb=" CB  PRO A 575 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.29    0.43 2.00e-01 2.50e+01 4.53e+00
  ... (remaining 1762 not shown)

  Planarity restraints: 1825
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 245 "   -1.054 9.50e-02 1.11e+02   4.72e-01 1.35e+02
        pdb=" NE  ARG A 245 "    0.063 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 245 "    0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 245 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 245 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 935 "    0.041 2.00e-02 2.50e+03   7.35e-02 5.41e+01
        pdb=" C   LEU A 935 "   -0.127 2.00e-02 2.50e+03
        pdb=" O   LEU A 935 "    0.048 2.00e-02 2.50e+03
        pdb=" N   ASN A 936 "    0.039 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 330 "    0.049 2.00e-02 2.50e+03   5.50e-02 3.78e+01
        pdb=" CG  ASN A 330 "   -0.018 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 330 "   -0.007 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 330 "   -0.089 2.00e-02 2.50e+03
        pdb=" C1  NAG B   1 "    0.066 2.00e-02 2.50e+03
  ... (remaining 1822 not shown)

  Histogram of nonbonded interaction distances:
        1.97 -     2.55: 144
        2.55 -     3.14: 9304
        3.14 -     3.73: 15820
        3.73 -     4.31: 22555
        4.31 -     4.90: 33847
  Nonbonded interactions: 81670
  Sorted by model distance:
  nonbonded pdb=" SD  MET A1477 "
            pdb=" OD2 ASP A1499 "
     model   vdw
     1.965 3.400
  nonbonded pdb=" O   LEU A 531 "
            pdb=" OG1 THR A 534 "
     model   vdw
     1.973 3.040
  nonbonded pdb=" CE1 PHE A 401 "
            pdb=" OH  TYR A1406 "
     model   vdw
     2.009 3.340
  nonbonded pdb=" O   ILE A1330 "
            pdb=" N   ASP A1332 "
     model   vdw
     2.025 3.120
  nonbonded pdb=" O   GLY A 221 "
            pdb=" ND1 HIS A 222 "
     model   vdw
     2.025 3.120
  ... (remaining 81665 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 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.570
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     11.880
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5675
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      :  0.010   0.307  10952  Z= 0.555
  Angle     :  1.475  29.579  14944  Z= 0.902
  Chirality :  0.059   0.653   1765
  Planarity :  0.013   0.472   1818
  Dihedral  : 24.001 133.913   4058
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 54.20
  Ramachandran Plot:
    Outliers :  5.24 %
    Allowed  : 12.91 %
    Favored  : 81.85 %
  Rotamer:
    Outliers : 11.48 %
    Allowed  : 12.14 %
    Favored  : 76.38 %
  Cbeta Deviations :  0.16 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.08 %
    Twisted Proline : 48.94 %
    Twisted General : 7.70 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.95 (0.16), residues: 1317
  helix: -3.44 (0.12), residues: 821
  sheet:  None (None), residues: 0
  loop : -4.70 (0.20), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 305 
 TYR   0.081   0.002   TYR A1089 
 PHE   0.036   0.001   PHE A 684 
 TRP   0.048   0.002   TRP A 316 
 HIS   0.012   0.002   HIS A 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00862 (10927)
  covalent geometry    : angle       1.40698 (14874)
  SS BOND              : bond        0.18901 (    5)
  SS BOND              : angle      11.37339 (   10)
  hydrogen bonds       : bond        0.30330 (  549)
  hydrogen bonds       : angle      11.03970 ( 1584)
  link_BETA1-3         : bond        0.00305 (    1)
  link_BETA1-3         : angle       2.31723 (    3)
  link_BETA1-4         : bond        0.00663 (   11)
  link_BETA1-4         : angle       4.48506 (   33)
  link_BETA1-6         : bond        0.00219 (    1)
  link_BETA1-6         : angle       3.29527 (    3)
  link_NAG-ASN         : bond        0.01327 (    7)
  link_NAG-ASN         : angle       7.13685 (   21)

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

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

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  501 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 121
    poor density    : 380
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 PHE cc_start: 0.6576 (t80) cc_final: 0.5715 (m-80)
REVERT: A  183 LYS cc_start: 0.8446 (mmtt) cc_final: 0.7788 (mtmt)
REVERT: A  219 ASP cc_start: 0.0666 (OUTLIER) cc_final: 0.0054 (t0)
REVERT: A  227 ARG cc_start: 0.6226 (mmt90) cc_final: 0.6004 (mmt180)
REVERT: A  259 LYS cc_start: 0.2473 (OUTLIER) cc_final: 0.1820 (mtmt)
REVERT: A  281 MET cc_start: 0.7065 (ttp) cc_final: 0.6278 (ttm)
REVERT: A  331 SER cc_start: 0.6957 (m) cc_final: 0.6741 (t)
REVERT: A  379 ASP cc_start: 0.5424 (OUTLIER) cc_final: 0.5114 (t0)
REVERT: A  425 ARG cc_start: 0.4644 (OUTLIER) cc_final: 0.4195 (ttm-80)
REVERT: A  556 TYR cc_start: 0.8356 (m-80) cc_final: 0.6459 (t80)
REVERT: A  557 ILE cc_start: 0.8727 (mt) cc_final: 0.8349 (mt)
REVERT: A  590 ILE cc_start: 0.7398 (mm) cc_final: 0.7171 (mt)
REVERT: A  613 ARG cc_start: 0.8334 (mtt180) cc_final: 0.7611 (ttm110)
REVERT: A  631 MET cc_start: 0.6904 (tpt) cc_final: 0.6377 (tmm)
REVERT: A  706 MET cc_start: 0.7510 (ttp) cc_final: 0.6787 (ttp)
REVERT: A  711 LEU cc_start: 0.7357 (tm) cc_final: 0.6322 (tm)
REVERT: A  735 LEU cc_start: 0.6008 (tp) cc_final: 0.5387 (tt)
REVERT: A  854 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.6219 (mmtm)
REVERT: A  856 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7333 (ptpt)
REVERT: A  905 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.7695 (tpp)
REVERT: A  966 ASN cc_start: 0.5686 (OUTLIER) cc_final: 0.5024 (t0)
REVERT: A 1003 LEU cc_start: 0.4543 (OUTLIER) cc_final: 0.4294 (pp)
REVERT: A 1010 LYS cc_start: 0.7082 (OUTLIER) cc_final: 0.6811 (pttm)
REVERT: A 1015 ASN cc_start: 0.6776 (m-40) cc_final: 0.6505 (m-40)
REVERT: A 1017 THR cc_start: 0.6255 (p) cc_final: 0.5519 (m)
REVERT: A 1032 HIS cc_start: 0.6870 (t70) cc_final: 0.6592 (t70)
REVERT: A 1074 ARG cc_start: 0.7304 (pmt-80) cc_final: 0.6546 (pmt-80)
REVERT: A 1125 LEU cc_start: 0.4952 (OUTLIER) cc_final: 0.3200 (mt)
REVERT: A 1131 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.6762 (tpt170)
REVERT: A 1134 LEU cc_start: 0.8728 (mt) cc_final: 0.8497 (mt)
REVERT: A 1135 ILE cc_start: 0.8360 (mt) cc_final: 0.7973 (mt)
REVERT: A 1136 TYR cc_start: 0.7168 (m-80) cc_final: 0.6914 (m-80)
REVERT: A 1147 LYS cc_start: 0.8683 (mttt) cc_final: 0.8433 (mmtt)
REVERT: A 1149 VAL cc_start: 0.7673 (t) cc_final: 0.7169 (t)
REVERT: A 1156 THR cc_start: 0.6576 (OUTLIER) cc_final: 0.6209 (m)
REVERT: A 1170 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.6442 (ttp80)
REVERT: A 1187 MET cc_start: 0.6390 (mtm) cc_final: 0.5825 (mtm)
REVERT: A 1197 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7450 (mt-10)
REVERT: A 1258 PHE cc_start: 0.5884 (OUTLIER) cc_final: 0.5517 (m-80)
REVERT: A 1268 ARG cc_start: 0.7180 (ttp-170) cc_final: 0.6810 (ttp80)
REVERT: A 1276 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7091 (mt)
REVERT: A 1277 ARG cc_start: 0.6410 (OUTLIER) cc_final: 0.6157 (mtt180)
REVERT: A 1310 MET cc_start: 0.6467 (OUTLIER) cc_final: 0.6109 (mtp)
REVERT: A 1316 PHE cc_start: 0.6896 (OUTLIER) cc_final: 0.5988 (m-80)
REVERT: A 1319 GLU cc_start: 0.7070 (mm-30) cc_final: 0.6715 (mm-30)
REVERT: A 1338 THR cc_start: 0.7453 (p) cc_final: 0.7034 (t)
REVERT: A 1346 LEU cc_start: 0.5034 (OUTLIER) cc_final: 0.4800 (pp)
REVERT: A 1378 PRO cc_start: 0.5105 (Cg_exo) cc_final: 0.4047 (Cg_endo)
REVERT: A 1406 TYR cc_start: 0.5478 (OUTLIER) cc_final: 0.4995 (t80)
REVERT: A 1416 GLU cc_start: 0.6875 (tt0) cc_final: 0.6467 (tt0)
REVERT: A 1429 ASP cc_start: 0.6592 (OUTLIER) cc_final: 0.6388 (t70)
REVERT: A 1432 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7805 (ppp)
REVERT: A 1438 GLN cc_start: 0.8691 (tt0) cc_final: 0.8180 (tp-100)
REVERT: A 1455 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8693 (mm-30)
REVERT: A 1473 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8401 (mmtm)
REVERT: A 1479 ILE cc_start: 0.8730 (mt) cc_final: 0.8469 (mt)
REVERT: A 1494 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8079 (tp30)
  outliers start: 121
  outliers final: 11
  residues processed: 455
  average time/residue: 0.1216
  time to fit residues: 75.3798
Evaluate side-chains
  293 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 256
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 PHE
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  219 ASP
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  259 LYS
Chi-restraints excluded: chain A residue  343 CYS
Chi-restraints excluded: chain A residue  379 ASP
Chi-restraints excluded: chain A residue  425 ARG
Chi-restraints excluded: chain A residue  521 PHE
Chi-restraints excluded: chain A residue  596 LEU
Chi-restraints excluded: chain A residue  854 LYS
Chi-restraints excluded: chain A residue  856 LYS
Chi-restraints excluded: chain A residue  880 LEU
Chi-restraints excluded: chain A residue  897 LEU
Chi-restraints excluded: chain A residue  905 MET
Chi-restraints excluded: chain A residue  909 LEU
Chi-restraints excluded: chain A residue  966 ASN
Chi-restraints excluded: chain A residue 1003 LEU
Chi-restraints excluded: chain A residue 1010 LYS
Chi-restraints excluded: chain A residue 1125 LEU
Chi-restraints excluded: chain A residue 1131 ARG
Chi-restraints excluded: chain A residue 1156 THR
Chi-restraints excluded: chain A residue 1170 ARG
Chi-restraints excluded: chain A residue 1197 GLU
Chi-restraints excluded: chain A residue 1227 HIS
Chi-restraints excluded: chain A residue 1258 PHE
Chi-restraints excluded: chain A residue 1276 LEU
Chi-restraints excluded: chain A residue 1277 ARG
Chi-restraints excluded: chain A residue 1310 MET
Chi-restraints excluded: chain A residue 1316 PHE
Chi-restraints excluded: chain A residue 1346 LEU
Chi-restraints excluded: chain A residue 1406 TYR
Chi-restraints excluded: chain A residue 1425 LEU
Chi-restraints excluded: chain A residue 1429 ASP
Chi-restraints excluded: chain A residue 1432 MET
Chi-restraints excluded: chain A residue 1455 GLU
Chi-restraints excluded: chain A residue 1473 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    0.4980
   chunk 55 optimal weight:    0.8980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 153 HIS
A 286 GLN
A 291 HIS
A 382 GLN
A 392 HIS
** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 661 GLN
A 670 ASN
A1002 GLN
A1021 HIS
** A1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1068 ASN
A1079 GLN
A1194 GLN
** A1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1446 GLN
A1465 GLN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.184885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.151637 restraints weight = 16225.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.153388 restraints weight = 10006.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.154746 restraints weight = 6948.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.154819 restraints weight = 5796.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.155067 restraints weight = 5677.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6506
moved from start:          0.4568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062  10952  Z= 0.226
  Angle     :  1.085  14.813  14944  Z= 0.531
  Chirality :  0.053   0.531   1765
  Planarity :  0.007   0.068   1818
  Dihedral  : 17.338  87.012   1936
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 13.88
  Ramachandran Plot:
    Outliers :  1.90 %
    Allowed  : 10.25 %
    Favored  : 87.85 %
  Rotamer:
    Outliers :  6.17 %
    Allowed  : 19.26 %
    Favored  : 74.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.08 %
    Twisted Proline : 17.02 %
    Twisted General : 2.51 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.39 (0.22), residues: 1317
  helix: -1.34 (0.17), residues: 847
  sheet: -4.73 (0.97), residues: 20
  loop : -3.83 (0.27), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 681 
 TYR   0.040   0.003   TYR A1089 
 PHE   0.023   0.002   PHE A 653 
 TRP   0.033   0.003   TRP A 316 
 HIS   0.007   0.001   HIS A 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 (10927)
  covalent geometry    : angle       1.05566 (14874)
  SS BOND              : bond        0.01811 (    5)
  SS BOND              : angle       3.08780 (   10)
  hydrogen bonds       : bond        0.05962 (  549)
  hydrogen bonds       : angle       6.08310 ( 1584)
  link_BETA1-3         : bond        0.00546 (    1)
  link_BETA1-3         : angle       3.27671 (    3)
  link_BETA1-4         : bond        0.00614 (   11)
  link_BETA1-4         : angle       3.30364 (   33)
  link_BETA1-6         : bond        0.00709 (    1)
  link_BETA1-6         : angle       4.77697 (    3)
  link_NAG-ASN         : bond        0.00532 (    7)
  link_NAG-ASN         : angle       4.69807 (   21)

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

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

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  380 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 315
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  556 TYR cc_start: 0.7436 (m-10) cc_final: 0.7062 (t80)
REVERT: A  580 LYS cc_start: 0.5818 (tptt) cc_final: 0.5428 (tttp)
REVERT: A  735 LEU cc_start: 0.7835 (tp) cc_final: 0.7341 (tt)
REVERT: A  859 GLN cc_start: 0.7766 (mt0) cc_final: 0.7558 (mm110)
REVERT: A  966 ASN cc_start: 0.6842 (t0) cc_final: 0.6543 (t0)
REVERT: A 1052 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7296 (mp)
REVERT: A 1074 ARG cc_start: 0.6922 (pmt-80) cc_final: 0.6264 (tpt170)
REVERT: A 1079 GLN cc_start: 0.7812 (tp40) cc_final: 0.7555 (tp-100)
REVERT: A 1170 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.6664 (ttt90)
REVERT: A 1310 MET cc_start: 0.6130 (mtp) cc_final: 0.5901 (mtp)
REVERT: A 1373 HIS cc_start: 0.7276 (t-90) cc_final: 0.6449 (t-90)
REVERT: A 1438 GLN cc_start: 0.7952 (tt0) cc_final: 0.7564 (tt0)
REVERT: A 1439 GLN cc_start: 0.8506 (tm-30) cc_final: 0.7926 (tm-30)
REVERT: A 1455 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7574 (mm-30)
REVERT: A 1473 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8470 (mmtm)
  outliers start: 65
  outliers final: 21
  residues processed: 353
  average time/residue: 0.1052
  time to fit residues: 52.5570
Evaluate side-chains
  270 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 245
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  375 ASP
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  398 ILE
Chi-restraints excluded: chain A residue  862 VAL
Chi-restraints excluded: chain A residue  880 LEU
Chi-restraints excluded: chain A residue  891 LEU
Chi-restraints excluded: chain A residue  892 TYR
Chi-restraints excluded: chain A residue  897 LEU
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue  949 THR
Chi-restraints excluded: chain A residue 1003 LEU
Chi-restraints excluded: chain A residue 1052 LEU
Chi-restraints excluded: chain A residue 1057 VAL
Chi-restraints excluded: chain A residue 1143 THR
Chi-restraints excluded: chain A residue 1170 ARG
Chi-restraints excluded: chain A residue 1226 HIS
Chi-restraints excluded: chain A residue 1266 ILE
Chi-restraints excluded: chain A residue 1281 SER
Chi-restraints excluded: chain A residue 1318 MET
Chi-restraints excluded: chain A residue 1436 VAL
Chi-restraints excluded: chain A residue 1455 GLU
Chi-restraints excluded: chain A residue 1473 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 93 optimal weight:    2.9990
   chunk 39 optimal weight:   20.0000
   chunk 40 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0010
   chunk 101 optimal weight:    8.9990
   chunk 62 optimal weight:    3.9990
   chunk 27 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 70 optimal weight:    5.9990
   overall best weight:    1.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 153 HIS
A 286 GLN
** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 555 ASN
** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1160 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.179261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.146285 restraints weight = 15928.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.146581 restraints weight = 9568.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.147851 restraints weight = 7415.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.148679 restraints weight = 6137.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.148961 restraints weight = 5390.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6856
moved from start:          0.6398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  10952  Z= 0.199
  Angle     :  0.962  19.936  14944  Z= 0.464
  Chirality :  0.049   0.275   1765
  Planarity :  0.007   0.140   1818
  Dihedral  : 12.059  70.308   1860
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 14.03
  Ramachandran Plot:
    Outliers :  0.99 %
    Allowed  : 11.69 %
    Favored  : 87.32 %
  Rotamer:
    Outliers :  5.69 %
    Allowed  : 21.16 %
    Favored  : 73.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.08 %
    Twisted Proline : 8.51 %
    Twisted General : 1.49 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.54 (0.22), residues: 1317
  helix: -0.69 (0.17), residues: 870
  sheet:  None (None), residues: 0
  loop : -3.68 (0.28), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A1074 
 TYR   0.026   0.002   TYR A1240 
 PHE   0.021   0.002   PHE A 653 
 TRP   0.035   0.002   TRP A 707 
 HIS   0.008   0.002   HIS A 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 (10927)
  covalent geometry    : angle       0.93114 (14874)
  SS BOND              : bond        0.00413 (    5)
  SS BOND              : angle       1.83279 (   10)
  hydrogen bonds       : bond        0.05020 (  549)
  hydrogen bonds       : angle       5.42939 ( 1584)
  link_BETA1-3         : bond        0.00598 (    1)
  link_BETA1-3         : angle       2.65561 (    3)
  link_BETA1-4         : bond        0.00795 (   11)
  link_BETA1-4         : angle       3.42643 (   33)
  link_BETA1-6         : bond        0.00771 (    1)
  link_BETA1-6         : angle       5.20241 (    3)
  link_NAG-ASN         : bond        0.00359 (    7)
  link_NAG-ASN         : angle       4.35262 (   21)

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

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

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  350 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 290
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  402 TYR cc_start: 0.7876 (m-80) cc_final: 0.7525 (m-80)
REVERT: A  427 ASP cc_start: 0.5950 (t0) cc_final: 0.5641 (t70)
REVERT: A  556 TYR cc_start: 0.7469 (m-10) cc_final: 0.6425 (t80)
REVERT: A  580 LYS cc_start: 0.5817 (tptt) cc_final: 0.5396 (tttp)
REVERT: A  651 LEU cc_start: 0.8116 (tt) cc_final: 0.7829 (tt)
REVERT: A  662 LEU cc_start: 0.7685 (tt) cc_final: 0.7436 (tp)
REVERT: A  692 MET cc_start: 0.7455 (tpp) cc_final: 0.7188 (tpp)
REVERT: A  908 MET cc_start: 0.7601 (tpp) cc_final: 0.7361 (tpp)
REVERT: A  966 ASN cc_start: 0.7518 (t0) cc_final: 0.7208 (t0)
REVERT: A 1052 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7709 (mt)
REVERT: A 1151 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8274 (tpp80)
REVERT: A 1160 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7845 (mp10)
REVERT: A 1163 MET cc_start: 0.7254 (mtt) cc_final: 0.6878 (mtp)
REVERT: A 1170 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.6684 (ttt90)
REVERT: A 1196 MET cc_start: 0.6783 (mmp) cc_final: 0.6536 (ppp)
REVERT: A 1200 GLU cc_start: 0.7452 (tt0) cc_final: 0.7226 (tt0)
REVERT: A 1227 HIS cc_start: 0.6938 (OUTLIER) cc_final: 0.6641 (m90)
REVERT: A 1288 LEU cc_start: 0.8838 (tt) cc_final: 0.8489 (tt)
REVERT: A 1335 ASN cc_start: 0.7649 (p0) cc_final: 0.7366 (p0)
REVERT: A 1432 MET cc_start: 0.6815 (ppp) cc_final: 0.6094 (ppp)
REVERT: A 1438 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7437 (tt0)
REVERT: A 1439 GLN cc_start: 0.8587 (tm-30) cc_final: 0.7811 (tm-30)
REVERT: A 1455 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7623 (mm-30)
REVERT: A 1473 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8526 (mptt)
  outliers start: 60
  outliers final: 33
  residues processed: 315
  average time/residue: 0.0936
  time to fit residues: 43.0696
Evaluate side-chains
  286 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 245
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  375 ASP
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  555 ASN
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain A residue  693 ILE
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  880 LEU
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  891 LEU
Chi-restraints excluded: chain A residue  892 TYR
Chi-restraints excluded: chain A residue  897 LEU
Chi-restraints excluded: chain A residue  909 LEU
Chi-restraints excluded: chain A residue  938 VAL
Chi-restraints excluded: chain A residue  955 VAL
Chi-restraints excluded: chain A residue  988 VAL
Chi-restraints excluded: chain A residue 1003 LEU
Chi-restraints excluded: chain A residue 1052 LEU
Chi-restraints excluded: chain A residue 1109 CYS
Chi-restraints excluded: chain A residue 1143 THR
Chi-restraints excluded: chain A residue 1151 ARG
Chi-restraints excluded: chain A residue 1160 GLN
Chi-restraints excluded: chain A residue 1170 ARG
Chi-restraints excluded: chain A residue 1226 HIS
Chi-restraints excluded: chain A residue 1227 HIS
Chi-restraints excluded: chain A residue 1231 ASP
Chi-restraints excluded: chain A residue 1266 ILE
Chi-restraints excluded: chain A residue 1281 SER
Chi-restraints excluded: chain A residue 1396 ILE
Chi-restraints excluded: chain A residue 1436 VAL
Chi-restraints excluded: chain A residue 1438 GLN
Chi-restraints excluded: chain A residue 1455 GLU
Chi-restraints excluded: chain A residue 1456 LEU
Chi-restraints excluded: chain A residue 1473 LYS
Chi-restraints excluded: chain A residue 1492 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 62 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9980
   chunk 95 optimal weight:    5.9990
   chunk 118 optimal weight:    5.9990
   chunk 29 optimal weight:    6.9990
   chunk 77 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9980
   chunk 85 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 153 HIS
** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 541 HIS
** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 948 GLN
** A1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1301 ASN
A1348 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.179099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.147894 restraints weight = 15867.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.147049 restraints weight = 10626.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.147642 restraints weight = 9025.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.147924 restraints weight = 7662.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.149984 restraints weight = 6933.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6965
moved from start:          0.7119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10952  Z= 0.172
  Angle     :  0.876  20.732  14944  Z= 0.425
  Chirality :  0.046   0.207   1765
  Planarity :  0.005   0.092   1818
  Dihedral  : 10.157  61.379   1860
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 13.22
  Ramachandran Plot:
    Outliers :  0.91 %
    Allowed  : 10.86 %
    Favored  : 88.23 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 25.05 %
    Favored  : 69.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.08 %
    Twisted Proline : 8.51 %
    Twisted General : 1.26 %

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 aren not related in a simple way.
  whole: -2.11 (0.22), residues: 1317
  helix: -0.39 (0.17), residues: 873
  sheet:  None (None), residues: 0
  loop : -3.46 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 613 
 TYR   0.024   0.002   TYR A1089 
 PHE   0.025   0.001   PHE A 687 
 TRP   0.031   0.002   TRP A 715 
 HIS   0.006   0.001   HIS A 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 (10927)
  covalent geometry    : angle       0.85276 (14874)
  SS BOND              : bond        0.00368 (    5)
  SS BOND              : angle       2.06837 (   10)
  hydrogen bonds       : bond        0.04553 (  549)
  hydrogen bonds       : angle       5.08304 ( 1584)
  link_BETA1-3         : bond        0.00628 (    1)
  link_BETA1-3         : angle       2.26336 (    3)
  link_BETA1-4         : bond        0.00607 (   11)
  link_BETA1-4         : angle       2.92171 (   33)
  link_BETA1-6         : bond        0.00633 (    1)
  link_BETA1-6         : angle       4.25622 (    3)
  link_NAG-ASN         : bond        0.00386 (    7)
  link_NAG-ASN         : angle       3.50031 (   21)

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

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

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  313 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 257
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  393 ILE cc_start: 0.7440 (OUTLIER) cc_final: 0.7047 (pt)
REVERT: A  402 TYR cc_start: 0.8017 (m-80) cc_final: 0.7673 (m-80)
REVERT: A  542 ASP cc_start: 0.6332 (m-30) cc_final: 0.5468 (p0)
REVERT: A  556 TYR cc_start: 0.7358 (m-10) cc_final: 0.6876 (t80)
REVERT: A  580 LYS cc_start: 0.5921 (tptt) cc_final: 0.5328 (ttmm)
REVERT: A  662 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7402 (tp)
REVERT: A  905 MET cc_start: 0.7975 (tpp) cc_final: 0.7602 (tpt)
REVERT: A  956 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.8398 (t80)
REVERT: A  966 ASN cc_start: 0.7719 (t0) cc_final: 0.7458 (t0)
REVERT: A 1074 ARG cc_start: 0.6266 (OUTLIER) cc_final: 0.6056 (tpp-160)
REVERT: A 1151 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.7901 (tpp80)
REVERT: A 1170 ARG cc_start: 0.7402 (mmt90) cc_final: 0.6853 (ttt90)
REVERT: A 1227 HIS cc_start: 0.7159 (m90) cc_final: 0.6677 (m-70)
REVERT: A 1288 LEU cc_start: 0.8818 (tt) cc_final: 0.8512 (tt)
REVERT: A 1432 MET cc_start: 0.6771 (ppp) cc_final: 0.6123 (ppp)
REVERT: A 1438 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7284 (tt0)
REVERT: A 1439 GLN cc_start: 0.8595 (tm-30) cc_final: 0.7927 (tm-30)
REVERT: A 1455 GLU cc_start: 0.8022 (tp30) cc_final: 0.7667 (mm-30)
REVERT: A 1473 LYS cc_start: 0.8910 (mmtp) cc_final: 0.8519 (mmtm)
  outliers start: 56
  outliers final: 26
  residues processed: 282
  average time/residue: 0.0988
  time to fit residues: 40.2766
Evaluate side-chains
  273 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 241
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  375 ASP
Chi-restraints excluded: chain A residue  393 ILE
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  891 LEU
Chi-restraints excluded: chain A residue  892 TYR
Chi-restraints excluded: chain A residue  893 VAL
Chi-restraints excluded: chain A residue  909 LEU
Chi-restraints excluded: chain A residue  938 VAL
Chi-restraints excluded: chain A residue  956 PHE
Chi-restraints excluded: chain A residue  963 SER
Chi-restraints excluded: chain A residue 1074 ARG
Chi-restraints excluded: chain A residue 1079 GLN
Chi-restraints excluded: chain A residue 1109 CYS
Chi-restraints excluded: chain A residue 1143 THR
Chi-restraints excluded: chain A residue 1151 ARG
Chi-restraints excluded: chain A residue 1172 PHE
Chi-restraints excluded: chain A residue 1226 HIS
Chi-restraints excluded: chain A residue 1281 SER
Chi-restraints excluded: chain A residue 1396 ILE
Chi-restraints excluded: chain A residue 1438 GLN
Chi-restraints excluded: chain A residue 1456 LEU
Chi-restraints excluded: chain A residue 1479 ILE
Chi-restraints excluded: chain A residue 1492 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 14 optimal weight:    9.9990
   chunk 75 optimal weight:    5.9990
   chunk 116 optimal weight:    0.0570
   chunk 115 optimal weight:    0.9980
   chunk 39 optimal weight:    6.9990
   chunk 56 optimal weight:    0.4980
   chunk 76 optimal weight:    5.9990
   chunk 29 optimal weight:    0.4980
   chunk 119 optimal weight:    1.9990
   overall best weight:    0.8100

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

Flipped N/Q/H residues before XYZ refinement:
A 153 HIS
** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 555 ASN
** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1183 ASN
A1348 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.179793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.147864 restraints weight = 15838.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.148988 restraints weight = 9812.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.150094 restraints weight = 7378.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.150749 restraints weight = 6476.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.150654 restraints weight = 5843.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7010
moved from start:          0.7769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10952  Z= 0.157
  Angle     :  0.865  21.273  14944  Z= 0.417
  Chirality :  0.046   0.215   1765
  Planarity :  0.005   0.084   1818
  Dihedral  :  8.461  54.764   1841
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 12.36
  Ramachandran Plot:
    Outliers :  0.76 %
    Allowed  : 10.86 %
    Favored  : 88.38 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 27.23 %
    Favored  : 68.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.08 %
    Twisted Proline : 6.38 %
    Twisted General : 0.86 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.84 (0.23), residues: 1317
  helix: -0.15 (0.17), residues: 879
  sheet:  None (None), residues: 0
  loop : -3.48 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1142 
 TYR   0.024   0.002   TYR A1089 
 PHE   0.017   0.001   PHE A1434 
 TRP   0.027   0.002   TRP A 707 
 HIS   0.007   0.001   HIS A1077 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (10927)
  covalent geometry    : angle       0.84561 (14874)
  SS BOND              : bond        0.00328 (    5)
  SS BOND              : angle       1.49879 (   10)
  hydrogen bonds       : bond        0.04215 (  549)
  hydrogen bonds       : angle       4.82996 ( 1584)
  link_BETA1-3         : bond        0.00654 (    1)
  link_BETA1-3         : angle       1.86869 (    3)
  link_BETA1-4         : bond        0.00625 (   11)
  link_BETA1-4         : angle       2.68660 (   33)
  link_BETA1-6         : bond        0.00546 (    1)
  link_BETA1-6         : angle       3.23772 (    3)
  link_NAG-ASN         : bond        0.00388 (    7)
  link_NAG-ASN         : angle       3.39356 (   21)

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

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

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 258
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  202 ASN cc_start: 0.8071 (m-40) cc_final: 0.7823 (m110)
REVERT: A  393 ILE cc_start: 0.7284 (OUTLIER) cc_final: 0.6954 (pt)
REVERT: A  556 TYR cc_start: 0.7471 (m-10) cc_final: 0.6875 (t80)
REVERT: A  580 LYS cc_start: 0.5900 (tptt) cc_final: 0.5395 (tttp)
REVERT: A  610 ARG cc_start: 0.8189 (ttt-90) cc_final: 0.7976 (ttt90)
REVERT: A  661 GLN cc_start: 0.7347 (mt0) cc_final: 0.7139 (mt0)
REVERT: A  886 LEU cc_start: 0.8096 (mt) cc_final: 0.7795 (mt)
REVERT: A  905 MET cc_start: 0.8045 (tpp) cc_final: 0.7554 (tpt)
REVERT: A  908 MET cc_start: 0.7536 (tpp) cc_final: 0.7210 (tpp)
REVERT: A  966 ASN cc_start: 0.7804 (t0) cc_final: 0.7548 (t0)
REVERT: A 1151 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7872 (tpp80)
REVERT: A 1170 ARG cc_start: 0.7437 (mmt90) cc_final: 0.6891 (ttt90)
REVERT: A 1227 HIS cc_start: 0.7027 (m90) cc_final: 0.6688 (m-70)
REVERT: A 1283 ARG cc_start: 0.6717 (OUTLIER) cc_final: 0.6377 (tmm-80)
REVERT: A 1418 TYR cc_start: 0.7575 (m-80) cc_final: 0.7330 (m-80)
REVERT: A 1432 MET cc_start: 0.6734 (ppp) cc_final: 0.6178 (ppp)
REVERT: A 1438 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7278 (tt0)
REVERT: A 1439 GLN cc_start: 0.8603 (tm-30) cc_final: 0.7875 (tm-30)
REVERT: A 1455 GLU cc_start: 0.7960 (tp30) cc_final: 0.7547 (mm-30)
REVERT: A 1473 LYS cc_start: 0.8866 (mmtp) cc_final: 0.8517 (mmtm)
  outliers start: 48
  outliers final: 24
  residues processed: 284
  average time/residue: 0.1009
  time to fit residues: 41.1992
Evaluate side-chains
  261 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 233
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  393 ILE
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  892 TYR
Chi-restraints excluded: chain A residue  893 VAL
Chi-restraints excluded: chain A residue  938 VAL
Chi-restraints excluded: chain A residue  955 VAL
Chi-restraints excluded: chain A residue 1108 VAL
Chi-restraints excluded: chain A residue 1109 CYS
Chi-restraints excluded: chain A residue 1141 MET
Chi-restraints excluded: chain A residue 1143 THR
Chi-restraints excluded: chain A residue 1151 ARG
Chi-restraints excluded: chain A residue 1226 HIS
Chi-restraints excluded: chain A residue 1283 ARG
Chi-restraints excluded: chain A residue 1396 ILE
Chi-restraints excluded: chain A residue 1438 GLN
Chi-restraints excluded: chain A residue 1456 LEU
Chi-restraints excluded: chain A residue 1479 ILE
Chi-restraints excluded: chain A residue 1492 VAL
Chi-restraints excluded: chain A residue 1500 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 7 optimal weight:    0.0570
   chunk 125 optimal weight:    8.9990
   chunk 27 optimal weight:    0.0470
   chunk 61 optimal weight:    6.9990
   chunk 65 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 103 optimal weight:    6.9990
   chunk 68 optimal weight:    0.8980
   chunk 38 optimal weight:    8.9990
   chunk 4 optimal weight:    3.9990
   chunk 40 optimal weight:    9.9990
   overall best weight:    0.9598

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

Flipped N/Q/H residues before XYZ refinement:
A 153 HIS
** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1039 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1380 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.181485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.149860 restraints weight = 16161.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.150672 restraints weight = 10698.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.152066 restraints weight = 7602.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.152427 restraints weight = 6085.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.152595 restraints weight = 5548.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7128
moved from start:          0.8368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10952  Z= 0.159
  Angle     :  0.826  21.358  14944  Z= 0.400
  Chirality :  0.044   0.218   1765
  Planarity :  0.005   0.115   1818
  Dihedral  :  7.530  49.787   1841
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 12.07
  Ramachandran Plot:
    Outliers :  0.76 %
    Allowed  : 11.09 %
    Favored  : 88.15 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 29.70 %
    Favored  : 65.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.08 %
    Twisted Proline : 6.38 %
    Twisted General : 0.79 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.66 (0.23), residues: 1317
  helix: -0.00 (0.17), residues: 880
  sheet:  None (None), residues: 0
  loop : -3.44 (0.28), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1268 
 TYR   0.020   0.002   TYR A 224 
 PHE   0.025   0.001   PHE A 901 
 TRP   0.023   0.002   TRP A 316 
 HIS   0.004   0.001   HIS A1158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 (10927)
  covalent geometry    : angle       0.80856 (14874)
  SS BOND              : bond        0.01137 (    5)
  SS BOND              : angle       1.38341 (   10)
  hydrogen bonds       : bond        0.04107 (  549)
  hydrogen bonds       : angle       4.65630 ( 1584)
  link_BETA1-3         : bond        0.00648 (    1)
  link_BETA1-3         : angle       1.84148 (    3)
  link_BETA1-4         : bond        0.00534 (   11)
  link_BETA1-4         : angle       2.47131 (   33)
  link_BETA1-6         : bond        0.00688 (    1)
  link_BETA1-6         : angle       2.59994 (    3)
  link_NAG-ASN         : bond        0.00461 (    7)
  link_NAG-ASN         : angle       3.19175 (   21)

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

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

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 258
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 TRP cc_start: 0.7633 (t60) cc_final: 0.7305 (m100)
REVERT: A  252 SER cc_start: 0.8178 (t) cc_final: 0.7822 (m)
REVERT: A  292 PHE cc_start: 0.7636 (OUTLIER) cc_final: 0.7132 (m-80)
REVERT: A  393 ILE cc_start: 0.7496 (OUTLIER) cc_final: 0.7096 (pt)
REVERT: A  556 TYR cc_start: 0.7447 (m-10) cc_final: 0.6940 (t80)
REVERT: A  580 LYS cc_start: 0.5773 (tptt) cc_final: 0.5168 (ttmm)
REVERT: A  886 LEU cc_start: 0.8060 (mt) cc_final: 0.7780 (mt)
REVERT: A  905 MET cc_start: 0.7896 (tpp) cc_final: 0.7594 (tpt)
REVERT: A  908 MET cc_start: 0.7490 (tpp) cc_final: 0.7237 (tpp)
REVERT: A 1094 PHE cc_start: 0.7857 (t80) cc_final: 0.7622 (t80)
REVERT: A 1151 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7860 (tpp80)
REVERT: A 1170 ARG cc_start: 0.7269 (mmt90) cc_final: 0.6855 (ttt90)
REVERT: A 1220 LYS cc_start: 0.8750 (ttmt) cc_final: 0.8337 (ttpt)
REVERT: A 1227 HIS cc_start: 0.7072 (m90) cc_final: 0.6790 (m-70)
REVERT: A 1249 MET cc_start: 0.5024 (tpp) cc_final: 0.4529 (tpt)
REVERT: A 1288 LEU cc_start: 0.8886 (tt) cc_final: 0.8667 (tt)
REVERT: A 1418 TYR cc_start: 0.7604 (m-80) cc_final: 0.7396 (m-80)
REVERT: A 1432 MET cc_start: 0.6621 (ppp) cc_final: 0.6098 (ppp)
REVERT: A 1438 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7274 (tt0)
REVERT: A 1439 GLN cc_start: 0.8556 (tm-30) cc_final: 0.7893 (tm-30)
REVERT: A 1473 LYS cc_start: 0.8781 (mmtp) cc_final: 0.8503 (mmtm)
  outliers start: 48
  outliers final: 32
  residues processed: 283
  average time/residue: 0.0982
  time to fit residues: 40.2121
Evaluate side-chains
  266 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 230
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  292 PHE
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  393 ILE
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain A residue  733 LEU
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  739 LEU
Chi-restraints excluded: chain A residue  885 VAL
Chi-restraints excluded: chain A residue  892 TYR
Chi-restraints excluded: chain A residue  893 VAL
Chi-restraints excluded: chain A residue  938 VAL
Chi-restraints excluded: chain A residue  963 SER
Chi-restraints excluded: chain A residue 1023 ILE
Chi-restraints excluded: chain A residue 1032 HIS
Chi-restraints excluded: chain A residue 1042 MET
Chi-restraints excluded: chain A residue 1108 VAL
Chi-restraints excluded: chain A residue 1109 CYS
Chi-restraints excluded: chain A residue 1141 MET
Chi-restraints excluded: chain A residue 1143 THR
Chi-restraints excluded: chain A residue 1147 LYS
Chi-restraints excluded: chain A residue 1151 ARG
Chi-restraints excluded: chain A residue 1226 HIS
Chi-restraints excluded: chain A residue 1239 LEU
Chi-restraints excluded: chain A residue 1281 SER
Chi-restraints excluded: chain A residue 1322 MET
Chi-restraints excluded: chain A residue 1380 ASN
Chi-restraints excluded: chain A residue 1438 GLN
Chi-restraints excluded: chain A residue 1456 LEU
Chi-restraints excluded: chain A residue 1479 ILE
Chi-restraints excluded: chain A residue 1492 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 32 optimal weight:    0.5980
   chunk 126 optimal weight:    6.9990
   chunk 73 optimal weight:    2.9990
   chunk 107 optimal weight:    0.6980
   chunk 49 optimal weight:    9.9990
   chunk 78 optimal weight:    0.4980
   chunk 36 optimal weight:    1.9990
   chunk 12 optimal weight:    9.9990
   chunk 18 optimal weight:    6.9990
   chunk 50 optimal weight:    4.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 153 HIS
A 278 GLN
A 345 GLN
** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 532 ASN
** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1039 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.181357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.149951 restraints weight = 16023.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.151142 restraints weight = 10265.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.152481 restraints weight = 7079.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.152783 restraints weight = 5876.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.152943 restraints weight = 5342.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7184
moved from start:          0.8729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10952  Z= 0.154
  Angle     :  0.840  20.916  14944  Z= 0.403
  Chirality :  0.045   0.222   1765
  Planarity :  0.005   0.125   1818
  Dihedral  :  7.142  46.488   1841
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.76 %
    Allowed  : 10.86 %
    Favored  : 88.38 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 31.12 %
    Favored  : 64.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.08 %
    Twisted Proline : 4.26 %
    Twisted General : 0.86 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.47 (0.23), residues: 1317
  helix:  0.18 (0.17), residues: 878
  sheet:  None (None), residues: 0
  loop : -3.43 (0.28), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A1268 
 TYR   0.026   0.002   TYR A1334 
 PHE   0.020   0.001   PHE A 521 
 TRP   0.022   0.002   TRP A 316 
 HIS   0.004   0.001   HIS A1227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (10927)
  covalent geometry    : angle       0.82433 (14874)
  SS BOND              : bond        0.00351 (    5)
  SS BOND              : angle       1.18442 (   10)
  hydrogen bonds       : bond        0.04013 (  549)
  hydrogen bonds       : angle       4.56806 ( 1584)
  link_BETA1-3         : bond        0.00658 (    1)
  link_BETA1-3         : angle       1.86246 (    3)
  link_BETA1-4         : bond        0.00580 (   11)
  link_BETA1-4         : angle       2.37934 (   33)
  link_BETA1-6         : bond        0.00641 (    1)
  link_BETA1-6         : angle       2.36615 (    3)
  link_NAG-ASN         : bond        0.00458 (    7)
  link_NAG-ASN         : angle       3.16288 (   21)

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

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

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 242
  time to evaluate  : 0.394 
Fit side-chains
REVERT: A  203 TRP cc_start: 0.7646 (t60) cc_final: 0.7238 (m100)
REVERT: A  252 SER cc_start: 0.8227 (t) cc_final: 0.7889 (m)
REVERT: A  292 PHE cc_start: 0.7727 (OUTLIER) cc_final: 0.7295 (m-80)
REVERT: A  556 TYR cc_start: 0.7435 (m-10) cc_final: 0.6934 (t80)
REVERT: A  580 LYS cc_start: 0.5806 (tptt) cc_final: 0.5177 (ttmm)
REVERT: A  905 MET cc_start: 0.7827 (tpp) cc_final: 0.7464 (tpt)
REVERT: A  908 MET cc_start: 0.7549 (tpp) cc_final: 0.7241 (tpp)
REVERT: A 1094 PHE cc_start: 0.7961 (t80) cc_final: 0.7742 (t80)
REVERT: A 1170 ARG cc_start: 0.7288 (mmt90) cc_final: 0.6965 (ttt90)
REVERT: A 1249 MET cc_start: 0.4681 (tpp) cc_final: 0.3835 (tpt)
REVERT: A 1283 ARG cc_start: 0.6717 (OUTLIER) cc_final: 0.6464 (tmm-80)
REVERT: A 1418 TYR cc_start: 0.7601 (m-80) cc_final: 0.7291 (m-80)
REVERT: A 1432 MET cc_start: 0.6604 (ppp) cc_final: 0.6151 (ppp)
REVERT: A 1473 LYS cc_start: 0.8743 (mmtp) cc_final: 0.8396 (mmtm)
  outliers start: 41
  outliers final: 23
  residues processed: 267
  average time/residue: 0.0954
  time to fit residues: 37.2746
Evaluate side-chains
  252 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 227
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  292 PHE
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  739 LEU
Chi-restraints excluded: chain A residue  892 TYR
Chi-restraints excluded: chain A residue  906 ILE
Chi-restraints excluded: chain A residue  938 VAL
Chi-restraints excluded: chain A residue 1032 HIS
Chi-restraints excluded: chain A residue 1108 VAL
Chi-restraints excluded: chain A residue 1109 CYS
Chi-restraints excluded: chain A residue 1141 MET
Chi-restraints excluded: chain A residue 1147 LYS
Chi-restraints excluded: chain A residue 1226 HIS
Chi-restraints excluded: chain A residue 1239 LEU
Chi-restraints excluded: chain A residue 1283 ARG
Chi-restraints excluded: chain A residue 1322 MET
Chi-restraints excluded: chain A residue 1396 ILE
Chi-restraints excluded: chain A residue 1456 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 79 optimal weight:    3.9990
   chunk 123 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 129 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 73 optimal weight:    0.8980
   chunk 76 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 117 optimal weight:    9.9990
   chunk 93 optimal weight:    0.7980
   chunk 43 optimal weight:    6.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A 153 HIS
A 409 ASN
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1039 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1068 ASN
A1227 HIS
** A1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1380 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.174363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.142244 restraints weight = 16263.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.142981 restraints weight = 10224.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.144291 restraints weight = 7375.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.144584 restraints weight = 6554.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.144797 restraints weight = 5743.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7285
moved from start:          0.9219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10952  Z= 0.171
  Angle     :  0.839  20.304  14944  Z= 0.405
  Chirality :  0.046   0.231   1765
  Planarity :  0.005   0.123   1818
  Dihedral  :  6.865  43.331   1841
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.68 %
    Allowed  : 11.24 %
    Favored  : 88.08 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 31.78 %
    Favored  : 64.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.08 %
    Twisted Proline : 2.13 %
    Twisted General : 0.79 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.43 (0.23), residues: 1317
  helix:  0.18 (0.17), residues: 878
  sheet:  None (None), residues: 0
  loop : -3.35 (0.28), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A1268 
 TYR   0.018   0.002   TYR A1334 
 PHE   0.023   0.001   PHE A 521 
 TRP   0.028   0.002   TRP A 316 
 HIS   0.007   0.001   HIS A1227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 (10927)
  covalent geometry    : angle       0.82301 (14874)
  SS BOND              : bond        0.00606 (    5)
  SS BOND              : angle       1.38848 (   10)
  hydrogen bonds       : bond        0.04006 (  549)
  hydrogen bonds       : angle       4.55993 ( 1584)
  link_BETA1-3         : bond        0.00486 (    1)
  link_BETA1-3         : angle       1.78382 (    3)
  link_BETA1-4         : bond        0.00595 (   11)
  link_BETA1-4         : angle       2.31630 (   33)
  link_BETA1-6         : bond        0.00502 (    1)
  link_BETA1-6         : angle       2.24293 (    3)
  link_NAG-ASN         : bond        0.00476 (    7)
  link_NAG-ASN         : angle       3.18214 (   21)

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

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

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 258
  time to evaluate  : 0.384 
Fit side-chains
REVERT: A  252 SER cc_start: 0.8489 (t) cc_final: 0.8053 (m)
REVERT: A  292 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7579 (m-80)
REVERT: A  374 LEU cc_start: 0.8756 (tp) cc_final: 0.8516 (tp)
REVERT: A  556 TYR cc_start: 0.7516 (m-10) cc_final: 0.6869 (t80)
REVERT: A  580 LYS cc_start: 0.5865 (tptt) cc_final: 0.5255 (ttmm)
REVERT: A  905 MET cc_start: 0.8051 (tpp) cc_final: 0.7659 (tpt)
REVERT: A  908 MET cc_start: 0.7884 (tpp) cc_final: 0.7481 (tpp)
REVERT: A 1049 ASN cc_start: 0.8254 (m-40) cc_final: 0.7937 (m-40)
REVERT: A 1094 PHE cc_start: 0.8016 (t80) cc_final: 0.7778 (t80)
REVERT: A 1170 ARG cc_start: 0.7443 (mmt90) cc_final: 0.6922 (ttt90)
REVERT: A 1256 LYS cc_start: 0.4283 (OUTLIER) cc_final: 0.3084 (ttmt)
REVERT: A 1283 ARG cc_start: 0.6681 (OUTLIER) cc_final: 0.6438 (tmm-80)
REVERT: A 1373 HIS cc_start: 0.6050 (t-90) cc_final: 0.5820 (t-90)
REVERT: A 1418 TYR cc_start: 0.7783 (m-80) cc_final: 0.7427 (m-80)
REVERT: A 1429 ASP cc_start: 0.5726 (m-30) cc_final: 0.4937 (m-30)
REVERT: A 1432 MET cc_start: 0.6918 (ppp) cc_final: 0.6406 (ppp)
REVERT: A 1473 LYS cc_start: 0.8910 (mmtp) cc_final: 0.8528 (mmtm)
  outliers start: 41
  outliers final: 30
  residues processed: 281
  average time/residue: 0.0923
  time to fit residues: 38.4338
Evaluate side-chains
  270 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 237
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  292 PHE
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  409 ASN
Chi-restraints excluded: chain A residue  597 GLU
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain A residue  733 LEU
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  739 LEU
Chi-restraints excluded: chain A residue  880 LEU
Chi-restraints excluded: chain A residue  892 TYR
Chi-restraints excluded: chain A residue  906 ILE
Chi-restraints excluded: chain A residue  938 VAL
Chi-restraints excluded: chain A residue 1032 HIS
Chi-restraints excluded: chain A residue 1108 VAL
Chi-restraints excluded: chain A residue 1109 CYS
Chi-restraints excluded: chain A residue 1141 MET
Chi-restraints excluded: chain A residue 1143 THR
Chi-restraints excluded: chain A residue 1147 LYS
Chi-restraints excluded: chain A residue 1226 HIS
Chi-restraints excluded: chain A residue 1239 LEU
Chi-restraints excluded: chain A residue 1256 LYS
Chi-restraints excluded: chain A residue 1283 ARG
Chi-restraints excluded: chain A residue 1322 MET
Chi-restraints excluded: chain A residue 1324 ILE
Chi-restraints excluded: chain A residue 1380 ASN
Chi-restraints excluded: chain A residue 1396 ILE
Chi-restraints excluded: chain A residue 1456 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 121 optimal weight:    0.7980
   chunk 119 optimal weight:    2.9990
   chunk 17 optimal weight:   10.0000
   chunk 62 optimal weight:    3.9990
   chunk 48 optimal weight:    4.9990
   chunk 118 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 97 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9980
   chunk 123 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
A 153 HIS
A 345 GLN
A 409 ASN
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 882 GLN
** A1039 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.171113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.138748 restraints weight = 16388.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.140842 restraints weight = 9893.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.141667 restraints weight = 7446.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.142015 restraints weight = 5817.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.142148 restraints weight = 5409.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.9838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071  10952  Z= 0.206
  Angle     :  0.896  21.561  14944  Z= 0.434
  Chirality :  0.048   0.496   1765
  Planarity :  0.006   0.133   1818
  Dihedral  :  6.910  44.835   1841
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 13.31
  Ramachandran Plot:
    Outliers :  0.76 %
    Allowed  : 10.78 %
    Favored  : 88.46 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 32.26 %
    Favored  : 63.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.08 %
    Twisted Proline : 4.26 %
    Twisted General : 0.86 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.45 (0.23), residues: 1317
  helix:  0.19 (0.17), residues: 870
  sheet: -1.12 (1.61), residues: 10
  loop : -3.41 (0.28), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A1503 
 TYR   0.022   0.002   TYR A1089 
 PHE   0.033   0.002   PHE A 521 
 TRP   0.033   0.003   TRP A 316 
 HIS   0.005   0.001   HIS A 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00476 (10927)
  covalent geometry    : angle       0.88104 (14874)
  SS BOND              : bond        0.00780 (    5)
  SS BOND              : angle       2.06531 (   10)
  hydrogen bonds       : bond        0.04212 (  549)
  hydrogen bonds       : angle       4.64969 ( 1584)
  link_BETA1-3         : bond        0.00553 (    1)
  link_BETA1-3         : angle       1.77490 (    3)
  link_BETA1-4         : bond        0.00576 (   11)
  link_BETA1-4         : angle       2.25307 (   33)
  link_BETA1-6         : bond        0.00475 (    1)
  link_BETA1-6         : angle       2.30820 (    3)
  link_NAG-ASN         : bond        0.00479 (    7)
  link_NAG-ASN         : angle       3.25500 (   21)

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

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

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 257
  time to evaluate  : 0.478 
Fit side-chains
REVERT: A  292 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.7592 (m-80)
REVERT: A  556 TYR cc_start: 0.7529 (m-10) cc_final: 0.6933 (t80)
REVERT: A  580 LYS cc_start: 0.6253 (tptt) cc_final: 0.5497 (ttmm)
REVERT: A  886 LEU cc_start: 0.8396 (mt) cc_final: 0.8080 (mt)
REVERT: A  905 MET cc_start: 0.8117 (tpp) cc_final: 0.7761 (tpt)
REVERT: A  926 ASP cc_start: 0.7224 (t70) cc_final: 0.7019 (t0)
REVERT: A 1049 ASN cc_start: 0.8256 (m-40) cc_final: 0.8008 (m-40)
REVERT: A 1094 PHE cc_start: 0.8046 (t80) cc_final: 0.7801 (t80)
REVERT: A 1170 ARG cc_start: 0.7565 (mmt90) cc_final: 0.7062 (ttt90)
REVERT: A 1220 LYS cc_start: 0.8748 (ttmt) cc_final: 0.8410 (ttpt)
REVERT: A 1256 LYS cc_start: 0.4617 (OUTLIER) cc_final: 0.3449 (ttmt)
REVERT: A 1373 HIS cc_start: 0.6127 (t-90) cc_final: 0.5925 (t-90)
REVERT: A 1418 TYR cc_start: 0.7918 (m-80) cc_final: 0.7422 (m-80)
REVERT: A 1429 ASP cc_start: 0.5728 (m-30) cc_final: 0.5134 (m-30)
REVERT: A 1432 MET cc_start: 0.6853 (ppp) cc_final: 0.6337 (ppp)
REVERT: A 1473 LYS cc_start: 0.8923 (mmtp) cc_final: 0.8557 (mmtm)
  outliers start: 40
  outliers final: 29
  residues processed: 279
  average time/residue: 0.0907
  time to fit residues: 37.5247
Evaluate side-chains
  277 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 246
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  292 PHE
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  597 GLU
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain A residue  733 LEU
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  739 LEU
Chi-restraints excluded: chain A residue  892 TYR
Chi-restraints excluded: chain A residue  894 ASP
Chi-restraints excluded: chain A residue  906 ILE
Chi-restraints excluded: chain A residue  938 VAL
Chi-restraints excluded: chain A residue 1032 HIS
Chi-restraints excluded: chain A residue 1108 VAL
Chi-restraints excluded: chain A residue 1109 CYS
Chi-restraints excluded: chain A residue 1141 MET
Chi-restraints excluded: chain A residue 1143 THR
Chi-restraints excluded: chain A residue 1147 LYS
Chi-restraints excluded: chain A residue 1226 HIS
Chi-restraints excluded: chain A residue 1239 LEU
Chi-restraints excluded: chain A residue 1256 LYS
Chi-restraints excluded: chain A residue 1322 MET
Chi-restraints excluded: chain A residue 1324 ILE
Chi-restraints excluded: chain A residue 1396 ILE
Chi-restraints excluded: chain A residue 1401 VAL
Chi-restraints excluded: chain A residue 1456 LEU
Chi-restraints excluded: chain A residue 1497 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 107 optimal weight:    7.9990
   chunk 1 optimal weight:   30.0000
   chunk 77 optimal weight:    0.9990
   chunk 118 optimal weight:    5.9990
   chunk 73 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 52 optimal weight:    0.5980
   chunk 105 optimal weight:    2.9990
   chunk 87 optimal weight:    3.9990
   overall best weight:    1.5188

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

Flipped N/Q/H residues before XYZ refinement:
A 345 GLN
A 532 ASN
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.171396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.139212 restraints weight = 16377.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.139007 restraints weight = 9821.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.140091 restraints weight = 7800.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.140945 restraints weight = 7029.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.140872 restraints weight = 6127.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7457
moved from start:          1.0305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10952  Z= 0.178
  Angle     :  0.871  22.036  14944  Z= 0.418
  Chirality :  0.046   0.239   1765
  Planarity :  0.006   0.131   1818
  Dihedral  :  6.715  46.709   1841
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.68 %
    Allowed  : 10.93 %
    Favored  : 88.38 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 33.11 %
    Favored  : 63.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.08 %
    Twisted Proline : 2.13 %
    Twisted General : 0.71 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.26 (0.23), residues: 1317
  helix:  0.30 (0.17), residues: 863
  sheet: -0.90 (1.63), residues: 10
  loop : -3.20 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A1268 
 TYR   0.032   0.002   TYR A1089 
 PHE   0.034   0.002   PHE A 521 
 TRP   0.029   0.003   TRP A 316 
 HIS   0.005   0.001   HIS A1227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 (10927)
  covalent geometry    : angle       0.85603 (14874)
  SS BOND              : bond        0.00482 (    5)
  SS BOND              : angle       2.15153 (   10)
  hydrogen bonds       : bond        0.04025 (  549)
  hydrogen bonds       : angle       4.58662 ( 1584)
  link_BETA1-3         : bond        0.00524 (    1)
  link_BETA1-3         : angle       1.73171 (    3)
  link_BETA1-4         : bond        0.00600 (   11)
  link_BETA1-4         : angle       2.20921 (   33)
  link_BETA1-6         : bond        0.00515 (    1)
  link_BETA1-6         : angle       2.14281 (    3)
  link_NAG-ASN         : bond        0.00487 (    7)
  link_NAG-ASN         : angle       3.20706 (   21)

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

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

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2634 Ramachandran restraints generated.
    1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  296 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 263
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  202 ASN cc_start: 0.8145 (m-40) cc_final: 0.7938 (t0)
REVERT: A  292 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7683 (m-80)
REVERT: A  556 TYR cc_start: 0.7819 (m-10) cc_final: 0.6950 (t80)
REVERT: A  580 LYS cc_start: 0.6333 (tptt) cc_final: 0.5551 (ttmm)
REVERT: A  886 LEU cc_start: 0.8494 (mt) cc_final: 0.8171 (mt)
REVERT: A  905 MET cc_start: 0.8277 (tpp) cc_final: 0.7946 (tpt)
REVERT: A  908 MET cc_start: 0.7841 (tpp) cc_final: 0.7592 (tpp)
REVERT: A 1094 PHE cc_start: 0.8064 (t80) cc_final: 0.7807 (t80)
REVERT: A 1170 ARG cc_start: 0.7780 (mmt90) cc_final: 0.6946 (ttt90)
REVERT: A 1198 PHE cc_start: 0.7293 (m-10) cc_final: 0.7057 (m-10)
REVERT: A 1256 LYS cc_start: 0.4689 (OUTLIER) cc_final: 0.3525 (ttmt)
REVERT: A 1285 MET cc_start: 0.7455 (tpp) cc_final: 0.7056 (mmp)
REVERT: A 1373 HIS cc_start: 0.6156 (t-90) cc_final: 0.5877 (t-90)
REVERT: A 1418 TYR cc_start: 0.7912 (m-80) cc_final: 0.7396 (m-80)
REVERT: A 1455 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7877 (mm-30)
REVERT: A 1473 LYS cc_start: 0.9017 (mmtp) cc_final: 0.8675 (mmtm)
  outliers start: 33
  outliers final: 29
  residues processed: 283
  average time/residue: 0.0911
  time to fit residues: 39.1088
Evaluate side-chains
  277 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 246
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  292 PHE
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  529 ILE
Chi-restraints excluded: chain A residue  597 GLU
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain A residue  733 LEU
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  739 LEU
Chi-restraints excluded: chain A residue  892 TYR
Chi-restraints excluded: chain A residue  938 VAL
Chi-restraints excluded: chain A residue 1023 ILE
Chi-restraints excluded: chain A residue 1032 HIS
Chi-restraints excluded: chain A residue 1108 VAL
Chi-restraints excluded: chain A residue 1109 CYS
Chi-restraints excluded: chain A residue 1141 MET
Chi-restraints excluded: chain A residue 1143 THR
Chi-restraints excluded: chain A residue 1147 LYS
Chi-restraints excluded: chain A residue 1226 HIS
Chi-restraints excluded: chain A residue 1239 LEU
Chi-restraints excluded: chain A residue 1256 LYS
Chi-restraints excluded: chain A residue 1322 MET
Chi-restraints excluded: chain A residue 1324 ILE
Chi-restraints excluded: chain A residue 1396 ILE
Chi-restraints excluded: chain A residue 1401 VAL
Chi-restraints excluded: chain A residue 1456 LEU
Chi-restraints excluded: chain A residue 1497 VAL
Chi-restraints excluded: chain A residue 1500 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 44 optimal weight:    5.9990
   chunk 65 optimal weight:    2.9990
   chunk 15 optimal weight:    0.1980
   chunk 0 optimal weight:   40.0000
   chunk 115 optimal weight:    0.3980
   chunk 116 optimal weight:    2.9990
   chunk 49 optimal weight:   10.0000
   chunk 39 optimal weight:    6.9990
   chunk 29 optimal weight:    0.8980
   chunk 35 optimal weight:    0.6980
   chunk 95 optimal weight:   10.0000
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 532 ASN
** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1039 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.172567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.139243 restraints weight = 16294.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.140309 restraints weight = 9884.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.141185 restraints weight = 7549.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.141367 restraints weight = 6410.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.142517 restraints weight = 5935.678|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7465
moved from start:          1.0559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10952  Z= 0.158
  Angle     :  0.876  21.514  14944  Z= 0.417
  Chirality :  0.046   0.237   1765
  Planarity :  0.006   0.133   1818
  Dihedral  :  6.566  44.780   1841
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 13.12
  Ramachandran Plot:
    Outliers :  0.76 %
    Allowed  : 10.78 %
    Favored  : 88.46 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 33.49 %
    Favored  : 63.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.08 %
    Twisted Proline : 2.13 %
    Twisted General : 0.71 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.20 (0.23), residues: 1317
  helix:  0.40 (0.18), residues: 857
  sheet: -0.90 (1.66), residues: 10
  loop : -3.23 (0.28), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1268 
 TYR   0.027   0.002   TYR A1089 
 PHE   0.038   0.002   PHE A 593 
 TRP   0.039   0.002   TRP A 922 
 HIS   0.008   0.001   HIS A1227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 (10927)
  covalent geometry    : angle       0.86332 (14874)
  SS BOND              : bond        0.00384 (    5)
  SS BOND              : angle       1.25791 (   10)
  hydrogen bonds       : bond        0.03992 (  549)
  hydrogen bonds       : angle       4.55933 ( 1584)
  link_BETA1-3         : bond        0.00541 (    1)
  link_BETA1-3         : angle       1.66659 (    3)
  link_BETA1-4         : bond        0.00613 (   11)
  link_BETA1-4         : angle       2.13937 (   33)
  link_BETA1-6         : bond        0.00541 (    1)
  link_BETA1-6         : angle       1.99533 (    3)
  link_NAG-ASN         : bond        0.00491 (    7)
  link_NAG-ASN         : angle       3.11010 (   21)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1942.35 seconds
wall clock time: 34 minutes 23.45 seconds (2063.45 seconds total)