Starting phenix.real_space_refine
on Fri Jul 25 19:21:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7dfz_30668/07_2025/7dfz_30668_neut_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7dfz_30668/07_2025/7dfz_30668.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7dfz_30668/07_2025/7dfz_30668.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7dfz_30668/07_2025/7dfz_30668.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7dfz_30668/07_2025/7dfz_30668_neut_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7dfz_30668/07_2025/7dfz_30668_neut_trim.cif"
  }
  resolution = 3.58
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.008
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: 5
    Type Number    sf(0)   Gaussians
     S      41      5.16       5
     C    4862      2.51       5
     N    1150      2.21       5
     O    1357      1.98       5
     F       2      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 42 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 7412
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 7004
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 897, 7004
          Classifications: {'peptide': 897}
          Link IDs: {'PTRANS': 46, 'TRANS': 850}
          Chain breaks: 2
    Chain: "E"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          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: "H"
      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: "J"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          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: "P"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          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: "T"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 212
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 212
          Unusual residues: {'CLR': 4, 'H56': 1, 'NAG': 5}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
  Time building chain proxies: 5.41, per 1000 atoms: 0.73
  Number of scatterers: 7412
  At special positions: 0
  Unit cell: (88.371, 76.37, 134.193, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      41     16.00
     F       2      9.00
     O    1357      8.00
     N    1150      7.00
     C    4862      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 471 " - pdb=" SG  CYS A 485 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 525 " - pdb=" SG  CYS A 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 920 " - pdb=" SG  CYS A 925 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 966 " - pdb=" SG  CYS A1024 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 967 " - pdb=" SG  CYS A 993 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 980 " - pdb=" SG  CYS A 989 " distance=2.04

  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
      " NAG E   2 " - " NAG E   3 "
      " NAG H   1 " - " NAG H   2 "
      " NAG P   2 " - " NAG P   3 "
    BETA1-4
      " NAG E   1 " - " NAG E   2 "
      " NAG J   1 " - " NAG J   2 "
      " NAG J   2 " - " NAG J   3 "
      " NAG P   1 " - " NAG P   2 "
      " NAG T   1 " - " NAG T   2 "
      " NAG T   2 " - " NAG T   3 "
    NAG-ASN
      " NAG A1301 " - " ASN A 431 "
      " NAG A1302 " - " ASN A 927 "
      " NAG A1303 " - " ASN A 416 "
      " NAG A1304 " - " ASN A1075 "
      " NAG A1305 " - " ASN A 479 "
      " NAG E   1 " - " ASN A 464 "
      " NAG H   1 " - " ASN A 506 "
      " NAG J   1 " - " ASN A 497 "
      " NAG P   1 " - " ASN A 909 "
      " NAG T   1 " - " ASN A1037 "
  Time building additional restraints: 2.34
  Conformation dependent library (CDL) restraints added in 893.4 milliseconds
  

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1686

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 7 sheets defined
      59.4% alpha, 5.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 332 through 351
      removed outlier: 3.647A  pdb=" N   LEU A 336 " --> pdb=" O   SER A 332 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LEU A 337 " --> pdb=" O   THR A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 373
      Proline residue:  A 362  - end of helix
      removed outlier: 4.133A  pdb=" N   ALA A 365 " --> pdb=" O   ILE A 361 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   LEU A 366 " --> pdb=" O   PRO A 362 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   GLY A 369 " --> pdb=" O   ALA A 365 " (cutoff:3.500A)
      removed outlier: 4.432A  pdb=" N   LEU A 370 " --> pdb=" O   LEU A 366 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   VAL A 371 " --> pdb=" O   ALA A 367 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   THR A 373 " --> pdb=" O   GLY A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 402
      removed outlier: 3.605A  pdb=" N   LYS A 394 " --> pdb=" O   ALA A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 437 through 453
      removed outlier: 3.536A  pdb=" N   LEU A 441 " --> pdb=" O   ASP A 437 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   LEU A 442 " --> pdb=" O   LEU A 438 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   GLU A 443 " --> pdb=" O   ASP A 439 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   LEU A 447 " --> pdb=" O   GLU A 443 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   ARG A 450 " --> pdb=" O   GLU A 446 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   HIS A 453 " --> pdb=" O   GLU A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 485
      removed outlier: 4.116A  pdb=" N   CYS A 485 " --> pdb=" O   LEU A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 489 through 494
    Processing helix  chain 'A' and resid 497 through 502
    Processing helix  chain 'A' and resid 517 through 528
      removed outlier: 3.773A  pdb=" N   HIS A 521 " --> pdb=" O   ASP A 517 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ASN A 527 " --> pdb=" O   LEU A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 554
    Processing helix  chain 'A' and resid 583 through 607
      removed outlier: 3.610A  pdb=" N   ALA A 587 " --> pdb=" O   ASP A 583 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   LEU A 591 " --> pdb=" O   ALA A 587 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   TRP A 592 " --> pdb=" O   GLN A 588 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   GLU A 593 " --> pdb=" O   ALA A 589 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   GLU A 594 " --> pdb=" O   LYS A 590 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ALA A 595 " --> pdb=" O   LEU A 591 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   ALA A 602 " --> pdb=" O   GLU A 598 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ARG A 605 " --> pdb=" O   ARG A 601 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   MET A 607 " --> pdb=" O   PHE A 603 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 617 through 623
      removed outlier: 4.125A  pdb=" N   LEU A 621 " --> pdb=" O   ALA A 617 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   GLU A 622 " --> pdb=" O   GLU A 618 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 624 through 631
      removed outlier: 3.759A  pdb=" N   THR A 628 " --> pdb=" O   GLU A 624 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   THR A 629 " --> pdb=" O   ILE A 625 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 638 through 648
      removed outlier: 4.833A  pdb=" N   PHE A 644 " --> pdb=" O   TYR A 640 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   LEU A 645 " --> pdb=" O   ILE A 641 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   TYR A 646 " --> pdb=" O   VAL A 642 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   ILE A 647 " --> pdb=" O   ILE A 643 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   SER A 648 " --> pdb=" O   PHE A 644 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 669 through 691
      removed outlier: 4.184A  pdb=" N   PHE A 687 " --> pdb=" O   ALA A 683 " (cutoff:3.500A)
      removed outlier: 4.753A  pdb=" N   SER A 688 " --> pdb=" O   MET A 684 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   TYR A 689 " --> pdb=" O   GLY A 685 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   LEU A 690 " --> pdb=" O   PHE A 686 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 697 through 701
      removed outlier: 3.630A  pdb=" N   GLN A 700 " --> pdb=" O   VAL A 697 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   VAL A 701 " --> pdb=" O   ILE A 698 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 697 through 701'
    Processing helix  chain 'A' and resid 702 through 722
      removed outlier: 4.933A  pdb=" N   SER A 708 " --> pdb=" O   PHE A 704 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   VAL A 709 " --> pdb=" O   LEU A 705 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   ASP A 712 " --> pdb=" O   SER A 708 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   ASN A 713 " --> pdb=" O   VAL A 709 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   ILE A 714 " --> pdb=" O   GLY A 710 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 731 through 742
      removed outlier: 4.383A  pdb=" N   GLY A 737 " --> pdb=" O   GLU A 733 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   ARG A 742 " --> pdb=" O   ARG A 738 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 743 through 750
      removed outlier: 3.624A  pdb=" N   CYS A 750 " --> pdb=" O   SER A 746 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 754 through 761
    Processing helix  chain 'A' and resid 762 through 764
      No H-bonds generated for 'chain 'A' and resid 762 through 764'
    Processing helix  chain 'A' and resid 766 through 780
      removed outlier: 3.612A  pdb=" N   VAL A 780 " --> pdb=" O   SER A 776 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 780 through 785
      removed outlier: 3.710A  pdb=" N   LEU A 785 " --> pdb=" O   ILE A 781 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 790 through 798
    Processing helix  chain 'A' and resid 828 through 840
      removed outlier: 4.061A  pdb=" N   LYS A 834 " --> pdb=" O   GLY A 830 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   ALA A 835 " --> pdb=" O   PHE A 831 " (cutoff:3.500A)
      Proline residue:  A 838  - end of helix
    Processing helix  chain 'A' and resid 848 through 864
      removed outlier: 3.870A  pdb=" N   TYR A 862 " --> pdb=" O   GLY A 858 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 865 through 867
      No H-bonds generated for 'chain 'A' and resid 865 through 867'
    Processing helix  chain 'A' and resid 872 through 877
      removed outlier: 3.643A  pdb=" N   LEU A 875 " --> pdb=" O   ASP A 872 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   ALA A 876 " --> pdb=" O   GLN A 873 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LEU A 877 " --> pdb=" O   GLU A 874 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 872 through 877'
    Processing helix  chain 'A' and resid 881 through 894
      removed outlier: 4.136A  pdb=" N   ASP A 885 " --> pdb=" O   SER A 881 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ARG A 892 " --> pdb=" O   LEU A 888 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   PHE A 894 " --> pdb=" O   LEU A 890 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 912 through 917
      removed outlier: 3.934A  pdb=" N   ASN A 917 " --> pdb=" O   GLU A 913 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 929 through 939
      removed outlier: 3.733A  pdb=" N   GLN A 935 " --> pdb=" O   THR A 931 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   GLU A 939 " --> pdb=" O   GLN A 935 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 952 through 961
      removed outlier: 3.788A  pdb=" N   ASP A 956 " --> pdb=" O   SER A 952 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1005 through 1016
      removed outlier: 3.770A  pdb=" N   HIS A1009 " --> pdb=" O   VAL A1005 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   LYS A1010 " --> pdb=" O   GLU A1006 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   TYR A1011 " --> pdb=" O   GLN A1007 " (cutoff:3.500A)
      Proline residue:  A1013  - end of helix
    Processing helix  chain 'A' and resid 1058 through 1081
      removed outlier: 3.591A  pdb=" N   TYR A1062 " --> pdb=" O   ASN A1058 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   THR A1063 " --> pdb=" O   SER A1059 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   GLU A1064 " --> pdb=" O   GLN A1060 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   LEU A1072 " --> pdb=" O   ALA A1068 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1103 through 1108
      removed outlier: 3.677A  pdb=" N   LEU A1106 " --> pdb=" O   GLU A1103 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   ILE A1108 " --> pdb=" O   TYR A1105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1109 through 1120
      removed outlier: 4.003A  pdb=" N   MET A1115 " --> pdb=" O   GLU A1111 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LEU A1120 " --> pdb=" O   LEU A1116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1120 through 1131
      removed outlier: 3.584A  pdb=" N   VAL A1126 " --> pdb=" O   PRO A1122 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   LEU A1129 " --> pdb=" O   ALA A1125 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   LEU A1131 " --> pdb=" O   SER A1127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1135 through 1160
    Processing helix  chain 'A' and resid 1168 through 1178
    Processing helix  chain 'A' and resid 1178 through 1192
      removed outlier: 3.518A  pdb=" N   VAL A1182 " --> pdb=" O   SER A1178 " (cutoff:3.500A)
      removed outlier: 4.677A  pdb=" N   HIS A1184 " --> pdb=" O   GLU A1180 " (cutoff:3.500A)
      removed outlier: 5.148A  pdb=" N   ILE A1185 " --> pdb=" O   PHE A1181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1196 through 1225
      removed outlier: 4.173A  pdb=" N   ALA A1201 " --> pdb=" O   TRP A1197 " (cutoff:3.500A)
      removed outlier: 5.530A  pdb=" N   LYS A1202 " --> pdb=" O   LEU A1198 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   GLU A1203 " --> pdb=" O   GLU A1199 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   ALA A1204 " --> pdb=" O   ARG A1200 " (cutoff:3.500A)
      removed outlier: 5.022A  pdb=" N   SER A1210 " --> pdb=" O   ILE A1206 " (cutoff:3.500A)
      removed outlier: 4.659A  pdb=" N   ALA A1211 " --> pdb=" O   SER A1207 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   THR A1219 " --> pdb=" O   GLY A1215 " (cutoff:3.500A)
      Proline residue:  A1222  - end of helix
    Processing helix  chain 'A' and resid 1226 through 1230
      removed outlier: 3.867A  pdb=" N   ALA A1230 " --> pdb=" O   LEU A1227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1232 through 1239
    Processing helix  chain 'A' and resid 1242 through 1251
    Processing helix  chain 'A' and resid 1251 through 1256
      removed outlier: 3.506A  pdb=" N   VAL A1256 " --> pdb=" O   LEU A1252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1257 through 1263
    Processing sheet with id=AA1, first strand: chain 'A' and resid 487 through 488
      removed outlier: 3.802A  pdb=" N   ALA A 569 " --> pdb=" O   GLY A 557 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 487 through 488
    Processing sheet with id=AA3, first strand: chain 'A' and resid 422 through 424
    Processing sheet with id=AA4, first strand: chain 'A' and resid 505 through 506
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1050 through 1052
    Processing sheet with id=AA6, first strand: chain 'A' and resid 968 through 969
      removed outlier: 3.722A  pdb=" N   LYS A 991 " --> pdb=" O   LEU A 969 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1036 through 1038
      removed outlier: 6.872A  pdb=" N   ASN A1037 " --> pdb=" O   LEU A1045 " (cutoff:3.500A)

    288 hydrogen bonds defined for protein.
    828 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.22

  Time building geometry restraints manager: 2.69 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1123
        1.31 -     1.44: 2107
        1.44 -     1.56: 4298
        1.56 -     1.69: 9
        1.69 -     1.82: 65
  Bond restraints: 7602
  Sorted by residual:
  bond pdb=" C1  H56 A1306 "
       pdb=" N1  H56 A1306 "
    ideal  model  delta    sigma   weight residual
    1.365  1.759 -0.394 2.00e-02 2.50e+03 3.89e+02
  bond pdb=" C2  H56 A1306 "
       pdb=" C9  H56 A1306 "
    ideal  model  delta    sigma   weight residual
    1.555  1.345  0.210 2.00e-02 2.50e+03 1.10e+02
  bond pdb=" C20 H56 A1306 "
       pdb=" C21 H56 A1306 "
    ideal  model  delta    sigma   weight residual
    1.383  1.539 -0.156 2.00e-02 2.50e+03 6.06e+01
  bond pdb=" C5  H56 A1306 "
       pdb=" C6  H56 A1306 "
    ideal  model  delta    sigma   weight residual
    1.380  1.532 -0.152 2.00e-02 2.50e+03 5.81e+01
  bond pdb=" C19 H56 A1306 "
       pdb=" C24 H56 A1306 "
    ideal  model  delta    sigma   weight residual
    1.389  1.541 -0.152 2.00e-02 2.50e+03 5.80e+01
  ... (remaining 7597 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.61: 10087
        2.61 -     5.21: 250
        5.21 -     7.82: 33
        7.82 -    10.42: 6
       10.42 -    13.03: 4
  Bond angle restraints: 10380
  Sorted by residual:
  angle pdb=" N   ILE A 641 "
        pdb=" CA  ILE A 641 "
        pdb=" C   ILE A 641 "
      ideal   model   delta    sigma   weight residual
     113.53  107.33    6.20 9.80e-01 1.04e+00 4.01e+01
  angle pdb=" CA  VAL A 380 "
        pdb=" CB  VAL A 380 "
        pdb=" CG1 VAL A 380 "
      ideal   model   delta    sigma   weight residual
     110.40  118.03   -7.63 1.70e+00 3.46e-01 2.01e+01
  angle pdb=" C1  H56 A1306 "
        pdb=" N1  H56 A1306 "
        pdb=" C2  H56 A1306 "
      ideal   model   delta    sigma   weight residual
      95.10   82.07   13.03 3.00e+00 1.11e-01 1.89e+01
  angle pdb=" C1  H56 A1306 "
        pdb=" C9  H56 A1306 "
        pdb=" C2  H56 A1306 "
      ideal   model   delta    sigma   weight residual
      85.54   98.26  -12.72 3.00e+00 1.11e-01 1.80e+01
  angle pdb=" CA  GLU A 566 "
        pdb=" CB  GLU A 566 "
        pdb=" CG  GLU A 566 "
      ideal   model   delta    sigma   weight residual
     114.10  122.32   -8.22 2.00e+00 2.50e-01 1.69e+01
  ... (remaining 10375 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.91: 4561
       22.91 -    45.82: 317
       45.82 -    68.73: 28
       68.73 -    91.64: 16
       91.64 -   114.55: 7
  Dihedral angle restraints: 4929
    sinusoidal: 2316
      harmonic: 2613
  Sorted by residual:
  dihedral pdb=" CA  ILE A1022 "
           pdb=" C   ILE A1022 "
           pdb=" N   LYS A1023 "
           pdb=" CA  LYS A1023 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.64   30.36     0      5.00e+00 4.00e-02 3.69e+01
  dihedral pdb=" CA  CYS A 925 "
           pdb=" C   CYS A 925 "
           pdb=" N   ASN A 926 "
           pdb=" CA  ASN A 926 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.65  -27.35     0      5.00e+00 4.00e-02 2.99e+01
  dihedral pdb=" CA  GLN A 492 "
           pdb=" C   GLN A 492 "
           pdb=" N   TYR A 493 "
           pdb=" CA  TYR A 493 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.15   20.85     0      5.00e+00 4.00e-02 1.74e+01
  ... (remaining 4926 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 1081
       0.076 -    0.151: 163
       0.151 -    0.227: 15
       0.227 -    0.303: 4
       0.303 -    0.378: 3
  Chirality restraints: 1266
  Sorted by residual:
  chirality pdb=" C1  NAG H   2 "
            pdb=" O3  NAG H   1 "
            pdb=" C2  NAG H   2 "
            pdb=" O5  NAG H   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.14   -0.26 2.00e-02 2.50e+03 1.68e+02
  chirality pdb=" C1  NAG E   3 "
            pdb=" O3  NAG E   2 "
            pdb=" C2  NAG E   3 "
            pdb=" O5  NAG E   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.20   -0.20 2.00e-02 2.50e+03 1.02e+02
  chirality pdb=" C1  NAG P   3 "
            pdb=" O3  NAG P   2 "
            pdb=" C2  NAG P   3 "
            pdb=" O5  NAG P   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.30   -0.10 2.00e-02 2.50e+03 2.54e+01
  ... (remaining 1263 not shown)

  Planarity restraints: 1264
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG P   3 "    0.351 2.00e-02 2.50e+03   3.04e-01 1.15e+03
        pdb=" C7  NAG P   3 "   -0.082 2.00e-02 2.50e+03
        pdb=" C8  NAG P   3 "    0.091 2.00e-02 2.50e+03
        pdb=" N2  NAG P   3 "   -0.539 2.00e-02 2.50e+03
        pdb=" O7  NAG P   3 "    0.179 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG T   3 "    0.346 2.00e-02 2.50e+03   2.99e-01 1.11e+03
        pdb=" C7  NAG T   3 "   -0.080 2.00e-02 2.50e+03
        pdb=" C8  NAG T   3 "    0.066 2.00e-02 2.50e+03
        pdb=" N2  NAG T   3 "   -0.527 2.00e-02 2.50e+03
        pdb=" O7  NAG T   3 "    0.195 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG T   2 "   -0.344 2.00e-02 2.50e+03   2.98e-01 1.11e+03
        pdb=" C7  NAG T   2 "    0.082 2.00e-02 2.50e+03
        pdb=" C8  NAG T   2 "   -0.095 2.00e-02 2.50e+03
        pdb=" N2  NAG T   2 "    0.530 2.00e-02 2.50e+03
        pdb=" O7  NAG T   2 "   -0.172 2.00e-02 2.50e+03
  ... (remaining 1261 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 214
        2.71 -     3.25: 7575
        3.25 -     3.80: 11132
        3.80 -     4.35: 13825
        4.35 -     4.90: 23417
  Nonbonded interactions: 56163
  Sorted by model distance:
  nonbonded pdb=" O   ALA A 923 "
            pdb=" OG  SER A1000 "
     model   vdw
     2.157 3.040
  nonbonded pdb=" OE1 GLN A 409 "
            pdb=" OH  TYR A 886 "
     model   vdw
     2.167 3.040
  nonbonded pdb=" OH  TYR A 836 "
            pdb=" O   LEU A1255 "
     model   vdw
     2.172 3.040
  nonbonded pdb=" O3  NAG E   2 "
            pdb=" O6  NAG E   2 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" O4  NAG P   3 "
            pdb=" O6  NAG P   3 "
     model   vdw
     2.266 3.040
  ... (remaining 56158 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 'E'
  selection = chain 'J'
  selection = chain 'P'
  selection = chain 'T'
}

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:             2.900
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.140
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
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   0.394   7627  Z= 0.477
  Angle     :  1.032  13.027  10449  Z= 0.502
  Chirality :  0.057   0.378   1266
  Planarity :  0.029   0.304   1254
  Dihedral  : 15.654 114.555   3225
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 18.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.07 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.56 (0.23), residues: 891
  helix: -2.33 (0.19), residues: 484
  sheet: -1.83 (0.66), residues: 57
  loop : -2.28 (0.30), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 953 
 HIS   0.008   0.002   HIS A 400 
 PHE   0.053   0.003   PHE A 704 
 TYR   0.016   0.002   TYR A1032 
 ARG   0.023   0.001   ARG A1187 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00887 (   10)
  link_NAG-ASN         : angle       5.31583 (   30)
  link_BETA1-4         : bond        0.00476 (    6)
  link_BETA1-4         : angle       1.39709 (   18)
  hydrogen bonds       : bond        0.15848 (  286)
  hydrogen bonds       : angle       6.08551 (  828)
  SS BOND              : bond        0.00336 (    6)
  SS BOND              : angle       1.96300 (   12)
  link_BETA1-3         : bond        0.01087 (    3)
  link_BETA1-3         : angle       2.94316 (    9)
  covalent geometry    : bond        0.00979 ( 7602)
  covalent geometry    : angle       0.98759 (10380)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.847 
Fit side-chains
   revert: symmetry clash
REVERT: A  789 SER cc_start: 0.8420 (t) cc_final: 0.8114 (t)
REVERT: A  983 THR cc_start: 0.9345 (t) cc_final: 0.9080 (p)
REVERT: A  998 MET cc_start: 0.6458 (tmm) cc_final: 0.6200 (tmm)
REVERT: A 1115 MET cc_start: 0.8406 (ttm) cc_final: 0.8176 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.1631
  time to fit residues: 25.5941
Evaluate side-chains
  87 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 37 optimal weight:    0.1980
   chunk 23 optimal weight:    0.0170
   chunk 45 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   chunk 69 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 51 optimal weight:    0.5980
   chunk 80 optimal weight:    0.7980
   overall best weight:    0.4618

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

Flipped N/Q/H residues before XYZ refinement:
** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.122995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.097782 restraints weight = 12493.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.100858 restraints weight = 6882.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.102881 restraints weight = 4719.211|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.1160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7627  Z= 0.156
  Angle     :  0.855  12.344  10449  Z= 0.374
  Chirality :  0.052   0.393   1266
  Planarity :  0.005   0.053   1254
  Dihedral  : 13.822 113.819   1642
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  :  9.54 %
    Favored  : 89.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.37 (0.27), residues: 891
  helix: -1.19 (0.23), residues: 496
  sheet: -1.75 (0.62), residues: 57
  loop : -1.93 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 953 
 HIS   0.003   0.001   HIS A1184 
 PHE   0.024   0.002   PHE A1124 
 TYR   0.011   0.001   TYR A1032 
 ARG   0.004   0.000   ARG A 968 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01040 (   10)
  link_NAG-ASN         : angle       5.25104 (   30)
  link_BETA1-4         : bond        0.00884 (    6)
  link_BETA1-4         : angle       2.77642 (   18)
  hydrogen bonds       : bond        0.04215 (  286)
  hydrogen bonds       : angle       4.47175 (  828)
  SS BOND              : bond        0.00398 (    6)
  SS BOND              : angle       0.92239 (   12)
  link_BETA1-3         : bond        0.02181 (    3)
  link_BETA1-3         : angle       5.11797 (    9)
  covalent geometry    : bond        0.00338 ( 7602)
  covalent geometry    : angle       0.78705 (10380)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 0.783 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  593 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7512 (mt-10)
REVERT: A  693 ARG cc_start: 0.8082 (mtm180) cc_final: 0.7624 (mtp85)
REVERT: A  747 MET cc_start: 0.8314 (tmm) cc_final: 0.7659 (tmm)
REVERT: A  760 LEU cc_start: 0.8741 (tp) cc_final: 0.8478 (tt)
REVERT: A  781 ILE cc_start: 0.8825 (tt) cc_final: 0.8561 (tp)
REVERT: A  788 MET cc_start: 0.7287 (mtt) cc_final: 0.6839 (mtt)
REVERT: A  983 THR cc_start: 0.9368 (t) cc_final: 0.9094 (p)
REVERT: A 1050 MET cc_start: 0.8552 (ttp) cc_final: 0.8327 (ttp)
REVERT: A 1111 GLU cc_start: 0.7143 (tp30) cc_final: 0.6448 (tm-30)
  outliers start: 9
  outliers final: 7
  residues processed: 101
  average time/residue: 0.1733
  time to fit residues: 25.1971
Evaluate side-chains
  92 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  622 GLU
Chi-restraints excluded: chain A residue  785 LEU
Chi-restraints excluded: chain A residue  796 SER
Chi-restraints excluded: chain A residue  861 LEU
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1265 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9980
   chunk 72 optimal weight:    0.8980
   chunk 20 optimal weight:    0.0010
   chunk 70 optimal weight:    0.8980
   chunk 61 optimal weight:    6.9990
   chunk 41 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 77 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.6786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.122126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.097009 restraints weight = 12674.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.100096 restraints weight = 6919.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.102147 restraints weight = 4721.583|
|-----------------------------------------------------------------------------|
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.1471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7627  Z= 0.155
  Angle     :  0.784  11.832  10449  Z= 0.345
  Chirality :  0.049   0.377   1266
  Planarity :  0.004   0.049   1254
  Dihedral  : 13.057 112.894   1642
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 13.07 %
    Favored  : 84.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.92 (0.28), residues: 891
  helix: -0.79 (0.24), residues: 497
  sheet: -1.58 (0.62), residues: 57
  loop : -1.79 (0.33), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 344 
 HIS   0.003   0.001   HIS A1184 
 PHE   0.023   0.001   PHE A 372 
 TYR   0.009   0.001   TYR A 640 
 ARG   0.002   0.000   ARG A 968 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00925 (   10)
  link_NAG-ASN         : angle       4.86130 (   30)
  link_BETA1-4         : bond        0.00607 (    6)
  link_BETA1-4         : angle       1.96564 (   18)
  hydrogen bonds       : bond        0.03796 (  286)
  hydrogen bonds       : angle       4.23464 (  828)
  SS BOND              : bond        0.00301 (    6)
  SS BOND              : angle       0.60955 (   12)
  link_BETA1-3         : bond        0.01839 (    3)
  link_BETA1-3         : angle       4.16345 (    9)
  covalent geometry    : bond        0.00359 ( 7602)
  covalent geometry    : angle       0.72653 (10380)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.768 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  339 GLN cc_start: 0.7159 (tt0) cc_final: 0.6890 (mt0)
REVERT: A  693 ARG cc_start: 0.8088 (mtm180) cc_final: 0.7652 (mtp85)
REVERT: A  783 ASP cc_start: 0.8576 (OUTLIER) cc_final: 0.8373 (t0)
REVERT: A  788 MET cc_start: 0.7545 (mtt) cc_final: 0.7154 (mtt)
REVERT: A  983 THR cc_start: 0.9340 (t) cc_final: 0.9043 (p)
REVERT: A 1050 MET cc_start: 0.8538 (ttp) cc_final: 0.8319 (ttp)
REVERT: A 1111 GLU cc_start: 0.7214 (tp30) cc_final: 0.6586 (tm-30)
  outliers start: 16
  outliers final: 8
  residues processed: 109
  average time/residue: 0.1573
  time to fit residues: 24.8292
Evaluate side-chains
  98 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  783 ASP
Chi-restraints excluded: chain A residue  796 SER
Chi-restraints excluded: chain A residue  861 LEU
Chi-restraints excluded: chain A residue  938 THR
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1221 LEU
Chi-restraints excluded: chain A residue 1265 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 83 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 23 optimal weight:    0.4980
   chunk 31 optimal weight:    2.9990
   chunk 72 optimal weight:    0.7980
   chunk 27 optimal weight:    0.5980
   chunk 24 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.121992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.096813 restraints weight = 12595.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.099862 restraints weight = 6901.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.101941 restraints weight = 4723.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.1643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7627  Z= 0.154
  Angle     :  0.778  11.746  10449  Z= 0.340
  Chirality :  0.050   0.376   1266
  Planarity :  0.004   0.050   1254
  Dihedral  : 12.647 113.569   1642
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 17.12 %
    Favored  : 80.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.75 (0.28), residues: 891
  helix: -0.63 (0.24), residues: 496
  sheet: -1.38 (0.63), residues: 57
  loop : -1.79 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 953 
 HIS   0.003   0.001   HIS A 735 
 PHE   0.024   0.001   PHE A 372 
 TYR   0.009   0.001   TYR A 640 
 ARG   0.002   0.000   ARG A 738 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00888 (   10)
  link_NAG-ASN         : angle       4.75119 (   30)
  link_BETA1-4         : bond        0.00588 (    6)
  link_BETA1-4         : angle       1.93966 (   18)
  hydrogen bonds       : bond        0.03608 (  286)
  hydrogen bonds       : angle       4.18504 (  828)
  SS BOND              : bond        0.00294 (    6)
  SS BOND              : angle       0.79722 (   12)
  link_BETA1-3         : bond        0.01666 (    3)
  link_BETA1-3         : angle       4.11272 (    9)
  covalent geometry    : bond        0.00358 ( 7602)
  covalent geometry    : angle       0.72312 (10380)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.767 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  339 GLN cc_start: 0.7249 (tt0) cc_final: 0.6987 (mt0)
REVERT: A  693 ARG cc_start: 0.8073 (mtm180) cc_final: 0.7628 (mtp85)
REVERT: A  783 ASP cc_start: 0.8600 (t0) cc_final: 0.8386 (t0)
REVERT: A  788 MET cc_start: 0.7704 (mtt) cc_final: 0.7320 (mtt)
REVERT: A  983 THR cc_start: 0.9325 (t) cc_final: 0.9022 (p)
REVERT: A 1050 MET cc_start: 0.8543 (ttp) cc_final: 0.8336 (ttp)
REVERT: A 1111 GLU cc_start: 0.7191 (tp30) cc_final: 0.6594 (tm-30)
REVERT: A 1187 ARG cc_start: 0.8174 (tpp80) cc_final: 0.7200 (tmm160)
  outliers start: 15
  outliers final: 12
  residues processed: 104
  average time/residue: 0.1627
  time to fit residues: 24.4349
Evaluate side-chains
  101 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  699 LEU
Chi-restraints excluded: chain A residue  796 SER
Chi-restraints excluded: chain A residue  861 LEU
Chi-restraints excluded: chain A residue  906 LEU
Chi-restraints excluded: chain A residue  916 MET
Chi-restraints excluded: chain A residue  938 THR
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1131 LEU
Chi-restraints excluded: chain A residue 1140 LEU
Chi-restraints excluded: chain A residue 1221 LEU
Chi-restraints excluded: chain A residue 1265 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 85 optimal weight:    0.8980
   chunk 49 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 61 optimal weight:    5.9990
   chunk 68 optimal weight:    0.7980
   chunk 21 optimal weight:    0.5980
   chunk 48 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 400 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.121904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.096590 restraints weight = 12665.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.099648 restraints weight = 6968.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.101677 restraints weight = 4786.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.1790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   7627  Z= 0.153
  Angle     :  0.773  11.722  10449  Z= 0.337
  Chirality :  0.050   0.374   1266
  Planarity :  0.004   0.049   1254
  Dihedral  : 12.228 113.170   1642
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 17.39 %
    Favored  : 79.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.61 (0.28), residues: 891
  helix: -0.50 (0.24), residues: 492
  sheet: -1.23 (0.64), residues: 57
  loop : -1.74 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 953 
 HIS   0.003   0.001   HIS A1184 
 PHE   0.019   0.001   PHE A 372 
 TYR   0.009   0.001   TYR A 640 
 ARG   0.001   0.000   ARG A 738 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00868 (   10)
  link_NAG-ASN         : angle       4.69510 (   30)
  link_BETA1-4         : bond        0.00574 (    6)
  link_BETA1-4         : angle       1.87659 (   18)
  hydrogen bonds       : bond        0.03570 (  286)
  hydrogen bonds       : angle       4.12857 (  828)
  SS BOND              : bond        0.00298 (    6)
  SS BOND              : angle       0.75463 (   12)
  link_BETA1-3         : bond        0.01639 (    3)
  link_BETA1-3         : angle       4.00420 (    9)
  covalent geometry    : bond        0.00357 ( 7602)
  covalent geometry    : angle       0.71948 (10380)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 96
  time to evaluate  : 0.763 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  339 GLN cc_start: 0.7298 (tt0) cc_final: 0.7021 (mt0)
REVERT: A  566 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7692 (tt0)
REVERT: A  693 ARG cc_start: 0.8042 (mtm180) cc_final: 0.7561 (mtp85)
REVERT: A  766 MET cc_start: 0.7714 (mmp) cc_final: 0.7356 (mmp)
REVERT: A  788 MET cc_start: 0.7677 (mtt) cc_final: 0.7310 (mtt)
REVERT: A  789 SER cc_start: 0.8847 (t) cc_final: 0.8529 (t)
REVERT: A  983 THR cc_start: 0.9317 (t) cc_final: 0.9027 (p)
REVERT: A 1111 GLU cc_start: 0.7189 (tp30) cc_final: 0.6586 (tm-30)
REVERT: A 1187 ARG cc_start: 0.8142 (tpp80) cc_final: 0.7207 (tmm160)
  outliers start: 24
  outliers final: 15
  residues processed: 113
  average time/residue: 0.1603
  time to fit residues: 26.0362
Evaluate side-chains
  106 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  566 GLU
Chi-restraints excluded: chain A residue  675 VAL
Chi-restraints excluded: chain A residue  699 LEU
Chi-restraints excluded: chain A residue  756 ILE
Chi-restraints excluded: chain A residue  785 LEU
Chi-restraints excluded: chain A residue  796 SER
Chi-restraints excluded: chain A residue  861 LEU
Chi-restraints excluded: chain A residue  906 LEU
Chi-restraints excluded: chain A residue  938 THR
Chi-restraints excluded: chain A residue 1063 THR
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1140 LEU
Chi-restraints excluded: chain A residue 1221 LEU
Chi-restraints excluded: chain A residue 1265 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 79 optimal weight:    0.4980
   chunk 10 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0170
   chunk 1 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   chunk 13 optimal weight:    0.0870
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.3996

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

Flipped N/Q/H residues before XYZ refinement:
A1233 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.121657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.095659 restraints weight = 12823.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.099010 restraints weight = 6627.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.101222 restraints weight = 4382.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.2004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   7627  Z= 0.125
  Angle     :  0.755  11.506  10449  Z= 0.329
  Chirality :  0.048   0.373   1266
  Planarity :  0.004   0.048   1254
  Dihedral  : 11.695 113.134   1642
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 18.43 %
    Favored  : 79.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.46 (0.29), residues: 891
  helix: -0.37 (0.25), residues: 489
  sheet: -1.35 (0.63), residues: 60
  loop : -1.66 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 953 
 HIS   0.005   0.001   HIS A 521 
 PHE   0.023   0.001   PHE A1124 
 TYR   0.008   0.001   TYR A 901 
 ARG   0.002   0.000   ARG A 498 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00901 (   10)
  link_NAG-ASN         : angle       4.57130 (   30)
  link_BETA1-4         : bond        0.00580 (    6)
  link_BETA1-4         : angle       1.84014 (   18)
  hydrogen bonds       : bond        0.03245 (  286)
  hydrogen bonds       : angle       4.02606 (  828)
  SS BOND              : bond        0.00242 (    6)
  SS BOND              : angle       0.65435 (   12)
  link_BETA1-3         : bond        0.01592 (    3)
  link_BETA1-3         : angle       3.89886 (    9)
  covalent geometry    : bond        0.00281 ( 7602)
  covalent geometry    : angle       0.70308 (10380)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.741 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  339 GLN cc_start: 0.7303 (tt0) cc_final: 0.7018 (mt0)
REVERT: A  559 TYR cc_start: 0.8940 (p90) cc_final: 0.8399 (p90)
REVERT: A  693 ARG cc_start: 0.8015 (mtm180) cc_final: 0.7587 (mtp85)
REVERT: A  766 MET cc_start: 0.7758 (mmp) cc_final: 0.7531 (mmp)
REVERT: A  788 MET cc_start: 0.7616 (mtt) cc_final: 0.7350 (mtt)
REVERT: A  789 SER cc_start: 0.8880 (t) cc_final: 0.8580 (t)
REVERT: A  983 THR cc_start: 0.9289 (t) cc_final: 0.9036 (p)
REVERT: A 1111 GLU cc_start: 0.7338 (tp30) cc_final: 0.6709 (tm-30)
REVERT: A 1187 ARG cc_start: 0.8183 (tpp80) cc_final: 0.7273 (tmm160)
  outliers start: 19
  outliers final: 15
  residues processed: 108
  average time/residue: 0.1604
  time to fit residues: 24.9491
Evaluate side-chains
  104 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  675 VAL
Chi-restraints excluded: chain A residue  699 LEU
Chi-restraints excluded: chain A residue  781 ILE
Chi-restraints excluded: chain A residue  785 LEU
Chi-restraints excluded: chain A residue  796 SER
Chi-restraints excluded: chain A residue  861 LEU
Chi-restraints excluded: chain A residue  906 LEU
Chi-restraints excluded: chain A residue 1063 THR
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1140 LEU
Chi-restraints excluded: chain A residue 1221 LEU
Chi-restraints excluded: chain A residue 1265 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 62 optimal weight:    6.9990
   chunk 19 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 58 optimal weight:    0.2980
   chunk 48 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 72 optimal weight:    0.6980
   chunk 13 optimal weight:    0.0770
   chunk 1 optimal weight:    0.7980
   chunk 44 optimal weight:    0.5980
   chunk 61 optimal weight:    2.9990
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1253 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.122522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.096166 restraints weight = 12729.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.099580 restraints weight = 6501.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.101869 restraints weight = 4303.898|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.2113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7627  Z= 0.132
  Angle     :  0.759  11.346  10449  Z= 0.330
  Chirality :  0.048   0.375   1266
  Planarity :  0.004   0.048   1254
  Dihedral  : 11.283 112.878   1642
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 20.13 %
    Favored  : 76.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.29), residues: 891
  helix: -0.23 (0.25), residues: 489
  sheet: -1.29 (0.63), residues: 60
  loop : -1.63 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 953 
 HIS   0.003   0.000   HIS A1184 
 PHE   0.027   0.001   PHE A 832 
 TYR   0.009   0.001   TYR A 901 
 ARG   0.001   0.000   ARG A1048 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00835 (   10)
  link_NAG-ASN         : angle       4.53510 (   30)
  link_BETA1-4         : bond        0.00566 (    6)
  link_BETA1-4         : angle       1.84096 (   18)
  hydrogen bonds       : bond        0.03223 (  286)
  hydrogen bonds       : angle       3.97548 (  828)
  SS BOND              : bond        0.00621 (    6)
  SS BOND              : angle       0.94364 (   12)
  link_BETA1-3         : bond        0.01527 (    3)
  link_BETA1-3         : angle       3.80887 (    9)
  covalent geometry    : bond        0.00302 ( 7602)
  covalent geometry    : angle       0.70822 (10380)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 96
  time to evaluate  : 0.874 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  339 GLN cc_start: 0.7484 (tt0) cc_final: 0.7113 (mt0)
REVERT: A  559 TYR cc_start: 0.8906 (p90) cc_final: 0.8376 (p90)
REVERT: A  566 GLU cc_start: 0.8144 (tt0) cc_final: 0.7631 (tt0)
REVERT: A  591 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8874 (tt)
REVERT: A  693 ARG cc_start: 0.8067 (mtm180) cc_final: 0.7648 (mtp85)
REVERT: A  766 MET cc_start: 0.7747 (mmp) cc_final: 0.7534 (mmp)
REVERT: A  788 MET cc_start: 0.7676 (mtt) cc_final: 0.7385 (mtt)
REVERT: A  789 SER cc_start: 0.8940 (t) cc_final: 0.8674 (t)
REVERT: A  983 THR cc_start: 0.9280 (t) cc_final: 0.9011 (p)
REVERT: A 1111 GLU cc_start: 0.7312 (tp30) cc_final: 0.6659 (tm-30)
REVERT: A 1187 ARG cc_start: 0.8135 (tpp80) cc_final: 0.7192 (tmm160)
  outliers start: 23
  outliers final: 16
  residues processed: 111
  average time/residue: 0.1634
  time to fit residues: 26.4165
Evaluate side-chains
  111 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  636 PHE
Chi-restraints excluded: chain A residue  675 VAL
Chi-restraints excluded: chain A residue  781 ILE
Chi-restraints excluded: chain A residue  785 LEU
Chi-restraints excluded: chain A residue  796 SER
Chi-restraints excluded: chain A residue  861 LEU
Chi-restraints excluded: chain A residue  906 LEU
Chi-restraints excluded: chain A residue 1063 THR
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1140 LEU
Chi-restraints excluded: chain A residue 1221 LEU
Chi-restraints excluded: chain A residue 1265 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 13 optimal weight:    0.1980
   chunk 27 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0370
   chunk 71 optimal weight:    0.8980
   chunk 53 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.5258

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

Flipped N/Q/H residues before XYZ refinement:
** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.122488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.096128 restraints weight = 12852.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.099555 restraints weight = 6509.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.101841 restraints weight = 4301.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.2197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7627  Z= 0.135
  Angle     :  0.763  11.057  10449  Z= 0.332
  Chirality :  0.048   0.371   1266
  Planarity :  0.004   0.048   1254
  Dihedral  : 10.985 112.968   1642
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 20.26 %
    Favored  : 76.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.29), residues: 891
  helix: -0.12 (0.25), residues: 478
  sheet: -1.25 (0.63), residues: 60
  loop : -1.56 (0.34), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 953 
 HIS   0.003   0.000   HIS A1184 
 PHE   0.035   0.001   PHE A 832 
 TYR   0.010   0.001   TYR A 901 
 ARG   0.001   0.000   ARG A1048 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00842 (   10)
  link_NAG-ASN         : angle       4.48520 (   30)
  link_BETA1-4         : bond        0.00554 (    6)
  link_BETA1-4         : angle       1.85861 (   18)
  hydrogen bonds       : bond        0.03195 (  286)
  hydrogen bonds       : angle       4.00652 (  828)
  SS BOND              : bond        0.00169 (    6)
  SS BOND              : angle       2.15515 (   12)
  link_BETA1-3         : bond        0.01489 (    3)
  link_BETA1-3         : angle       3.73369 (    9)
  covalent geometry    : bond        0.00313 ( 7602)
  covalent geometry    : angle       0.71029 (10380)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.894 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  339 GLN cc_start: 0.7542 (tt0) cc_final: 0.7124 (mt0)
REVERT: A  559 TYR cc_start: 0.8909 (p90) cc_final: 0.8496 (p90)
REVERT: A  566 GLU cc_start: 0.8150 (tt0) cc_final: 0.7695 (tt0)
REVERT: A  591 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8881 (tt)
REVERT: A  693 ARG cc_start: 0.8078 (mtm180) cc_final: 0.7664 (mtp85)
REVERT: A  747 MET cc_start: 0.7953 (ttt) cc_final: 0.7712 (tmm)
REVERT: A  788 MET cc_start: 0.7793 (mtt) cc_final: 0.7507 (mtt)
REVERT: A  789 SER cc_start: 0.8916 (t) cc_final: 0.8670 (t)
REVERT: A  983 THR cc_start: 0.9244 (t) cc_final: 0.8976 (p)
REVERT: A 1111 GLU cc_start: 0.7300 (tp30) cc_final: 0.6695 (tm-30)
REVERT: A 1187 ARG cc_start: 0.8143 (tpp80) cc_final: 0.7178 (tmm160)
REVERT: A 1218 MET cc_start: 0.6269 (tpp) cc_final: 0.5649 (tpp)
  outliers start: 22
  outliers final: 18
  residues processed: 113
  average time/residue: 0.1666
  time to fit residues: 27.1832
Evaluate side-chains
  114 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  636 PHE
Chi-restraints excluded: chain A residue  675 VAL
Chi-restraints excluded: chain A residue  699 LEU
Chi-restraints excluded: chain A residue  781 ILE
Chi-restraints excluded: chain A residue  785 LEU
Chi-restraints excluded: chain A residue  796 SER
Chi-restraints excluded: chain A residue  861 LEU
Chi-restraints excluded: chain A residue  906 LEU
Chi-restraints excluded: chain A residue  931 THR
Chi-restraints excluded: chain A residue 1063 THR
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1140 LEU
Chi-restraints excluded: chain A residue 1221 LEU
Chi-restraints excluded: chain A residue 1265 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 67 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 70 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9990
   chunk 84 optimal weight:    0.8980
   chunk 85 optimal weight:    0.6980
   chunk 73 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 612 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.121805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.095664 restraints weight = 12875.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.098965 restraints weight = 6650.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.101168 restraints weight = 4444.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.2190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   7627  Z= 0.164
  Angle     :  0.792  10.959  10449  Z= 0.347
  Chirality :  0.049   0.372   1266
  Planarity :  0.004   0.048   1254
  Dihedral  : 10.852 112.846   1642
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 20.65 %
    Favored  : 76.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.29), residues: 891
  helix: -0.16 (0.25), residues: 484
  sheet: -1.38 (0.63), residues: 61
  loop : -1.67 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 953 
 HIS   0.003   0.001   HIS A1184 
 PHE   0.028   0.001   PHE A 832 
 TYR   0.009   0.001   TYR A 901 
 ARG   0.001   0.000   ARG A 585 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00783 (   10)
  link_NAG-ASN         : angle       4.51714 (   30)
  link_BETA1-4         : bond        0.00539 (    6)
  link_BETA1-4         : angle       1.91007 (   18)
  hydrogen bonds       : bond        0.03390 (  286)
  hydrogen bonds       : angle       4.03918 (  828)
  SS BOND              : bond        0.00251 (    6)
  SS BOND              : angle       2.53250 (   12)
  link_BETA1-3         : bond        0.01512 (    3)
  link_BETA1-3         : angle       3.72973 (    9)
  covalent geometry    : bond        0.00387 ( 7602)
  covalent geometry    : angle       0.73903 (10380)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 0.766 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  339 GLN cc_start: 0.7544 (tt0) cc_final: 0.7184 (mt0)
REVERT: A  559 TYR cc_start: 0.8928 (p90) cc_final: 0.8347 (p90)
REVERT: A  566 GLU cc_start: 0.8255 (tt0) cc_final: 0.7726 (tt0)
REVERT: A  591 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8849 (tt)
REVERT: A  693 ARG cc_start: 0.8099 (mtm180) cc_final: 0.7645 (mtp85)
REVERT: A  747 MET cc_start: 0.8031 (ttt) cc_final: 0.7667 (tmm)
REVERT: A  766 MET cc_start: 0.7675 (mmp) cc_final: 0.7404 (mmp)
REVERT: A  788 MET cc_start: 0.7847 (mtt) cc_final: 0.7547 (mtt)
REVERT: A  789 SER cc_start: 0.8937 (t) cc_final: 0.8681 (t)
REVERT: A  983 THR cc_start: 0.9258 (t) cc_final: 0.8966 (p)
REVERT: A  998 MET cc_start: 0.5825 (tmm) cc_final: 0.5392 (tmm)
REVERT: A 1111 GLU cc_start: 0.7284 (tp30) cc_final: 0.6678 (tm-30)
REVERT: A 1180 GLU cc_start: 0.8274 (mm-30) cc_final: 0.8014 (mm-30)
REVERT: A 1187 ARG cc_start: 0.8144 (tpp80) cc_final: 0.7163 (tmm160)
  outliers start: 22
  outliers final: 18
  residues processed: 106
  average time/residue: 0.1600
  time to fit residues: 24.6341
Evaluate side-chains
  112 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  636 PHE
Chi-restraints excluded: chain A residue  675 VAL
Chi-restraints excluded: chain A residue  699 LEU
Chi-restraints excluded: chain A residue  781 ILE
Chi-restraints excluded: chain A residue  785 LEU
Chi-restraints excluded: chain A residue  796 SER
Chi-restraints excluded: chain A residue  861 LEU
Chi-restraints excluded: chain A residue  906 LEU
Chi-restraints excluded: chain A residue  938 THR
Chi-restraints excluded: chain A residue 1063 THR
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1140 LEU
Chi-restraints excluded: chain A residue 1221 LEU
Chi-restraints excluded: chain A residue 1265 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 21 optimal weight:    0.3980
   chunk 82 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 61 optimal weight:    0.3980
   chunk 15 optimal weight:    0.6980
   chunk 13 optimal weight:    0.8980
   chunk 78 optimal weight:    0.2980
   chunk 12 optimal weight:    0.0670
   overall best weight:    0.3718

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

Flipped N/Q/H residues before XYZ refinement:
** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.122806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.096536 restraints weight = 12957.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.099817 restraints weight = 6768.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.101978 restraints weight = 4554.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.2344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7627  Z= 0.125
  Angle     :  0.763  10.699  10449  Z= 0.333
  Chirality :  0.048   0.374   1266
  Planarity :  0.004   0.048   1254
  Dihedral  : 10.529 112.720   1642
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 21.05 %
    Favored  : 76.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.12 (0.29), residues: 891
  helix: -0.04 (0.25), residues: 478
  sheet: -1.32 (0.62), residues: 61
  loop : -1.51 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 953 
 HIS   0.003   0.000   HIS A1184 
 PHE   0.044   0.001   PHE A 832 
 TYR   0.008   0.001   TYR A 901 
 ARG   0.002   0.000   ARG A 968 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00844 (   10)
  link_NAG-ASN         : angle       4.39453 (   30)
  link_BETA1-4         : bond        0.00565 (    6)
  link_BETA1-4         : angle       1.87797 (   18)
  hydrogen bonds       : bond        0.03007 (  286)
  hydrogen bonds       : angle       3.99808 (  828)
  SS BOND              : bond        0.00173 (    6)
  SS BOND              : angle       2.01332 (   12)
  link_BETA1-3         : bond        0.01456 (    3)
  link_BETA1-3         : angle       3.54864 (    9)
  covalent geometry    : bond        0.00283 ( 7602)
  covalent geometry    : angle       0.71357 (10380)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 0.821 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  339 GLN cc_start: 0.7466 (tt0) cc_final: 0.7082 (mt0)
REVERT: A  559 TYR cc_start: 0.8898 (p90) cc_final: 0.8515 (p90)
REVERT: A  566 GLU cc_start: 0.8082 (tt0) cc_final: 0.7668 (tt0)
REVERT: A  591 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8872 (tt)
REVERT: A  693 ARG cc_start: 0.8020 (mtm180) cc_final: 0.7680 (mtp85)
REVERT: A  766 MET cc_start: 0.7766 (mmp) cc_final: 0.7511 (mmp)
REVERT: A  789 SER cc_start: 0.8915 (t) cc_final: 0.8666 (t)
REVERT: A  998 MET cc_start: 0.5857 (tmm) cc_final: 0.5452 (tmm)
REVERT: A 1111 GLU cc_start: 0.7239 (tp30) cc_final: 0.6691 (tm-30)
REVERT: A 1187 ARG cc_start: 0.8072 (tpp80) cc_final: 0.7107 (tmm160)
REVERT: A 1218 MET cc_start: 0.6176 (tpp) cc_final: 0.5933 (mmp)
  outliers start: 18
  outliers final: 16
  residues processed: 112
  average time/residue: 0.1616
  time to fit residues: 25.9209
Evaluate side-chains
  116 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  636 PHE
Chi-restraints excluded: chain A residue  675 VAL
Chi-restraints excluded: chain A residue  699 LEU
Chi-restraints excluded: chain A residue  781 ILE
Chi-restraints excluded: chain A residue  785 LEU
Chi-restraints excluded: chain A residue  796 SER
Chi-restraints excluded: chain A residue  861 LEU
Chi-restraints excluded: chain A residue  906 LEU
Chi-restraints excluded: chain A residue  931 THR
Chi-restraints excluded: chain A residue 1063 THR
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1140 LEU
Chi-restraints excluded: chain A residue 1221 LEU
Chi-restraints excluded: chain A residue 1265 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 63 optimal weight:    0.5980
   chunk 69 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 82 optimal weight:    4.9990
   chunk 28 optimal weight:    0.5980
   chunk 34 optimal weight:    0.1980
   chunk 40 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.121718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.095743 restraints weight = 12889.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.098918 restraints weight = 6860.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.101006 restraints weight = 4671.153|
|-----------------------------------------------------------------------------|
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.2379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7627  Z= 0.146
  Angle     :  0.786  11.003  10449  Z= 0.343
  Chirality :  0.049   0.370   1266
  Planarity :  0.004   0.048   1254
  Dihedral  : 10.404 112.512   1642
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 21.83 %
    Favored  : 75.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.29), residues: 891
  helix: -0.01 (0.25), residues: 476
  sheet: -1.29 (0.62), residues: 61
  loop : -1.49 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 953 
 HIS   0.002   0.001   HIS A1184 
 PHE   0.038   0.001   PHE A 832 
 TYR   0.008   0.001   TYR A 901 
 ARG   0.001   0.000   ARG A1002 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00797 (   10)
  link_NAG-ASN         : angle       4.39400 (   30)
  link_BETA1-4         : bond        0.00546 (    6)
  link_BETA1-4         : angle       1.88026 (   18)
  hydrogen bonds       : bond        0.03235 (  286)
  hydrogen bonds       : angle       4.01479 (  828)
  SS BOND              : bond        0.00213 (    6)
  SS BOND              : angle       1.77186 (   12)
  link_BETA1-3         : bond        0.01468 (    3)
  link_BETA1-3         : angle       3.54555 (    9)
  covalent geometry    : bond        0.00343 ( 7602)
  covalent geometry    : angle       0.73889 (10380)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2502.05 seconds
wall clock time: 44 minutes 39.39 seconds (2679.39 seconds total)