Starting phenix.real_space_refine
on Mon Dec 11 13:22:08 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qed_18352/12_2023/8qed_18352_trim_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qed_18352/12_2023/8qed_18352.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.27
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qed_18352/12_2023/8qed_18352.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qed_18352/12_2023/8qed_18352.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qed_18352/12_2023/8qed_18352_trim_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qed_18352/12_2023/8qed_18352_trim_updated.pdb"
  }
  resolution = 3.27
  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=  -0.001 sd=   0.030
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: 6
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      57      5.16       5
     C    5901      2.51       5
     N    1406      2.21       5
     O    1666      1.98       5
     H    8712      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A PHE  333": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A PHE  350": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A PHE  456": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A PHE  623": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU 1068": "OE1" <-> "OE2"
    Residue "A PHE 1077": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP 1087": "OD1" <-> "OD2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 17743
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 17523
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1101, 17523
          Classifications: {'peptide': 1101}
          Link IDs: {'PTRANS': 47, 'TRANS': 1053}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 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: "D"
      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: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 108
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 108
          Unusual residues: {'ERG': 2, 'PTY': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 8.08, per 1000 atoms: 0.46
  Number of scatterers: 17743
  At special positions: 0
  Unit cell: (84.63, 104.16, 161.448, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      57     16.00
     P       1     15.00
     O    1666      8.00
     N    1406      7.00
     C    5901      6.00
     H    8712      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=14, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  23 " - pdb=" SG  CYS A  75 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  29 " - pdb=" SG  CYS A  41 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  64 " - pdb=" SG  CYS A 110 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  76 " - pdb=" SG  CYS A 114 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  98 " - pdb=" SG  CYS A 230 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 101 " - pdb=" SG  CYS A 156 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 223 " - pdb=" SG  CYS A 235 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 232 " - pdb=" SG  CYS A 239 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 438 " - pdb=" SG  CYS A 447 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 473 " - pdb=" SG  CYS A 480 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 822 " - pdb=" SG  CYS A 828 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 868 " - pdb=" SG  CYS A 925 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 869 " - pdb=" SG  CYS A 891 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 879 " - pdb=" SG  CYS A 888 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
    NAG-ASN
      " NAG B   1 " - " ASN A 900 "
      " NAG C   1 " - " ASN A 513 "
      " NAG D   1 " - " ASN A 940 "
      " NAG E   1 " - " ASN A 401 "
  Time building additional restraints: 14.10
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2102

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      47 helices and 4 sheets defined
      53.1% alpha, 4.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 3.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 54 through 63
      removed outlier: 3.675A  pdb=" N   LEU A  59 " --> pdb=" O   GLU A  55 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   GLU A  62 " --> pdb=" O   LYS A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 68
      No H-bonds generated for 'chain 'A' and resid 66 through 68'
    Processing helix  chain 'A' and resid 78 through 95
      removed outlier: 3.507A  pdb=" N   VAL A  82 " --> pdb=" O   LYS A  78 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLN A  89 " --> pdb=" O   ARG A  85 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   LYS A  90 " --> pdb=" O   ASP A  86 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   ALA A  91 " --> pdb=" O   ASN A  87 " (cutoff:3.500A)
      Proline residue:  A  93  - end of helix
    Processing helix  chain 'A' and resid 99 through 114
    Processing helix  chain 'A' and resid 118 through 120
      No H-bonds generated for 'chain 'A' and resid 118 through 120'
    Processing helix  chain 'A' and resid 148 through 155
    Processing helix  chain 'A' and resid 168 through 172
      removed outlier: 4.000A  pdb=" N   ILE A 172 " --> pdb=" O   MET A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 187
    Processing helix  chain 'A' and resid 232 through 234
      No H-bonds generated for 'chain 'A' and resid 232 through 234'
    Processing helix  chain 'A' and resid 257 through 278
      removed outlier: 3.888A  pdb=" N   TYR A 278 " --> pdb=" O   PHE A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 336
      removed outlier: 3.797A  pdb=" N   ASN A 314 " --> pdb=" O   GLU A 310 " (cutoff:3.500A)
      removed outlier: 5.085A  pdb=" N   GLU A 315 " --> pdb=" O   SER A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 358
      removed outlier: 3.786A  pdb=" N   THR A 344 " --> pdb=" O   LYS A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 368
      No H-bonds generated for 'chain 'A' and resid 366 through 368'
    Processing helix  chain 'A' and resid 376 through 388
      removed outlier: 3.643A  pdb=" N   LYS A 381 " --> pdb=" O   LYS A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 409 through 424
      removed outlier: 3.553A  pdb=" N   ASN A 420 " --> pdb=" O   PHE A 416 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   PHE A 421 " --> pdb=" O   ASP A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 436
      No H-bonds generated for 'chain 'A' and resid 434 through 436'
    Processing helix  chain 'A' and resid 452 through 456
    Processing helix  chain 'A' and resid 466 through 475
    Processing helix  chain 'A' and resid 490 through 492
      No H-bonds generated for 'chain 'A' and resid 490 through 492'
    Processing helix  chain 'A' and resid 516 through 530
    Processing helix  chain 'A' and resid 547 through 554
      removed outlier: 3.741A  pdb=" N   ASN A 553 " --> pdb=" O   GLU A 549 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   ASN A 554 " --> pdb=" O   LYS A 550 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 575
    Processing helix  chain 'A' and resid 585 through 608
      removed outlier: 3.545A  pdb=" N   LEU A 608 " --> pdb=" O   GLY A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 615 through 645
      removed outlier: 3.873A  pdb=" N   VAL A 620 " --> pdb=" O   ILE A 616 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ILE A 621 " --> pdb=" O   ILE A 617 " (cutoff:3.500A)
      Proline residue:  A 622  - end of helix
      removed outlier: 3.523A  pdb=" N   ILE A 630 " --> pdb=" O   LEU A 626 " (cutoff:3.500A)
      removed outlier: 4.433A  pdb=" N   ASP A 631 " --> pdb=" O   ALA A 627 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   ASN A 632 " --> pdb=" O   ILE A 628 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   ILE A 633 " --> pdb=" O   GLY A 629 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   PHE A 634 " --> pdb=" O   ILE A 630 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   LEU A 635 " --> pdb=" O   ASP A 631 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   GLU A 645 " --> pdb=" O   ASP A 641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 652 through 662
      removed outlier: 3.505A  pdb=" N   ILE A 657 " --> pdb=" O   ASP A 653 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 664 through 683
      removed outlier: 3.527A  pdb=" N   CYS A 677 " --> pdb=" O   CYS A 673 " (cutoff:3.500A)
      removed outlier: 4.709A  pdb=" N   PHE A 678 " --> pdb=" O   GLN A 674 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   PHE A 683 " --> pdb=" O   LEU A 679 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 687 through 709
      removed outlier: 3.572A  pdb=" N   PHE A 692 " --> pdb=" O   ALA A 688 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   SER A 699 " --> pdb=" O   TYR A 695 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   ASN A 703 " --> pdb=" O   SER A 699 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 711 through 722
      removed outlier: 3.711A  pdb=" N   LYS A 720 " --> pdb=" O   SER A 716 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 745 through 747
      No H-bonds generated for 'chain 'A' and resid 745 through 747'
    Processing helix  chain 'A' and resid 749 through 763
    Processing helix  chain 'A' and resid 767 through 769
      No H-bonds generated for 'chain 'A' and resid 767 through 769'
    Processing helix  chain 'A' and resid 776 through 779
      No H-bonds generated for 'chain 'A' and resid 776 through 779'
    Processing helix  chain 'A' and resid 785 through 796
      removed outlier: 3.703A  pdb=" N   TYR A 789 " --> pdb=" O   TYR A 785 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   SER A 795 " --> pdb=" O   LYS A 791 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 815 through 820
      removed outlier: 4.097A  pdb=" N   LYS A 820 " --> pdb=" O   GLN A 816 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 833 through 842
      removed outlier: 4.460A  pdb=" N   HIS A 842 " --> pdb=" O   GLU A 838 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 853 through 861
      removed outlier: 3.640A  pdb=" N   LEU A 861 " --> pdb=" O   TYR A 857 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 907 through 918
      removed outlier: 3.731A  pdb=" N   TYR A 913 " --> pdb=" O   PHE A 910 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   SER A 915 " --> pdb=" O   GLU A 912 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ILE A 918 " --> pdb=" O   SER A 915 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 929 through 932
      No H-bonds generated for 'chain 'A' and resid 929 through 932'
    Processing helix  chain 'A' and resid 959 through 974
      removed outlier: 3.571A  pdb=" N   SER A 973 " --> pdb=" O   GLY A 969 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 997 through 1020
      removed outlier: 3.571A  pdb=" N   LEU A1002 " --> pdb=" O   GLY A 998 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ILE A1005 " --> pdb=" O   THR A1001 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1023 through 1047
      removed outlier: 3.738A  pdb=" N   LEU A1028 " --> pdb=" O   ARG A1024 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1053 through 1078
      removed outlier: 4.003A  pdb=" N   VAL A1063 " --> pdb=" O   LEU A1059 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   GLY A1064 " --> pdb=" O   ILE A1060 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   GLU A1068 " --> pdb=" O   GLY A1064 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   PHE A1069 " --> pdb=" O   LEU A1065 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   CYS A1070 " --> pdb=" O   GLY A1066 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   HIS A1072 " --> pdb=" O   GLU A1068 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   ILE A1073 " --> pdb=" O   PHE A1069 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1088 through 1098
    Processing helix  chain 'A' and resid 1100 through 1105
    Processing helix  chain 'A' and resid 1108 through 1119
      removed outlier: 3.976A  pdb=" N   VAL A1117 " --> pdb=" O   ILE A1113 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   LEU A1118 " --> pdb=" O   GLY A1114 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   ALA A1119 " --> pdb=" O   VAL A1115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1124 through 1129
    Processing helix  chain 'A' and resid 1132 through 1154
      removed outlier: 3.686A  pdb=" N   LEU A1146 " --> pdb=" O   ALA A1142 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   LEU A1149 " --> pdb=" O   ALA A1145 " (cutoff:3.500A)
      Proline residue:  A1150  - end of helix
    Processing sheet with id=  A, first strand: chain 'A' and resid 127 through 129
    Processing sheet with id=  B, first strand: chain 'A' and resid 199 through 203
      removed outlier: 6.325A  pdb=" N   ASP A 141 " --> pdb=" O   ILE A 124 " (cutoff:3.500A)
      removed outlier: 4.825A  pdb=" N   ILE A 124 " --> pdb=" O   ASP A 141 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   PHE A 143 " --> pdb=" O   VAL A 122 " (cutoff:3.500A)
      removed outlier: 5.820A  pdb=" N   VAL A 122 " --> pdb=" O   PHE A 143 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'A' and resid 504 through 507
    Processing sheet with id=  D, first strand: chain 'A' and resid 980 through 985
      removed outlier: 4.178A  pdb=" N   ASP A 980 " --> pdb=" O   LYS A 808 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   PHE A 949 " --> pdb=" O   MET A 805 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   VAL A 938 " --> pdb=" O   SER A 945 " (cutoff:3.500A)

    368 hydrogen bonds defined for protein.
    1068 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: 6.04

  Time building geometry restraints manager: 14.81 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 8702
        1.04 -     1.23: 188
        1.23 -     1.43: 3732
        1.43 -     1.63: 5268
        1.63 -     1.82: 78
  Bond restraints: 17968
  Sorted by residual:
  bond pdb=" C1  NAG B   2 "
       pdb=" O5  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.452 -0.046 2.00e-02 2.50e+03 5.18e+00
  bond pdb=" C1  NAG E   1 "
       pdb=" O5  NAG E   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.451 -0.045 2.00e-02 2.50e+03 4.96e+00
  bond pdb=" C6  ERG A1201 "
       pdb=" C7  ERG A1201 "
    ideal  model  delta    sigma   weight residual
    1.452  1.411  0.041 2.00e-02 2.50e+03 4.23e+00
  bond pdb=" C6  ERG A1200 "
       pdb=" C7  ERG A1200 "
    ideal  model  delta    sigma   weight residual
    1.452  1.414  0.038 2.00e-02 2.50e+03 3.60e+00
  bond pdb=" C1  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.431 -0.025 2.00e-02 2.50e+03 1.53e+00
  ... (remaining 17963 not shown)

  Histogram of bond angle deviations from ideal:
       73.98 -    85.98: 3
       85.98 -    97.99: 1
       97.99 -   110.00: 15213
      110.00 -   122.00: 14383
      122.00 -   134.01: 2774
  Bond angle restraints: 32374
  Sorted by residual:
  angle pdb=" C   GLU A 551 "
        pdb=" CA  GLU A 551 "
        pdb=" HA  GLU A 551 "
      ideal   model   delta    sigma   weight residual
     109.00   73.98   35.02 3.00e+00 1.11e-01 1.36e+02
  angle pdb=" N   GLU A 551 "
        pdb=" CA  GLU A 551 "
        pdb=" HA  GLU A 551 "
      ideal   model   delta    sigma   weight residual
     110.00   75.53   34.47 3.00e+00 1.11e-01 1.32e+02
  angle pdb=" CB  GLU A 551 "
        pdb=" CA  GLU A 551 "
        pdb=" HA  GLU A 551 "
      ideal   model   delta    sigma   weight residual
     109.00   76.41   32.59 3.00e+00 1.11e-01 1.18e+02
  angle pdb=" N   THR A 942 "
        pdb=" CA  THR A 942 "
        pdb=" C   THR A 942 "
      ideal   model   delta    sigma   weight residual
     114.62  111.04    3.58 1.14e+00 7.69e-01 9.87e+00
  angle pdb=" N   GLU A 551 "
        pdb=" CA  GLU A 551 "
        pdb=" C   GLU A 551 "
      ideal   model   delta    sigma   weight residual
     113.23  116.14   -2.91 1.24e+00 6.50e-01 5.52e+00
  ... (remaining 32369 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.64: 7772
       17.64 -    35.29: 666
       35.29 -    52.93: 153
       52.93 -    70.58: 31
       70.58 -    88.22: 18
  Dihedral angle restraints: 8640
    sinusoidal: 4644
      harmonic: 3996
  Sorted by residual:
  dihedral pdb=" CB  CYS A  98 "
           pdb=" SG  CYS A  98 "
           pdb=" SG  CYS A 230 "
           pdb=" CB  CYS A 230 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -142.90   56.90     1      1.00e+01 1.00e-02 4.36e+01
  dihedral pdb=" CB  CYS A 223 "
           pdb=" SG  CYS A 223 "
           pdb=" SG  CYS A 235 "
           pdb=" CB  CYS A 235 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -37.67  -48.33     1      1.00e+01 1.00e-02 3.22e+01
  dihedral pdb=" CB  CYS A 822 "
           pdb=" SG  CYS A 822 "
           pdb=" SG  CYS A 828 "
           pdb=" CB  CYS A 828 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -131.50   45.50     1      1.00e+01 1.00e-02 2.87e+01
  ... (remaining 8637 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 1359
       0.082 -    0.164: 77
       0.164 -    0.247: 1
       0.247 -    0.329: 2
       0.329 -    0.411: 1
  Chirality restraints: 1440
  Sorted by residual:
  chirality pdb=" CA  GLU A 551 "
            pdb=" N   GLU A 551 "
            pdb=" C   GLU A 551 "
            pdb=" CB  GLU A 551 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.23e+00
  chirality pdb=" C20 ERG A1200 "
            pdb=" C17 ERG A1200 "
            pdb=" C21 ERG A1200 "
            pdb=" C22 ERG A1200 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.58    2.30    0.28 2.00e-01 2.50e+01 1.99e+00
  chirality pdb=" C1  NAG B   1 "
            pdb=" ND2 ASN A 900 "
            pdb=" C2  NAG B   1 "
            pdb=" O5  NAG B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.15   -0.25 2.00e-01 2.50e+01 1.62e+00
  ... (remaining 1437 not shown)

  Planarity restraints: 2618
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 621 "   -0.019 5.00e-02 4.00e+02   2.95e-02 1.39e+00
        pdb=" N   PRO A 622 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO A 622 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 622 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 931 "    0.015 5.00e-02 4.00e+02   2.28e-02 8.32e-01
        pdb=" N   PRO A 932 "   -0.039 5.00e-02 4.00e+02
        pdb=" CA  PRO A 932 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A 932 "    0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 239 "   -0.014 5.00e-02 4.00e+02   2.17e-02 7.50e-01
        pdb=" N   PRO A 240 "    0.037 5.00e-02 4.00e+02
        pdb=" CA  PRO A 240 "   -0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO A 240 "   -0.012 5.00e-02 4.00e+02
  ... (remaining 2615 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.19: 824
        2.19 -     2.79: 35611
        2.79 -     3.39: 48867
        3.39 -     4.00: 62899
        4.00 -     4.60: 97251
  Nonbonded interactions: 245452
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 551 "
            pdb=" HG  SER A 784 "
     model   vdw
     1.582 1.850
  nonbonded pdb=" OE1 GLU A 410 "
            pdb=" H   GLU A 410 "
     model   vdw
     1.608 1.850
  nonbonded pdb=" HG  SER A 547 "
            pdb=" OH  TYR A 785 "
     model   vdw
     1.619 1.850
  nonbonded pdb=" H   GLU A 551 "
            pdb=" HA  GLU A 551 "
     model   vdw
     1.628 1.816
  nonbonded pdb=" OD1 ASN A 898 "
            pdb=" HG  SER A 902 "
     model   vdw
     1.631 1.850
  ... (remaining 245447 not shown)

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

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.260
  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:             0.270
  Extract box with map and model:          4.190
  Check model and map are aligned:         0.230
  Set scattering table:                    0.150
  Process input model:                     57.270
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   66.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
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      :  0.004   0.046   9256  Z= 0.235
  Angle     :  0.501   6.551  12565  Z= 0.249
  Chirality :  0.040   0.411   1440
  Planarity :  0.002   0.029   1563
  Dihedral  : 15.814  88.221   3591
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.75 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  : 11.94 %
    Favored  : 87.96 %
  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:  0.44 (0.26), residues: 1095
  helix:  1.19 (0.23), residues: 574
  sheet: -1.18 (0.66), residues: 71
  loop : -0.56 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.005   0.001   TRP A 415 
   HIS   0.004   0.001   HIS A 954 
   PHE   0.014   0.001   PHE A 982 
   TYR   0.009   0.001   TYR A 789 
   ARG   0.001   0.000   ARG A 539 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  147 is missing expected H atoms. Skipping.
Evaluate side-chains
  73 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 72
  time to evaluate  : 1.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 73
  average time/residue: 0.3625
  time to fit residues: 41.3328
Evaluate side-chains
  69 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 68
  time to evaluate  : 1.529 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 1
  average time/residue: 0.1899
  time to fit residues: 2.1090
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    0.7980
   chunk 83 optimal weight:    0.6980
   chunk 46 optimal weight:    0.6980
   chunk 28 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   chunk 99 optimal weight:    1.9990
   overall best weight:    0.8382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.0598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9256  Z= 0.199
  Angle     :  0.511   5.338  12565  Z= 0.272
  Chirality :  0.040   0.402   1440
  Planarity :  0.003   0.032   1563
  Dihedral  :  6.600  54.119   1518
  Min Nonbonded Distance : 1.917

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.47 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  : 11.84 %
    Favored  : 87.65 %
  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:  0.50 (0.26), residues: 1095
  helix:  1.20 (0.22), residues: 583
  sheet: -1.14 (0.65), residues: 71
  loop : -0.50 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.001   TRP A 415 
   HIS   0.004   0.001   HIS A 954 
   PHE   0.016   0.001   PHE A 505 
   TYR   0.010   0.001   TYR A 571 
   ARG   0.002   0.000   ARG A 815 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  147 is missing expected H atoms. Skipping.
Evaluate side-chains
  79 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 1.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 5
  outliers final: 3
  residues processed: 78
  average time/residue: 0.3496
  time to fit residues: 43.2470
Evaluate side-chains
  70 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 67
  time to evaluate  : 1.313 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 3
  outliers final: 1
  residues processed: 3
  average time/residue: 0.1993
  time to fit residues: 2.8634
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 83 optimal weight:    0.5980
   chunk 68 optimal weight:    4.9990
   chunk 27 optimal weight:    5.9990
   chunk 100 optimal weight:    1.9990
   chunk 108 optimal weight:    0.9980
   chunk 89 optimal weight:    0.5980
   chunk 99 optimal weight:    0.3980
   chunk 34 optimal weight:    1.9990
   chunk 80 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 227 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.0928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9256  Z= 0.164
  Angle     :  0.465   5.140  12565  Z= 0.241
  Chirality :  0.039   0.397   1440
  Planarity :  0.003   0.031   1563
  Dihedral  :  6.171  55.870   1518
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.02 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  : 11.23 %
    Favored  : 88.26 %
  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:  0.53 (0.26), residues: 1095
  helix:  1.24 (0.22), residues: 583
  sheet: -1.14 (0.66), residues: 71
  loop : -0.51 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.001   TRP A 415 
   HIS   0.004   0.001   HIS A 954 
   PHE   0.013   0.001   PHE A 505 
   TYR   0.016   0.001   TYR A 228 
   ARG   0.001   0.000   ARG A 524 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  147 is missing expected H atoms. Skipping.
Evaluate side-chains
  81 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 76
  time to evaluate  : 1.397 
Fit side-chains
  outliers start: 5
  outliers final: 3
  residues processed: 79
  average time/residue: 0.3314
  time to fit residues: 41.7468
Evaluate side-chains
  76 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 73
  time to evaluate  : 1.376 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 3
  outliers final: 1
  residues processed: 3
  average time/residue: 0.1985
  time to fit residues: 2.9454
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 11 optimal weight:    9.9990
   chunk 47 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 100 optimal weight:    0.4980
   chunk 106 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 95 optimal weight:    0.4980
   chunk 28 optimal weight:    4.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A 387 ASN
** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.1105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   9256  Z= 0.250
  Angle     :  0.488   5.538  12565  Z= 0.253
  Chirality :  0.039   0.406   1440
  Planarity :  0.003   0.031   1563
  Dihedral  :  6.239  57.117   1518
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.84 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 11.64 %
    Favored  : 87.65 %
  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:  0.51 (0.26), residues: 1095
  helix:  1.27 (0.22), residues: 586
  sheet: -1.22 (0.65), residues: 71
  loop : -0.58 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.001   TRP A 415 
   HIS   0.004   0.001   HIS A 954 
   PHE   0.018   0.001   PHE A 505 
   TYR   0.009   0.001   TYR A 409 
   ARG   0.002   0.000   ARG A 584 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  147 is missing expected H atoms. Skipping.
Evaluate side-chains
  84 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 1.404 
Fit side-chains
  outliers start: 7
  outliers final: 6
  residues processed: 83
  average time/residue: 0.3502
  time to fit residues: 46.0233
Evaluate side-chains
  75 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 1.310 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 6
  outliers final: 1
  residues processed: 6
  average time/residue: 0.1975
  time to fit residues: 4.1108
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 88 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 1 optimal weight:    0.1980
   chunk 79 optimal weight:    1.9990
   chunk 43 optimal weight:    0.2980
   chunk 90 optimal weight:    0.6980
   chunk 73 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 54 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   overall best weight:    0.5580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.1207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   9256  Z= 0.148
  Angle     :  0.456   5.067  12565  Z= 0.234
  Chirality :  0.038   0.395   1440
  Planarity :  0.003   0.031   1563
  Dihedral  :  5.956  59.216   1518
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.57 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 12.25 %
    Favored  : 87.35 %
  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:  0.70 (0.26), residues: 1095
  helix:  1.42 (0.22), residues: 586
  sheet: -1.09 (0.71), residues: 61
  loop : -0.53 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.001   TRP A 415 
   HIS   0.004   0.001   HIS A 954 
   PHE   0.014   0.001   PHE A 265 
   TYR   0.010   0.001   TYR A 228 
   ARG   0.001   0.000   ARG A  85 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  147 is missing expected H atoms. Skipping.
Evaluate side-chains
  78 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 74
  time to evaluate  : 1.466 
Fit side-chains
  outliers start: 4
  outliers final: 2
  residues processed: 78
  average time/residue: 0.3548
  time to fit residues: 43.8008
Evaluate side-chains
  73 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 71
  time to evaluate  : 1.387 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 2
  average time/residue: 0.1966
  time to fit residues: 2.4731
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9990
   chunk 21 optimal weight:    6.9990
   chunk 62 optimal weight:    1.9990
   chunk 26 optimal weight:    6.9990
   chunk 106 optimal weight:    1.9990
   chunk 88 optimal weight:    0.3980
   chunk 49 optimal weight:    0.9980
   chunk 8 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   chunk 102 optimal weight:    2.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
A 555 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.1292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   9256  Z= 0.257
  Angle     :  0.488   5.582  12565  Z= 0.252
  Chirality :  0.039   0.405   1440
  Planarity :  0.003   0.032   1563
  Dihedral  :  6.177  59.993   1518
  Min Nonbonded Distance : 1.911

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.93 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 12.35 %
    Favored  : 87.04 %
  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:  0.60 (0.26), residues: 1095
  helix:  1.37 (0.22), residues: 586
  sheet: -1.16 (0.71), residues: 61
  loop : -0.63 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP A 415 
   HIS   0.004   0.001   HIS A 954 
   PHE   0.018   0.001   PHE A 505 
   TYR   0.009   0.001   TYR A 409 
   ARG   0.002   0.000   ARG A 584 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  147 is missing expected H atoms. Skipping.
Evaluate side-chains
  76 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 1.432 
Fit side-chains
  outliers start: 6
  outliers final: 5
  residues processed: 76
  average time/residue: 0.3471
  time to fit residues: 41.8603
Evaluate side-chains
  75 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 70
  time to evaluate  : 1.259 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 5
  outliers final: 1
  residues processed: 5
  average time/residue: 0.1913
  time to fit residues: 3.3860
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 11 optimal weight:   10.0000
   chunk 60 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 89 optimal weight:    0.5980
   chunk 59 optimal weight:    1.9990
   chunk 106 optimal weight:    0.3980
   chunk 66 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.9582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.1405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9256  Z= 0.197
  Angle     :  0.468   6.218  12565  Z= 0.240
  Chirality :  0.039   0.399   1440
  Planarity :  0.003   0.031   1563
  Dihedral  :  6.100  59.225   1518
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.66 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  : 12.35 %
    Favored  : 87.35 %
  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:  0.66 (0.26), residues: 1095
  helix:  1.43 (0.22), residues: 587
  sheet: -1.22 (0.70), residues: 61
  loop : -0.60 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP A 415 
   HIS   0.004   0.001   HIS A 954 
   PHE   0.017   0.001   PHE A 505 
   TYR   0.013   0.001   TYR A 228 
   ARG   0.001   0.000   ARG A 584 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  147 is missing expected H atoms. Skipping.
Evaluate side-chains
  78 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 75
  time to evaluate  : 1.422 
Fit side-chains
  outliers start: 3
  outliers final: 3
  residues processed: 77
  average time/residue: 0.3338
  time to fit residues: 40.7598
Evaluate side-chains
  76 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 73
  time to evaluate  : 1.319 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 3
  outliers final: 1
  residues processed: 3
  average time/residue: 0.2196
  time to fit residues: 3.0029
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 67 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 9 optimal weight:   10.0000
   chunk 83 optimal weight:    2.9990
   chunk 96 optimal weight:    1.9990
   chunk 101 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   overall best weight:    1.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 555 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.1441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9256  Z= 0.274
  Angle     :  0.499   6.346  12565  Z= 0.257
  Chirality :  0.040   0.408   1440
  Planarity :  0.003   0.032   1563
  Dihedral  :  6.349  58.187   1518
  Min Nonbonded Distance : 1.895

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.02 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  : 12.75 %
    Favored  : 86.74 %
  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:  0.54 (0.26), residues: 1095
  helix:  1.34 (0.22), residues: 587
  sheet: -1.35 (0.66), residues: 68
  loop : -0.65 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP A 415 
   HIS   0.004   0.001   HIS A 954 
   PHE   0.019   0.001   PHE A 505 
   TYR   0.011   0.001   TYR A 228 
   ARG   0.001   0.000   ARG A 584 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  147 is missing expected H atoms. Skipping.
Evaluate side-chains
  76 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 71
  time to evaluate  : 1.450 
Fit side-chains
  outliers start: 5
  outliers final: 4
  residues processed: 76
  average time/residue: 0.3448
  time to fit residues: 41.4341
Evaluate side-chains
  75 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 71
  time to evaluate  : 1.397 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 4
  outliers final: 1
  residues processed: 4
  average time/residue: 0.2188
  time to fit residues: 3.3854
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 101 optimal weight:    0.9980
   chunk 59 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 89 optimal weight:    0.5980
   chunk 93 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 104 optimal weight:    2.9990
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 555 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.1503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   9256  Z= 0.170
  Angle     :  0.465   6.768  12565  Z= 0.237
  Chirality :  0.039   0.395   1440
  Planarity :  0.003   0.031   1563
  Dihedral  :  6.151  56.707   1518
  Min Nonbonded Distance : 1.908

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.20 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  : 13.26 %
    Favored  : 86.54 %
  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:  0.68 (0.26), residues: 1095
  helix:  1.46 (0.22), residues: 587
  sheet: -1.30 (0.66), residues: 68
  loop : -0.57 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.001   TRP A 415 
   HIS   0.004   0.001   HIS A 954 
   PHE   0.015   0.001   PHE A 505 
   TYR   0.009   0.001   TYR A 409 
   ARG   0.001   0.000   ARG A 843 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  147 is missing expected H atoms. Skipping.
Evaluate side-chains
  81 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 79
  time to evaluate  : 1.569 
Fit side-chains
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 81
  average time/residue: 0.3399
  time to fit residues: 44.0008
Evaluate side-chains
  74 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 73
  time to evaluate  : 1.387 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 1
  average time/residue: 0.2184
  time to fit residues: 2.2224
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 72 optimal weight:    0.9980
   chunk 109 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   chunk 87 optimal weight:    0.8980
   chunk 9 optimal weight:   10.0000
   chunk 67 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 69 optimal weight:    0.5980
   chunk 92 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 555 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.1549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9256  Z= 0.188
  Angle     :  0.469   7.116  12565  Z= 0.239
  Chirality :  0.039   0.397   1440
  Planarity :  0.003   0.032   1563
  Dihedral  :  6.112  55.041   1518
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.75 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 13.36 %
    Favored  : 86.23 %
  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:  0.72 (0.26), residues: 1095
  helix:  1.49 (0.22), residues: 588
  sheet: -1.17 (0.71), residues: 61
  loop : -0.61 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP A 415 
   HIS   0.004   0.001   HIS A 954 
   PHE   0.013   0.001   PHE A 505 
   TYR   0.009   0.001   TYR A 228 
   ARG   0.001   0.000   ARG A 584 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  147 is missing expected H atoms. Skipping.
Evaluate side-chains
  79 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 75
  time to evaluate  : 1.357 
Fit side-chains
   revert: symmetry clash
  outliers start: 4
  outliers final: 2
  residues processed: 78
  average time/residue: 0.3547
  time to fit residues: 43.6240
Evaluate side-chains
  77 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 75
  time to evaluate  : 1.337 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 2
  average time/residue: 0.2384
  time to fit residues: 2.5603
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 87 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 89 optimal weight:    0.7980
   chunk 11 optimal weight:   10.0000
   chunk 16 optimal weight:    8.9990
   chunk 76 optimal weight:    0.6980
   chunk 4 optimal weight:    8.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 555 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.147281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.104538 restraints weight = 36350.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 2.42
r_work: 0.3059 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2942 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.1588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9256  Z= 0.243
  Angle     :  0.491   6.883  12565  Z= 0.251
  Chirality :  0.039   0.405   1440
  Planarity :  0.003   0.032   1563
  Dihedral  :  6.304  55.296   1518
  Min Nonbonded Distance : 1.898

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.21 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 13.06 %
    Favored  : 86.54 %
  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:  0.63 (0.26), residues: 1095
  helix:  1.43 (0.22), residues: 588
  sheet: -1.22 (0.71), residues: 61
  loop : -0.68 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.008   0.001   TRP A 415 
   HIS   0.004   0.001   HIS A 954 
   PHE   0.019   0.001   PHE A 505 
   TYR   0.010   0.001   TYR A 228 
   ARG   0.002   0.000   ARG A 584 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3723.91 seconds
wall clock time: 66 minutes 46.24 seconds (4006.24 seconds total)