Starting phenix.real_space_refine
on Fri Mar 14 03:51:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6uox_20834/03_2025/6uox_20834.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6uox_20834/03_2025/6uox_20834.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.02
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6uox_20834/03_2025/6uox_20834.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6uox_20834/03_2025/6uox_20834.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6uox_20834/03_2025/6uox_20834.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6uox_20834/03_2025/6uox_20834.cif"
  }
  resolution = 4.02
  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=   0.001
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
     Br      1      7.06       5
     S      68      5.16       5
     Cl      2      4.86       5
     C    5882      2.51       5
     N    1468      2.21       5
     O    1717      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9138
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 8909
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1161, 8907
          Classifications: {'peptide': 1161}
          Incomplete info: {'truncation_to_alanine': 46}
          Link IDs: {'PTRANS': 62, 'TRANS': 1098}
          Chain breaks: 3
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 200
          Unresolved non-hydrogen angles: 262
          Unresolved non-hydrogen dihedrals: 180
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 124
      Conformer: "B"
        Number of residues, atoms: 1161, 8907
          Classifications: {'peptide': 1161}
          Incomplete info: {'truncation_to_alanine': 46}
          Link IDs: {'PTRANS': 62, 'TRANS': 1098}
          Chain breaks: 3
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 200
          Unresolved non-hydrogen angles: 262
          Unresolved non-hydrogen dihedrals: 180
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 124
          bond proxies already assigned to first conformer: 9126
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 162
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 162
          Unusual residues: {'NAG': 8, 'QDG': 1}
          Classifications: {'undetermined': 9}
          Link IDs: {None: 8}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 8
  Time building chain proxies: 12.14, per 1000 atoms: 1.33
  Number of scatterers: 9138
  At special positions: 0
  Unit cell: (112.86, 145.2, 114.84, 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)
     Br      1     34.99
     Cl      2     17.00
     S      68     16.00
     O    1717      8.00
     N    1468      7.00
     C    5882      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=15, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  25 " - pdb=" SG  CYS A  74 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  31 " - pdb=" SG  CYS A  42 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  63 " - pdb=" SG  CYS A 109 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  75 " - pdb=" SG  CYS A 113 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  97 " - pdb=" SG  CYS A 238 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 100 " - pdb=" SG  CYS A 160 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 177 " - pdb=" SG  CYS A 184 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 227 " - pdb=" SG  CYS A 243 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 240 " - pdb=" SG  CYS A 247 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 468 " - pdb=" SG  CYS A 479 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 516 " - pdb=" SG  CYS A 533 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 909 " - pdb=" SG  CYS A 914 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 956 " - pdb=" SG  CYS A1011 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 957 " - pdb=" SG  CYS A 979 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 967 " - pdb=" SG  CYS A 976 " distance=2.04

  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
    ALPHA1-3
      " NAG C   2 " - " MAN C   3 "
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG C   1 " - " NAG C   2 "
    NAG-ASN
      " NAG A1301 " - " ASN A 452 "
      " NAG A1302 " - " ASN A 459 "
      " NAG A1305 " - " ASN A 524 "
      " NAG A1309 " - " ASN A 598 "
      " NAG A1310 " - " ASN A 916 "
      " NAG A1311 " - " ASN A 931 "
      " NAG A1312 " - " ASN A 961 "
      " NAG A1313 " - " ASN A 968 "
      " NAG B   1 " - " ASN A 478 "
      " NAG C   1 " - " ASN A 557 "
  Time building additional restraints: 2.32
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2174

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 12 sheets defined
      51.5% alpha, 6.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.50
  Creating SS restraints...
    Processing helix  chain 'A' and resid 55 through 63
      removed outlier: 3.868A  pdb=" N   GLU A  61 " --> pdb=" O   ASP A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 87
      removed outlier: 3.736A  pdb=" N   LEU A  80 " --> pdb=" O   ASP A  76 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ASP A  85 " --> pdb=" O   GLN A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 94
    Processing helix  chain 'A' and resid 97 through 114
      removed outlier: 3.531A  pdb=" N   PHE A 101 " --> pdb=" O   CYS A  97 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   LEU A 104 " --> pdb=" O   CYS A 100 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   SER A 114 " --> pdb=" O   GLU A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 120
      removed outlier: 3.751A  pdb=" N   PHE A 120 " --> pdb=" O   ARG A 116 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 116 through 120'
    Processing helix  chain 'A' and resid 150 through 161
    Processing helix  chain 'A' and resid 171 through 178
      removed outlier: 4.107A  pdb=" N   LEU A 175 " --> pdb=" O   LYS A 171 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   LEU A 176 " --> pdb=" O   ALA A 172 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   GLY A 178 " --> pdb=" O   GLY A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 195
    Processing helix  chain 'A' and resid 270 through 278
      removed outlier: 3.579A  pdb=" N   ILE A 274 " --> pdb=" O   VAL A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 284
    Processing helix  chain 'A' and resid 335 through 349
      removed outlier: 3.589A  pdb=" N   PHE A 339 " --> pdb=" O   LEU A 335 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ARG A 341 " --> pdb=" O   ARG A 337 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   TRP A 342 " --> pdb=" O   LEU A 338 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   PHE A 345 " --> pdb=" O   ARG A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 365
      removed outlier: 3.804A  pdb=" N   PHE A 355 " --> pdb=" O   GLY A 351 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   PHE A 360 " --> pdb=" O   PHE A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 372
      removed outlier: 3.833A  pdb=" N   VAL A 371 " --> pdb=" O   GLY A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 393
    Processing helix  chain 'A' and resid 436 through 452
      removed outlier: 5.235A  pdb=" N   GLN A 442 " --> pdb=" O   GLN A 438 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   GLU A 451 " --> pdb=" O   GLN A 447 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ASN A 452 " --> pdb=" O   ILE A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 487
    Processing helix  chain 'A' and resid 508 through 516
    Processing helix  chain 'A' and resid 577 through 593
      removed outlier: 3.659A  pdb=" N   TRP A 583 " --> pdb=" O   ARG A 579 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   GLU A 586 " --> pdb=" O   ALA A 582 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 617
      removed outlier: 3.882A  pdb=" N   GLU A 612 " --> pdb=" O   SER A 608 " (cutoff:3.500A)
      removed outlier: 4.658A  pdb=" N   LEU A 613 " --> pdb=" O   ILE A 609 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ASN A 614 " --> pdb=" O   GLU A 610 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 618 through 620
      No H-bonds generated for 'chain 'A' and resid 618 through 620'
    Processing helix  chain 'A' and resid 621 through 638
      removed outlier: 3.775A  pdb=" N   ILE A 626 " --> pdb=" O   PHE A 622 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   SER A 627 " --> pdb=" O   THR A 623 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   MET A 631 " --> pdb=" O   SER A 627 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ILE A 635 " --> pdb=" O   MET A 631 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   SER A 636 " --> pdb=" O   PHE A 632 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 654 through 679
      removed outlier: 3.624A  pdb=" N   ALA A 669 " --> pdb=" O   LEU A 665 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   PHE A 675 " --> pdb=" O   SER A 671 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   TYR A 677 " --> pdb=" O   GLY A 673 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 685 through 711
      removed outlier: 3.596A  pdb=" N   VAL A 689 " --> pdb=" O   ILE A 685 " (cutoff:3.500A)
      Proline residue:  A 691  - end of helix
      removed outlier: 3.589A  pdb=" N   LEU A 695 " --> pdb=" O   PRO A 691 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   ASP A 700 " --> pdb=" O   ALA A 696 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ASN A 701 " --> pdb=" O   VAL A 697 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ILE A 702 " --> pdb=" O   GLY A 698 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ILE A 704 " --> pdb=" O   ASP A 700 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   GLN A 707 " --> pdb=" O   PHE A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 719 through 748
      Proline residue:  A 733  - end of helix
      removed outlier: 3.993A  pdb=" N   LEU A 737 " --> pdb=" O   PRO A 733 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   SER A 738 " --> pdb=" O   SER A 734 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   GLU A 742 " --> pdb=" O   SER A 738 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 757 through 776
      removed outlier: 4.170A  pdb=" N   LEU A 762 " --> pdb=" O   HIS A 758 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   PHE A 763 " --> pdb=" O   THR A 759 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   VAL A 768 " --> pdb=" O   ALA A 764 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ILE A 776 " --> pdb=" O   PHE A 772 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 777 through 782
      removed outlier: 3.951A  pdb=" N   SER A 781 " --> pdb=" O   THR A 777 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   LEU A 782 " --> pdb=" O   CYS A 778 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 777 through 782'
    Processing helix  chain 'A' and resid 782 through 792
    Processing helix  chain 'A' and resid 818 through 826
      removed outlier: 3.587A  pdb=" N   SER A 824 " --> pdb=" O   PHE A 820 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 836 through 852
      removed outlier: 3.959A  pdb=" N   PHE A 842 " --> pdb=" O   VAL A 838 " (cutoff:3.500A)
      removed outlier: 4.428A  pdb=" N   LEU A 846 " --> pdb=" O   PHE A 842 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ALA A 851 " --> pdb=" O   SER A 847 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   VAL A 852 " --> pdb=" O   PHE A 848 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 870 through 880
      removed outlier: 4.191A  pdb=" N   ASP A 874 " --> pdb=" O   SER A 870 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   SER A 880 " --> pdb=" O   PHE A 876 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 901 through 907
    Processing helix  chain 'A' and resid 918 through 928
      removed outlier: 4.137A  pdb=" N   GLN A 928 " --> pdb=" O   PHE A 924 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 942 through 951
      removed outlier: 3.569A  pdb=" N   PHE A 947 " --> pdb=" O   ILE A 943 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 952 through 955
      removed outlier: 4.185A  pdb=" N   SER A 955 " --> pdb=" O   PRO A 952 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 952 through 955'
    Processing helix  chain 'A' and resid 993 through 1004
      Proline residue:  A1000  - end of helix
    Processing helix  chain 'A' and resid 1047 through 1070
      removed outlier: 3.670A  pdb=" N   PHE A1051 " --> pdb=" O   THR A1047 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ILE A1052 " --> pdb=" O   SER A1048 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LYS A1057 " --> pdb=" O   ASP A1053 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   GLY A1070 " --> pdb=" O   THR A1066 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1089 through 1092
    Processing helix  chain 'A' and resid 1093 through 1118
      removed outlier: 3.670A  pdb=" N   ASP A1097 " --> pdb=" O   THR A1093 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   THR A1098 " --> pdb=" O   ILE A1094 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   ILE A1099 " --> pdb=" O   ILE A1095 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   GLY A1103 " --> pdb=" O   ILE A1099 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   THR A1113 " --> pdb=" O   ILE A1109 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   MET A1114 " --> pdb=" O   PHE A1110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1120 through 1146
      removed outlier: 3.669A  pdb=" N   ALA A1124 " --> pdb=" O   GLU A1120 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ILE A1126 " --> pdb=" O   TRP A1122 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   MET A1127 " --> pdb=" O   SER A1123 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   LEU A1135 " --> pdb=" O   ILE A1131 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ASN A1137 " --> pdb=" O   MET A1133 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   TRP A1143 " --> pdb=" O   PHE A1139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1150 through 1164
      removed outlier: 4.117A  pdb=" N   ASN A1156 " --> pdb=" O   VAL A1152 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   SER A1160 " --> pdb=" O   ASN A1156 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   CYS A1161 " --> pdb=" O   LEU A1157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1165 through 1177
      removed outlier: 4.279A  pdb=" N   HIS A1170 " --> pdb=" O   GLU A1166 " (cutoff:3.500A)
      removed outlier: 4.784A  pdb=" N   ILE A1171 " --> pdb=" O   PHE A1167 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   ALA A1174 " --> pdb=" O   HIS A1170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1182 through 1194
      removed outlier: 3.959A  pdb=" N   GLU A1188 " --> pdb=" O   VAL A1184 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   GLU A1189 " --> pdb=" O   GLU A1185 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ALA A1190 " --> pdb=" O   ARG A1186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1194 through 1201
    Processing helix  chain 'A' and resid 1202 through 1215
      removed outlier: 3.609A  pdb=" N   ILE A1210 " --> pdb=" O   LYS A1206 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   VAL A1211 " --> pdb=" O   PHE A1207 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   VAL A1212 " --> pdb=" O   GLY A1208 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LEU A1213 " --> pdb=" O   GLY A1209 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   PHE A1215 " --> pdb=" O   VAL A1211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1219 through 1224
    Processing helix  chain 'A' and resid 1226 through 1242
      removed outlier: 4.152A  pdb=" N   LEU A1235 " --> pdb=" O   ALA A1231 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   THR A1238 " --> pdb=" O   LEU A1234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1242 through 1249
      removed outlier: 4.239A  pdb=" N   VAL A1246 " --> pdb=" O   ILE A1242 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LEU A1247 " --> pdb=" O   PHE A1243 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 28
    Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 35
      removed outlier: 7.200A  pdb=" N   LYS A  38 " --> pdb=" O   ALA A  34 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 50
      removed outlier: 3.512A  pdb=" N   LEU A  73 " --> pdb=" O   LYS A  49 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 129
      removed outlier: 6.487A  pdb=" N   GLU A 143 " --> pdb=" O   THR A 124 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   THR A 126 " --> pdb=" O   VAL A 141 " (cutoff:3.500A)
      removed outlier: 7.310A  pdb=" N   VAL A 141 " --> pdb=" O   THR A 126 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   ASP A 128 " --> pdb=" O   THR A 139 " (cutoff:3.500A)
      removed outlier: 5.909A  pdb=" N   THR A 139 " --> pdb=" O   ASP A 128 " (cutoff:3.500A)
      removed outlier: 7.967A  pdb=" N   THR A 206 " --> pdb=" O   LYS A 142 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   LEU A 144 " --> pdb=" O   THR A 206 " (cutoff:3.500A)
      removed outlier: 7.560A  pdb=" N   VAL A 208 " --> pdb=" O   LEU A 144 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   TYR A 146 " --> pdb=" O   VAL A 208 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   SER A 210 " --> pdb=" O   TYR A 146 " (cutoff:3.500A)
      removed outlier: 5.426A  pdb=" N   VAL A 148 " --> pdb=" O   SER A 210 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 547 through 548
    Processing sheet with id=AA6, first strand: chain 'A' and resid 418 through 420
    Processing sheet with id=AA7, first strand: chain 'A' and resid 455 through 457
    Processing sheet with id=AA8, first strand: chain 'A' and resid 499 through 500
      removed outlier: 6.889A  pdb=" N   LYS A 499 " --> pdb=" O   TYR A 506 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1036 through 1037
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1036 through 1037
    Processing sheet with id=AB2, first strand: chain 'A' and resid 966 through 967
      removed outlier: 3.978A  pdb=" N   ARG A 958 " --> pdb=" O   CYS A 967 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1025 through 1027

    352 hydrogen bonds defined for protein.
    1014 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: 4.83

  Time building geometry restraints manager: 2.95 seconds

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

  Histogram of bond lengths:
        1.19 -     1.34: 2778
        1.34 -     1.49: 2650
        1.49 -     1.64: 3838
        1.64 -     1.79: 23
        1.79 -     1.94: 76
  Bond restraints: 9365
  Sorted by residual:
  bond pdb=" C17 QDG A1314 "
       pdb=" C49 QDG A1314 "
    ideal  model  delta    sigma   weight residual
    1.536  1.211  0.325 2.00e-02 2.50e+03 2.64e+02
  bond pdb=" C09 QDG A1314 "
       pdb=" O16 QDG A1314 "
    ideal  model  delta    sigma   weight residual
    1.396  1.197  0.199 2.00e-02 2.50e+03 9.90e+01
  bond pdb=" C45 QDG A1314 "
       pdb=" N44 QDG A1314 "
    ideal  model  delta    sigma   weight residual
    1.283  1.445 -0.162 2.00e-02 2.50e+03 6.58e+01
  bond pdb=" C17 QDG A1314 "
       pdb=" O16 QDG A1314 "
    ideal  model  delta    sigma   weight residual
    1.419  1.557 -0.138 2.00e-02 2.50e+03 4.77e+01
  bond pdb=" C40 QDG A1314 "
       pdb=" N39 QDG A1314 "
    ideal  model  delta    sigma   weight residual
    1.453  1.333  0.120 2.00e-02 2.50e+03 3.61e+01
  ... (remaining 9360 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.23: 11985
        2.23 -     4.46: 720
        4.46 -     6.68: 48
        6.68 -     8.91: 12
        8.91 -    11.14: 3
  Bond angle restraints: 12768
  Sorted by residual:
  angle pdb=" N   PRO A 132 "
        pdb=" CA  PRO A 132 "
        pdb=" CB  PRO A 132 "
      ideal   model   delta    sigma   weight residual
     103.25  110.45   -7.20 1.05e+00 9.07e-01 4.70e+01
  angle pdb=" N   PRO A 433 "
        pdb=" CA  PRO A 433 "
        pdb=" C   PRO A 433 "
      ideal   model   delta    sigma   weight residual
     110.70  118.24   -7.54 1.22e+00 6.72e-01 3.82e+01
  angle pdb=" N   ASP A 552 "
        pdb=" CA  ASP A 552 "
        pdb=" C   ASP A 552 "
      ideal   model   delta    sigma   weight residual
     110.80  121.94  -11.14 2.13e+00 2.20e-01 2.74e+01
  angle pdb=" N   TYR A 571 "
        pdb=" CA  TYR A 571 "
        pdb=" C   TYR A 571 "
      ideal   model   delta    sigma   weight residual
     111.33  117.17   -5.84 1.21e+00 6.83e-01 2.33e+01
  angle pdb=" N   ILE A 962 "
        pdb=" CA  ILE A 962 "
        pdb=" C   ILE A 962 "
      ideal   model   delta    sigma   weight residual
     111.90  115.78   -3.88 8.10e-01 1.52e+00 2.29e+01
  ... (remaining 12763 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.32: 5458
       22.32 -    44.65: 197
       44.65 -    66.97: 43
       66.97 -    89.29: 20
       89.29 -   111.61: 13
  Dihedral angle restraints: 5731
    sinusoidal: 2355
      harmonic: 3376
  Sorted by residual:
  dihedral pdb=" CB  CYS A 468 "
           pdb=" SG  CYS A 468 "
           pdb=" SG  CYS A 479 "
           pdb=" CB  CYS A 479 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -176.29   90.29     1      1.00e+01 1.00e-02 9.65e+01
  dihedral pdb=" CB  CYS A 957 "
           pdb=" SG  CYS A 957 "
           pdb=" SG  CYS A 979 "
           pdb=" CB  CYS A 979 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  173.40  -80.40     1      1.00e+01 1.00e-02 8.00e+01
  dihedral pdb=" CB  CYS A 909 "
           pdb=" SG  CYS A 909 "
           pdb=" SG  CYS A 914 "
           pdb=" CB  CYS A 914 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  162.63  -69.63     1      1.00e+01 1.00e-02 6.26e+01
  ... (remaining 5728 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.139: 1408
       0.139 -    0.277: 68
       0.277 -    0.415: 5
       0.415 -    0.554: 4
       0.554 -    0.692: 2
  Chirality restraints: 1487
  Sorted by residual:
  chirality pdb=" C1  NAG B   2 "
            pdb=" O4  NAG B   1 "
            pdb=" C2  NAG B   2 "
            pdb=" O5  NAG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.29   -0.11 2.00e-02 2.50e+03 3.05e+01
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.31   -0.09 2.00e-02 2.50e+03 2.12e+01
  chirality pdb=" C1  NAG B   1 "
            pdb=" ND2 ASN A 478 "
            pdb=" C2  NAG B   1 "
            pdb=" O5  NAG B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.71   -0.69 2.00e-01 2.50e+01 1.20e+01
  ... (remaining 1484 not shown)

  Planarity restraints: 1632
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 253 "   -0.053 5.00e-02 4.00e+02   8.06e-02 1.04e+01
        pdb=" N   PRO A 254 "    0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO A 254 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 254 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  89 "   -0.040 5.00e-02 4.00e+02   6.13e-02 6.01e+00
        pdb=" N   PRO A  90 "    0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO A  90 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A  90 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 254 "    0.032 5.00e-02 4.00e+02   4.96e-02 3.93e+00
        pdb=" N   PRO A 255 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A 255 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 255 "    0.027 5.00e-02 4.00e+02
  ... (remaining 1629 not shown)

  Histogram of nonbonded interaction distances:
        2.46 -     2.95: 3640
        2.95 -     3.44: 9311
        3.44 -     3.92: 14119
        3.92 -     4.41: 15218
        4.41 -     4.90: 25057
  Nonbonded interactions: 67345
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 849 "
            pdb=" O   VAL A1136 "
     model   vdw
     2.461 3.040
  nonbonded pdb=" OG1 THR A 454 "
            pdb=" OG1 THR A 461 "
     model   vdw
     2.494 3.040
  nonbonded pdb=" O   ALA A1062 "
            pdb=" OG1 THR A1066 "
     model   vdw
     2.496 3.040
  nonbonded pdb=" O   TYR A 932 "
            pdb=" NZ  LYS A1057 "
     model   vdw
     2.507 3.120
  nonbonded pdb=" OG  SER A 608 "
            pdb=" OH  TYR A 871 "
     model   vdw
     2.545 3.040
  ... (remaining 67340 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 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:             8.910
  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:          0.460
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     34.250
  Find NCS groups from input model:        0.190
  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:3.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
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   0.325   9365  Z= 0.684
  Angle     :  1.179  11.140  12768  Z= 0.752
  Chirality :  0.076   0.692   1487
  Planarity :  0.005   0.081   1622
  Dihedral  : 14.585 111.613   3512
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 0.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.15 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.23 %
    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: -4.01 (0.20), residues: 1153
  helix: -2.78 (0.16), residues: 549
  sheet: -2.22 (0.54), residues: 90
  loop : -2.48 (0.25), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A1145 
 HIS   0.004   0.001   HIS A 897 
 PHE   0.017   0.002   PHE A1139 
 TYR   0.015   0.002   TYR A 899 
 ARG   0.006   0.000   ARG A1227 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 1.039 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 ASP cc_start: 0.8849 (m-30) cc_final: 0.8550 (t0)
REVERT: A   85 ASP cc_start: 0.8768 (t70) cc_final: 0.8266 (t0)
REVERT: A  103 ASN cc_start: 0.9530 (m110) cc_final: 0.9082 (m110)
REVERT: A  106 ASN cc_start: 0.8784 (m-40) cc_final: 0.8504 (m-40)
REVERT: A  108 PHE cc_start: 0.8783 (m-80) cc_final: 0.8501 (m-80)
REVERT: A  355 PHE cc_start: 0.9111 (t80) cc_final: 0.8778 (t80)
REVERT: A  364 CYS cc_start: 0.8516 (m) cc_final: 0.8145 (m)
REVERT: A  406 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8226 (mt-10)
REVERT: A  593 ASN cc_start: 0.8958 (m-40) cc_final: 0.8434 (p0)
REVERT: A  634 TYR cc_start: 0.8639 (t80) cc_final: 0.8419 (t80)
REVERT: A  663 ILE cc_start: 0.9179 (mt) cc_final: 0.8893 (mt)
REVERT: A  689 VAL cc_start: 0.8739 (t) cc_final: 0.8266 (t)
REVERT: A  730 GLU cc_start: 0.9401 (tp30) cc_final: 0.8841 (tm-30)
REVERT: A  735 MET cc_start: 0.8544 (ttp) cc_final: 0.7998 (ttp)
REVERT: A  834 MET cc_start: 0.7817 (mtt) cc_final: 0.7404 (mmm)
REVERT: A  864 LEU cc_start: 0.8463 (mt) cc_final: 0.8200 (pp)
REVERT: A  872 MET cc_start: 0.8546 (mmm) cc_final: 0.7980 (mmm)
REVERT: A  922 GLN cc_start: 0.8907 (tp-100) cc_final: 0.8480 (tp-100)
REVERT: A  930 ASP cc_start: 0.8554 (p0) cc_final: 0.7879 (t0)
REVERT: A  933 THR cc_start: 0.8749 (t) cc_final: 0.8470 (t)
REVERT: A 1122 TRP cc_start: 0.7946 (m100) cc_final: 0.7449 (m-10)
REVERT: A 1150 ASN cc_start: 0.8223 (p0) cc_final: 0.7741 (p0)
REVERT: A 1156 ASN cc_start: 0.8981 (t0) cc_final: 0.8777 (t0)
REVERT: A 1179 MET cc_start: 0.7488 (mpp) cc_final: 0.7224 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 217
  average time/residue: 0.2486
  time to fit residues: 76.0073
Evaluate side-chains
  118 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 1.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    0.4980
   chunk 87 optimal weight:    7.9990
   chunk 48 optimal weight:    1.9990
   chunk 30 optimal weight:    8.9990
   chunk 59 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 90 optimal weight:    0.7980
   chunk 35 optimal weight:    9.9990
   chunk 55 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   chunk 105 optimal weight:    5.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
A 447 GLN
A 988 GLN
A1042 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.087647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.066383 restraints weight = 29957.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.068541 restraints weight = 16117.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.070024 restraints weight = 10740.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3242
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3242 r_free = 0.3242    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3242 r_free = 0.3242    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3242
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.2234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9365  Z= 0.198
  Angle     :  0.714   8.604  12768  Z= 0.352
  Chirality :  0.049   0.361   1487
  Planarity :  0.005   0.078   1622
  Dihedral  : 13.131  90.292   1547
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  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: -2.93 (0.22), residues: 1153
  helix: -1.58 (0.19), residues: 560
  sheet: -2.29 (0.50), residues: 100
  loop : -2.18 (0.26), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 583 
 HIS   0.003   0.001   HIS A 530 
 PHE   0.034   0.002   PHE A 937 
 TYR   0.015   0.001   TYR A1085 
 ARG   0.007   0.000   ARG A 958 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.982 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 ASN cc_start: 0.8778 (m-40) cc_final: 0.8280 (m-40)
REVERT: A  110 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7041 (mm-30)
REVERT: A  355 PHE cc_start: 0.8819 (t80) cc_final: 0.8570 (t80)
REVERT: A  586 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8717 (mt-10)
REVERT: A  593 ASN cc_start: 0.8663 (m-40) cc_final: 0.8389 (p0)
REVERT: A  676 SER cc_start: 0.9182 (m) cc_final: 0.8906 (p)
REVERT: A  730 GLU cc_start: 0.9225 (tp30) cc_final: 0.8656 (tm-30)
REVERT: A  774 LEU cc_start: 0.9432 (tp) cc_final: 0.9226 (tp)
REVERT: A  930 ASP cc_start: 0.8513 (p0) cc_final: 0.8248 (t0)
REVERT: A  935 ILE cc_start: 0.8195 (mt) cc_final: 0.7859 (mt)
REVERT: A 1150 ASN cc_start: 0.8739 (p0) cc_final: 0.8158 (p0)
REVERT: A 1156 ASN cc_start: 0.8731 (t0) cc_final: 0.8508 (t0)
REVERT: A 1175 PHE cc_start: 0.8314 (t80) cc_final: 0.7792 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 0.1770
  time to fit residues: 40.0789
Evaluate side-chains
  105 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 1.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 85 optimal weight:    4.9990
   chunk 87 optimal weight:    1.9990
   chunk 75 optimal weight:    8.9990
   chunk 20 optimal weight:    8.9990
   chunk 26 optimal weight:    9.9990
   chunk 104 optimal weight:    0.8980
   chunk 11 optimal weight:   50.0000
   chunk 91 optimal weight:    0.7980
   chunk 36 optimal weight:    4.9990
   chunk 19 optimal weight:    7.9990
   chunk 111 optimal weight:    8.9990
   overall best weight:    2.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 775 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.087525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.066763 restraints weight = 29564.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.068798 restraints weight = 16385.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.070170 restraints weight = 11148.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3251
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3251 r_free = 0.3251    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3251 r_free = 0.3251    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3251
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.2670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   9365  Z= 0.266
  Angle     :  0.718   8.287  12768  Z= 0.352
  Chirality :  0.047   0.349   1487
  Planarity :  0.005   0.075   1622
  Dihedral  : 11.211  84.868   1547
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -2.57 (0.23), residues: 1153
  helix: -1.16 (0.20), residues: 565
  sheet: -2.73 (0.46), residues: 105
  loop : -1.99 (0.26), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 583 
 HIS   0.011   0.002   HIS A1042 
 PHE   0.043   0.002   PHE A 632 
 TYR   0.013   0.002   TYR A1037 
 ARG   0.005   0.001   ARG A 411 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 1.093 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 ASP cc_start: 0.8809 (p0) cc_final: 0.8600 (m-30)
REVERT: A  632 PHE cc_start: 0.7941 (m-80) cc_final: 0.7716 (m-80)
REVERT: A  676 SER cc_start: 0.9312 (m) cc_final: 0.8994 (t)
REVERT: A  730 GLU cc_start: 0.9036 (tp30) cc_final: 0.8632 (tm-30)
REVERT: A  742 GLU cc_start: 0.8105 (pp20) cc_final: 0.7889 (pp20)
REVERT: A  774 LEU cc_start: 0.9421 (tp) cc_final: 0.9195 (tp)
REVERT: A  834 MET cc_start: 0.7519 (mmp) cc_final: 0.7282 (mmm)
REVERT: A  872 MET cc_start: 0.8059 (mmm) cc_final: 0.7851 (mmm)
REVERT: A  935 ILE cc_start: 0.8253 (mt) cc_final: 0.8035 (mt)
REVERT: A  996 MET cc_start: 0.9080 (mtp) cc_final: 0.8866 (ttm)
REVERT: A 1150 ASN cc_start: 0.8950 (p0) cc_final: 0.8323 (p0)
REVERT: A 1166 GLU cc_start: 0.8089 (tp30) cc_final: 0.7701 (tp30)
REVERT: A 1175 PHE cc_start: 0.8472 (t80) cc_final: 0.8150 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.2392
  time to fit residues: 49.2388
Evaluate side-chains
  99 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 1.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 74 optimal weight:    5.9990
   chunk 16 optimal weight:   10.0000
   chunk 105 optimal weight:    9.9990
   chunk 44 optimal weight:    7.9990
   chunk 9 optimal weight:    0.3980
   chunk 112 optimal weight:    2.9990
   chunk 60 optimal weight:    9.9990
   chunk 62 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   chunk 82 optimal weight:    0.4980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 568 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.089159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.068492 restraints weight = 29275.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.070602 restraints weight = 15812.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.072073 restraints weight = 10652.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3293
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3293 r_free = 0.3293    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3293 r_free = 0.3293    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3293
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.2896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9365  Z= 0.172
  Angle     :  0.658   8.450  12768  Z= 0.319
  Chirality :  0.045   0.344   1487
  Planarity :  0.005   0.076   1622
  Dihedral  :  9.858  87.262   1547
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  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: -2.19 (0.23), residues: 1153
  helix: -0.88 (0.21), residues: 560
  sheet: -2.38 (0.49), residues: 100
  loop : -1.81 (0.27), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 583 
 HIS   0.009   0.001   HIS A1042 
 PHE   0.040   0.001   PHE A 632 
 TYR   0.010   0.001   TYR A1037 
 ARG   0.005   0.000   ARG A 116 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 1.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 ASP cc_start: 0.8829 (p0) cc_final: 0.8623 (m-30)
REVERT: A  676 SER cc_start: 0.9287 (m) cc_final: 0.9001 (p)
REVERT: A  699 VAL cc_start: 0.8997 (m) cc_final: 0.8792 (t)
REVERT: A  730 GLU cc_start: 0.9007 (tp30) cc_final: 0.8664 (tm-30)
REVERT: A  872 MET cc_start: 0.7938 (mmm) cc_final: 0.7700 (mmm)
REVERT: A  945 ASP cc_start: 0.8596 (t70) cc_final: 0.8383 (t70)
REVERT: A  996 MET cc_start: 0.9047 (mtp) cc_final: 0.8844 (ttm)
REVERT: A  998 PHE cc_start: 0.8780 (m-80) cc_final: 0.8486 (m-80)
REVERT: A 1150 ASN cc_start: 0.8876 (p0) cc_final: 0.8261 (p0)
REVERT: A 1175 PHE cc_start: 0.8485 (t80) cc_final: 0.8160 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.2177
  time to fit residues: 46.9976
Evaluate side-chains
  103 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 1.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 66 optimal weight:    6.9990
   chunk 32 optimal weight:    4.9990
   chunk 103 optimal weight:    6.9990
   chunk 71 optimal weight:    7.9990
   chunk 70 optimal weight:    8.9990
   chunk 74 optimal weight:    3.9990
   chunk 90 optimal weight:    1.9990
   chunk 58 optimal weight:    9.9990
   chunk 94 optimal weight:    7.9990
   chunk 96 optimal weight:    3.9990
   chunk 24 optimal weight:    9.9990
   overall best weight:    4.3990

-------------------------------------------------------------------------------
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 = 0.3571 r_free = 0.3571 target = 0.085135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.064433 restraints weight = 30100.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.066321 restraints weight = 17228.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.067587 restraints weight = 11974.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3201
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3201 r_free = 0.3201    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3201 r_free = 0.3201    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3201
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.3274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058   9365  Z= 0.380
  Angle     :  0.775   8.434  12768  Z= 0.383
  Chirality :  0.049   0.359   1487
  Planarity :  0.005   0.074   1622
  Dihedral  :  9.164  84.030   1547
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.81 %
    Favored  : 92.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -2.22 (0.24), residues: 1153
  helix: -0.95 (0.20), residues: 569
  sheet: -2.72 (0.47), residues: 94
  loop : -1.70 (0.28), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 381 
 HIS   0.011   0.002   HIS A1042 
 PHE   0.024   0.003   PHE A 937 
 TYR   0.016   0.002   TYR A 709 
 ARG   0.009   0.001   ARG A 404 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 1.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 ASN cc_start: 0.8715 (m-40) cc_final: 0.8397 (m-40)
REVERT: A  531 ASP cc_start: 0.7919 (t0) cc_final: 0.7705 (t0)
REVERT: A  632 PHE cc_start: 0.7554 (m-80) cc_final: 0.7238 (m-80)
REVERT: A  676 SER cc_start: 0.9322 (m) cc_final: 0.9061 (p)
REVERT: A  730 GLU cc_start: 0.8917 (tp30) cc_final: 0.8562 (tm-30)
REVERT: A  834 MET cc_start: 0.7248 (mmm) cc_final: 0.6967 (mmm)
REVERT: A  872 MET cc_start: 0.7948 (mmm) cc_final: 0.7235 (mmm)
REVERT: A  875 TYR cc_start: 0.9016 (t80) cc_final: 0.8675 (t80)
REVERT: A  996 MET cc_start: 0.9082 (mtp) cc_final: 0.8794 (ttm)
REVERT: A 1150 ASN cc_start: 0.9063 (p0) cc_final: 0.8204 (p0)
REVERT: A 1166 GLU cc_start: 0.8094 (tp30) cc_final: 0.7822 (tp30)
REVERT: A 1175 PHE cc_start: 0.8484 (t80) cc_final: 0.7869 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.2681
  time to fit residues: 51.5720
Evaluate side-chains
  91 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 1.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 42 optimal weight:    8.9990
   chunk 10 optimal weight:    0.0770
   chunk 5 optimal weight:   20.0000
   chunk 27 optimal weight:    6.9990
   chunk 100 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 82 optimal weight:    0.8980
   chunk 83 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 84 optimal weight:    4.9990
   chunk 15 optimal weight:    6.9990
   overall best weight:    1.1942

-------------------------------------------------------------------------------
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 = 0.3617 r_free = 0.3617 target = 0.087802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.067144 restraints weight = 29567.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.069251 restraints weight = 16068.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.070670 restraints weight = 10800.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3268
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3268
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.3302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9365  Z= 0.181
  Angle     :  0.656   9.490  12768  Z= 0.317
  Chirality :  0.045   0.345   1487
  Planarity :  0.005   0.074   1622
  Dihedral  :  8.553  89.044   1547
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  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: -1.91 (0.24), residues: 1153
  helix: -0.64 (0.21), residues: 561
  sheet: -2.37 (0.49), residues: 94
  loop : -1.66 (0.28), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 583 
 HIS   0.007   0.001   HIS A1042 
 PHE   0.021   0.001   PHE A1243 
 TYR   0.025   0.001   TYR A1085 
 ARG   0.004   0.000   ARG A1227 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 1.047 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 ASN cc_start: 0.8647 (m-40) cc_final: 0.8355 (m-40)
REVERT: A  531 ASP cc_start: 0.7938 (t0) cc_final: 0.7688 (t0)
REVERT: A  632 PHE cc_start: 0.7659 (m-80) cc_final: 0.7357 (m-80)
REVERT: A  676 SER cc_start: 0.9305 (m) cc_final: 0.9017 (p)
REVERT: A  699 VAL cc_start: 0.9139 (m) cc_final: 0.8934 (t)
REVERT: A  730 GLU cc_start: 0.8991 (tp30) cc_final: 0.8650 (tm-30)
REVERT: A  872 MET cc_start: 0.7898 (mmm) cc_final: 0.7625 (mmt)
REVERT: A  945 ASP cc_start: 0.8637 (t70) cc_final: 0.8399 (t70)
REVERT: A  996 MET cc_start: 0.9112 (mtp) cc_final: 0.8841 (ttm)
REVERT: A 1063 SER cc_start: 0.9337 (t) cc_final: 0.9019 (p)
REVERT: A 1150 ASN cc_start: 0.8896 (p0) cc_final: 0.8186 (p0)
REVERT: A 1175 PHE cc_start: 0.8449 (t80) cc_final: 0.8042 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 0.1772
  time to fit residues: 35.6733
Evaluate side-chains
  101 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 26 optimal weight:   30.0000
   chunk 62 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0050
   chunk 31 optimal weight:    7.9990
   chunk 104 optimal weight:    6.9990
   chunk 3 optimal weight:    5.9990
   chunk 101 optimal weight:    0.7980
   chunk 83 optimal weight:    0.9980
   chunk 48 optimal weight:    5.9990
   chunk 67 optimal weight:    5.9990
   overall best weight:    1.1598

-------------------------------------------------------------------------------
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 = 0.3630 r_free = 0.3630 target = 0.088536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.067870 restraints weight = 30257.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.070032 restraints weight = 16308.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.071465 restraints weight = 10895.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3287
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3287 r_free = 0.3287    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3287 r_free = 0.3287    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3287
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.3463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9365  Z= 0.172
  Angle     :  0.649  11.938  12768  Z= 0.314
  Chirality :  0.044   0.335   1487
  Planarity :  0.004   0.073   1622
  Dihedral  :  7.955  85.729   1547
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  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: -1.73 (0.24), residues: 1153
  helix: -0.51 (0.21), residues: 563
  sheet: -2.41 (0.49), residues: 99
  loop : -1.51 (0.28), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1143 
 HIS   0.007   0.001   HIS A1042 
 PHE   0.014   0.001   PHE A1243 
 TYR   0.025   0.001   TYR A1085 
 ARG   0.004   0.000   ARG A1227 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 1.046 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 GLU cc_start: 0.7320 (mm-30) cc_final: 0.7055 (mm-30)
REVERT: A  531 ASP cc_start: 0.7932 (t0) cc_final: 0.7706 (t0)
REVERT: A  632 PHE cc_start: 0.7626 (m-80) cc_final: 0.7335 (m-80)
REVERT: A  676 SER cc_start: 0.9286 (m) cc_final: 0.9005 (p)
REVERT: A  730 GLU cc_start: 0.8916 (tp30) cc_final: 0.8617 (tm-30)
REVERT: A  872 MET cc_start: 0.7878 (mmm) cc_final: 0.7561 (mmt)
REVERT: A  907 MET cc_start: 0.8258 (mmm) cc_final: 0.8004 (mmm)
REVERT: A  945 ASP cc_start: 0.8639 (t70) cc_final: 0.8402 (t70)
REVERT: A  996 MET cc_start: 0.8948 (mtp) cc_final: 0.8675 (ttm)
REVERT: A 1063 SER cc_start: 0.9320 (t) cc_final: 0.8993 (p)
REVERT: A 1150 ASN cc_start: 0.8883 (p0) cc_final: 0.7982 (p0)
REVERT: A 1175 PHE cc_start: 0.8375 (t80) cc_final: 0.7681 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.1843
  time to fit residues: 37.3206
Evaluate side-chains
  100 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 10 optimal weight:   40.0000
   chunk 56 optimal weight:   10.0000
   chunk 81 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9980
   chunk 112 optimal weight:    8.9990
   chunk 94 optimal weight:    7.9990
   chunk 37 optimal weight:    1.9990
   chunk 9 optimal weight:    9.9990
   chunk 46 optimal weight:    1.9990
   chunk 89 optimal weight:    4.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 897 HIS
A1239 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.086743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.065853 restraints weight = 30923.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.067885 restraints weight = 16779.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.069290 restraints weight = 11366.012|
|-----------------------------------------------------------------------------|
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3240
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3240 r_free = 0.3240    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3240 r_free = 0.3240    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3240
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.3644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   9365  Z= 0.266
  Angle     :  0.680  10.213  12768  Z= 0.334
  Chirality :  0.047   0.425   1487
  Planarity :  0.005   0.073   1622
  Dihedral  :  8.191  82.189   1547
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  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: -1.71 (0.24), residues: 1153
  helix: -0.51 (0.21), residues: 570
  sheet: -2.39 (0.49), residues: 94
  loop : -1.51 (0.29), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 544 
 HIS   0.009   0.002   HIS A1042 
 PHE   0.026   0.002   PHE A 937 
 TYR   0.015   0.002   TYR A1085 
 ARG   0.007   0.001   ARG A1227 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.953 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 ASN cc_start: 0.8645 (m-40) cc_final: 0.8367 (m-40)
REVERT: A  110 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6922 (mm-30)
REVERT: A  194 PHE cc_start: 0.8989 (m-10) cc_final: 0.8772 (m-80)
REVERT: A  531 ASP cc_start: 0.8041 (t0) cc_final: 0.7801 (t0)
REVERT: A  632 PHE cc_start: 0.7671 (m-80) cc_final: 0.7358 (m-80)
REVERT: A  676 SER cc_start: 0.9304 (m) cc_final: 0.9035 (p)
REVERT: A  730 GLU cc_start: 0.8999 (tp30) cc_final: 0.8650 (tm-30)
REVERT: A  872 MET cc_start: 0.8016 (mmm) cc_final: 0.7494 (mmm)
REVERT: A  875 TYR cc_start: 0.9006 (t80) cc_final: 0.8692 (t80)
REVERT: A  996 MET cc_start: 0.9086 (mtp) cc_final: 0.8757 (ttm)
REVERT: A 1150 ASN cc_start: 0.8948 (p0) cc_final: 0.8060 (p0)
REVERT: A 1159 MET cc_start: 0.8491 (ttm) cc_final: 0.8143 (ttp)
REVERT: A 1166 GLU cc_start: 0.8259 (tp30) cc_final: 0.8013 (tp30)
REVERT: A 1175 PHE cc_start: 0.8407 (t80) cc_final: 0.7936 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.1679
  time to fit residues: 31.4023
Evaluate side-chains
  94 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 1.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 110 optimal weight:    1.9990
   chunk 55 optimal weight:    5.9990
   chunk 83 optimal weight:    3.9990
   chunk 23 optimal weight:    9.9990
   chunk 51 optimal weight:    3.9990
   chunk 34 optimal weight:    7.9990
   chunk 65 optimal weight:    8.9990
   chunk 15 optimal weight:    0.0370
   chunk 44 optimal weight:    4.9990
   chunk 33 optimal weight:    0.0980
   chunk 77 optimal weight:    7.9990
   overall best weight:    2.0264

-------------------------------------------------------------------------------
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 = 0.3609 r_free = 0.3609 target = 0.087288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.066568 restraints weight = 29766.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.068642 restraints weight = 16194.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.070044 restraints weight = 10975.876|
|-----------------------------------------------------------------------------|
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3255
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3255 r_free = 0.3255    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3255 r_free = 0.3255    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3255
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.3701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9365  Z= 0.217
  Angle     :  0.664  11.323  12768  Z= 0.325
  Chirality :  0.045   0.335   1487
  Planarity :  0.004   0.072   1622
  Dihedral  :  7.998  87.505   1547
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  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: -1.70 (0.24), residues: 1153
  helix: -0.48 (0.21), residues: 567
  sheet: -2.34 (0.50), residues: 94
  loop : -1.53 (0.29), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 544 
 HIS   0.009   0.001   HIS A1042 
 PHE   0.024   0.001   PHE A 937 
 TYR   0.027   0.001   TYR A 634 
 ARG   0.006   0.000   ARG A1227 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.975 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 ASN cc_start: 0.8640 (m-40) cc_final: 0.8320 (m-40)
REVERT: A  110 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6875 (mm-30)
REVERT: A  194 PHE cc_start: 0.9006 (m-10) cc_final: 0.8803 (m-80)
REVERT: A  531 ASP cc_start: 0.8002 (t0) cc_final: 0.7753 (t0)
REVERT: A  632 PHE cc_start: 0.7631 (m-80) cc_final: 0.7330 (m-80)
REVERT: A  676 SER cc_start: 0.9310 (m) cc_final: 0.9039 (p)
REVERT: A  730 GLU cc_start: 0.8988 (tp30) cc_final: 0.8642 (tm-30)
REVERT: A  872 MET cc_start: 0.7927 (mmm) cc_final: 0.7485 (mmm)
REVERT: A  996 MET cc_start: 0.9078 (mtp) cc_final: 0.8741 (ttm)
REVERT: A  999 LEU cc_start: 0.9575 (tp) cc_final: 0.9362 (tt)
REVERT: A 1063 SER cc_start: 0.9320 (t) cc_final: 0.9011 (p)
REVERT: A 1150 ASN cc_start: 0.8962 (p0) cc_final: 0.8089 (p0)
REVERT: A 1166 GLU cc_start: 0.8116 (tp30) cc_final: 0.7748 (tp30)
REVERT: A 1175 PHE cc_start: 0.8432 (t80) cc_final: 0.7998 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1719
  time to fit residues: 31.6788
Evaluate side-chains
  92 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 114 optimal weight:    3.9990
   chunk 100 optimal weight:    0.6980
   chunk 28 optimal weight:   10.0000
   chunk 99 optimal weight:    0.7980
   chunk 67 optimal weight:    0.0170
   chunk 32 optimal weight:    5.9990
   chunk 13 optimal weight:   10.0000
   chunk 55 optimal weight:    9.9990
   chunk 85 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.7022

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

Flipped N/Q/H residues before XYZ refinement:
A1239 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.088816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.068239 restraints weight = 30190.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.070432 restraints weight = 16034.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.071903 restraints weight = 10642.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3292
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3292 r_free = 0.3292    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3292 r_free = 0.3292    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3292
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.3818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9365  Z= 0.159
  Angle     :  0.639  11.959  12768  Z= 0.310
  Chirality :  0.044   0.324   1487
  Planarity :  0.004   0.072   1622
  Dihedral  :  7.473  83.267   1547
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  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: -1.57 (0.24), residues: 1153
  helix: -0.35 (0.21), residues: 566
  sheet: -1.91 (0.55), residues: 85
  loop : -1.61 (0.28), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 544 
 HIS   0.008   0.001   HIS A1042 
 PHE   0.022   0.001   PHE A 937 
 TYR   0.023   0.001   TYR A 634 
 ARG   0.004   0.000   ARG A1227 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.932 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 ASN cc_start: 0.8584 (m-40) cc_final: 0.8296 (m-40)
REVERT: A  110 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6862 (mm-30)
REVERT: A  194 PHE cc_start: 0.9002 (m-10) cc_final: 0.8789 (m-80)
REVERT: A  531 ASP cc_start: 0.7911 (t0) cc_final: 0.7686 (t0)
REVERT: A  632 PHE cc_start: 0.7613 (m-80) cc_final: 0.7310 (m-80)
REVERT: A  676 SER cc_start: 0.9298 (m) cc_final: 0.9050 (p)
REVERT: A  730 GLU cc_start: 0.8905 (tp30) cc_final: 0.8609 (tm-30)
REVERT: A  872 MET cc_start: 0.7765 (mmm) cc_final: 0.7426 (mmt)
REVERT: A  945 ASP cc_start: 0.8692 (t70) cc_final: 0.8438 (t70)
REVERT: A  996 MET cc_start: 0.8972 (mtp) cc_final: 0.8651 (ttm)
REVERT: A  999 LEU cc_start: 0.9561 (tp) cc_final: 0.9343 (tt)
REVERT: A 1063 SER cc_start: 0.9255 (t) cc_final: 0.8942 (p)
REVERT: A 1150 ASN cc_start: 0.8850 (p0) cc_final: 0.7958 (p0)
REVERT: A 1159 MET cc_start: 0.8413 (ttm) cc_final: 0.8043 (ttp)
REVERT: A 1166 GLU cc_start: 0.8005 (tp30) cc_final: 0.7568 (tp30)
REVERT: A 1175 PHE cc_start: 0.8463 (t80) cc_final: 0.8046 (t80)
REVERT: A 1194 MET cc_start: 0.8036 (ptm) cc_final: 0.7594 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1679
  time to fit residues: 31.4628
Evaluate side-chains
  97 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 99 optimal weight:    3.9990
   chunk 18 optimal weight:   20.0000
   chunk 69 optimal weight:    2.9990
   chunk 83 optimal weight:    4.9990
   chunk 49 optimal weight:    1.9990
   chunk 30 optimal weight:    8.9990
   chunk 92 optimal weight:   10.0000
   chunk 104 optimal weight:    5.9990
   chunk 0 optimal weight:   30.0000
   chunk 3 optimal weight:    8.9990
   chunk 82 optimal weight:    0.0970
   overall best weight:    2.8186

-------------------------------------------------------------------------------
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 = 0.3596 r_free = 0.3596 target = 0.086585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.065969 restraints weight = 30174.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.068029 restraints weight = 16436.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.069383 restraints weight = 11083.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3242
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3242 r_free = 0.3242    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3242 r_free = 0.3242    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3242
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.3925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   9365  Z= 0.259
  Angle     :  0.680  10.516  12768  Z= 0.334
  Chirality :  0.046   0.334   1487
  Planarity :  0.004   0.072   1622
  Dihedral  :  7.476  82.815   1547
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  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: -1.47 (0.25), residues: 1153
  helix: -0.31 (0.21), residues: 567
  sheet: -2.21 (0.51), residues: 94
  loop : -1.41 (0.29), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 833 
 HIS   0.009   0.002   HIS A1042 
 PHE   0.018   0.002   PHE A1139 
 TYR   0.023   0.002   TYR A 634 
 ARG   0.007   0.001   ARG A  78 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4330.59 seconds
wall clock time: 79 minutes 3.61 seconds (4743.61 seconds total)