Starting phenix.real_space_refine on Thu Feb 5 12:04:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bop_44747/02_2026/9bop_44747.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bop_44747/02_2026/9bop_44747.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bop_44747/02_2026/9bop_44747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bop_44747/02_2026/9bop_44747.map" model { file = "/net/cci-nas-00/data/ceres_data/9bop_44747/02_2026/9bop_44747.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bop_44747/02_2026/9bop_44747.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 10693 2.51 5 N 2763 2.21 5 O 3324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16858 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 919 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "B" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 810 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "M" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 915 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "N" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 806 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "O" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 891 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain breaks: 1 Chain: "P" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 719 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain breaks: 3 Chain: "S" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1824 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 12, 'TRANS': 221} Chain breaks: 1 Chain: "V" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 853 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain breaks: 1 Chain: "C" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 919 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "E" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 919 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "D" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 810 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "F" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 810 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "W" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 853 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain breaks: 1 Chain: "X" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 853 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain breaks: 1 Chain: "T" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1824 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 12, 'TRANS': 221} Chain breaks: 1 Chain: "U" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1824 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 12, 'TRANS': 221} Chain breaks: 1 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.30, per 1000 atoms: 0.26 Number of scatterers: 16858 At special positions: 0 Unit cell: (138.445, 149.094, 135.117, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 3324 8.00 N 2763 7.00 C 10693 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=25, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 98 " distance=2.03 Simple disulfide: pdb=" SG CYS A 36 " - pdb=" SG CYS A 51 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 21 " - pdb=" SG CYS M 93 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS O 21 " - pdb=" SG CYS O 93 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 Simple disulfide: pdb=" SG CYS S 108 " - pdb=" SG CYS S 135 " distance=2.03 Simple disulfide: pdb=" SG CYS S 121 " - pdb=" SG CYS S 147 " distance=2.03 Simple disulfide: pdb=" SG CYS V 511 " - pdb=" SG CYS V 556 " distance=2.03 Simple disulfide: pdb=" SG CYS V 601 " - pdb=" SG CYS V 608 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 98 " distance=2.03 Simple disulfide: pdb=" SG CYS C 36 " - pdb=" SG CYS C 51 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 98 " distance=2.03 Simple disulfide: pdb=" SG CYS E 36 " - pdb=" SG CYS E 51 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS W 511 " - pdb=" SG CYS W 556 " distance=2.03 Simple disulfide: pdb=" SG CYS W 601 " - pdb=" SG CYS W 608 " distance=2.03 Simple disulfide: pdb=" SG CYS X 511 " - pdb=" SG CYS X 556 " distance=2.03 Simple disulfide: pdb=" SG CYS X 601 " - pdb=" SG CYS X 608 " distance=2.03 Simple disulfide: pdb=" SG CYS T 108 " - pdb=" SG CYS T 135 " distance=2.03 Simple disulfide: pdb=" SG CYS T 121 " - pdb=" SG CYS T 147 " distance=2.03 Simple disulfide: pdb=" SG CYS U 108 " - pdb=" SG CYS U 135 " distance=2.03 Simple disulfide: pdb=" SG CYS U 121 " - pdb=" SG CYS U 147 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG S 401 " - " NAG S 402 " " NAG T 401 " - " NAG T 402 " " NAG U 401 " - " NAG U 402 " NAG-ASN " NAG G 1 " - " ASN V 563 " " NAG H 1 " - " ASN W 563 " " NAG I 1 " - " ASN X 563 " " NAG S 401 " - " ASN S 257 " " NAG S 403 " - " ASN S 228 " " NAG T 401 " - " ASN T 257 " " NAG T 403 " - " ASN T 228 " " NAG U 401 " - " ASN U 257 " " NAG U 403 " - " ASN U 228 " Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 627.7 milliseconds 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3888 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 49 sheets defined 10.6% alpha, 37.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.801A pdb=" N THR A 93 " --> pdb=" O ALA A 90 " (cutoff:3.500A) Processing helix chain 'M' and resid 27 through 31 removed outlier: 3.725A pdb=" N TYR M 31 " --> pdb=" O LEU M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 63 removed outlier: 3.502A pdb=" N LYS M 63 " --> pdb=" O SER M 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 60 through 63' Processing helix chain 'M' and resid 84 through 88 removed outlier: 4.107A pdb=" N THR M 88 " --> pdb=" O THR M 85 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 4.021A pdb=" N ALA N 83 " --> pdb=" O CYS N 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 71 through 74 Processing helix chain 'S' and resid 78 through 83 Processing helix chain 'S' and resid 249 through 264 Processing helix chain 'V' and resid 553 through 576 removed outlier: 3.545A pdb=" N GLN V 560 " --> pdb=" O CYS V 556 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR V 566 " --> pdb=" O ALA V 562 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLN V 567 " --> pdb=" O ASN V 563 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ALA V 568 " --> pdb=" O GLU V 564 " (cutoff:3.500A) Processing helix chain 'V' and resid 583 through 597 Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.952A pdb=" N THR C 93 " --> pdb=" O ALA C 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 93 Processing helix chain 'W' and resid 553 through 576 removed outlier: 3.679A pdb=" N GLN W 560 " --> pdb=" O CYS W 556 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN W 563 " --> pdb=" O ARG W 559 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR W 566 " --> pdb=" O ALA W 562 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N GLN W 567 " --> pdb=" O ASN W 563 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA W 568 " --> pdb=" O GLU W 564 " (cutoff:3.500A) Processing helix chain 'W' and resid 583 through 597 Processing helix chain 'X' and resid 553 through 576 removed outlier: 3.688A pdb=" N THR X 566 " --> pdb=" O ALA X 562 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N GLN X 567 " --> pdb=" O ASN X 563 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ALA X 568 " --> pdb=" O GLU X 564 " (cutoff:3.500A) Processing helix chain 'X' and resid 583 through 597 Processing helix chain 'T' and resid 71 through 74 Processing helix chain 'T' and resid 78 through 83 Processing helix chain 'T' and resid 249 through 264 Processing helix chain 'U' and resid 71 through 74 Processing helix chain 'U' and resid 78 through 83 Processing helix chain 'U' and resid 249 through 264 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 7 removed outlier: 4.083A pdb=" N THR A 82 " --> pdb=" O SER A 74 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 63 removed outlier: 6.727A pdb=" N TRP A 37 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N CYS A 51 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ARG A 35 " --> pdb=" O CYS A 51 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N TRP A 34 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 11.333A pdb=" N CYS A 98 " --> pdb=" O ASN A 113 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N ASN A 113 " --> pdb=" O CYS A 98 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ARG A 100 " --> pdb=" O PHE A 111 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N PHE A 111 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY A 102 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 63 removed outlier: 6.727A pdb=" N TRP A 37 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N CYS A 51 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ARG A 35 " --> pdb=" O CYS A 51 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N TRP A 34 " --> pdb=" O ALA A 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.522A pdb=" N VAL B 11 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.522A pdb=" N VAL B 11 " --> pdb=" O VAL B 109 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 19 through 24 removed outlier: 3.581A pdb=" N TYR B 71 " --> pdb=" O CYS B 23 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 2 through 6 Processing sheet with id=AA8, first strand: chain 'M' and resid 56 through 58 removed outlier: 6.821A pdb=" N TRP M 35 " --> pdb=" O ILE M 47 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL M 49 " --> pdb=" O MET M 33 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N MET M 33 " --> pdb=" O VAL M 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 96 through 97 removed outlier: 3.502A pdb=" N ALA M 108 " --> pdb=" O LEU M 97 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 4 through 6 removed outlier: 3.698A pdb=" N GLU N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.486A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'O' and resid 2 through 6 removed outlier: 3.640A pdb=" N LEU O 17 " --> pdb=" O ILE O 80 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'O' and resid 2 through 6 Processing sheet with id=AB5, first strand: chain 'O' and resid 56 through 58 removed outlier: 6.860A pdb=" N TRP O 35 " --> pdb=" O ILE O 47 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL O 49 " --> pdb=" O MET O 33 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N MET O 33 " --> pdb=" O VAL O 49 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ARG O 95 " --> pdb=" O ASP O 110 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP O 110 " --> pdb=" O ARG O 95 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 56 through 58 removed outlier: 6.860A pdb=" N TRP O 35 " --> pdb=" O ILE O 47 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL O 49 " --> pdb=" O MET O 33 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N MET O 33 " --> pdb=" O VAL O 49 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 4 through 6 removed outlier: 3.625A pdb=" N GLU P 70 " --> pdb=" O SER P 67 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'P' and resid 10 through 11 removed outlier: 3.581A pdb=" N GLN P 38 " --> pdb=" O THR P 85 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N TYR P 49 " --> pdb=" O LEU P 33 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'S' and resid 42 through 45 removed outlier: 3.888A pdb=" N ILE S 38 " --> pdb=" O ILE S 185 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'S' and resid 42 through 45 removed outlier: 3.888A pdb=" N ILE S 38 " --> pdb=" O ILE S 185 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'S' and resid 86 through 89 Processing sheet with id=AC3, first strand: chain 'S' and resid 165 through 167 removed outlier: 7.067A pdb=" N VAL S 96 " --> pdb=" O THR V 581 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'S' and resid 101 through 103 Processing sheet with id=AC5, first strand: chain 'S' and resid 105 through 114 removed outlier: 6.316A pdb=" N GLU S 106 " --> pdb=" O TYR S 137 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N HIS S 139 " --> pdb=" O GLU S 106 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N CYS S 108 " --> pdb=" O HIS S 139 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL S 141 " --> pdb=" O CYS S 108 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ASN S 110 " --> pdb=" O VAL S 141 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N GLY S 143 " --> pdb=" O ASN S 110 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLU S 112 " --> pdb=" O GLY S 143 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER S 142 " --> pdb=" O TYR S 220 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ARG S 219 " --> pdb=" O GLU S 235 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N VAL S 277 " --> pdb=" O GLN S 243 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'V' and resid 601 through 602 removed outlier: 6.649A pdb=" N CYS V 601 " --> pdb=" O GLU W 611 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'V' and resid 610 through 611 removed outlier: 3.670A pdb=" N GLU V 611 " --> pdb=" O CYS X 601 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 6 through 7 Processing sheet with id=AC9, first strand: chain 'C' and resid 62 through 63 removed outlier: 6.732A pdb=" N TRP C 37 " --> pdb=" O ILE C 49 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N CYS C 51 " --> pdb=" O ARG C 35 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ARG C 35 " --> pdb=" O CYS C 51 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N TRP C 34 " --> pdb=" O ALA C 101 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA C 101 " --> pdb=" O TRP C 34 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ARG C 100 " --> pdb=" O ASN C 113 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N PHE C 111 " --> pdb=" O GLY C 102 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASP C 104 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA C 109 " --> pdb=" O ASP C 104 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 62 through 63 removed outlier: 6.732A pdb=" N TRP C 37 " --> pdb=" O ILE C 49 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N CYS C 51 " --> pdb=" O ARG C 35 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ARG C 35 " --> pdb=" O CYS C 51 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N TRP C 34 " --> pdb=" O ALA C 101 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA C 101 " --> pdb=" O TRP C 34 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 6 through 7 removed outlier: 4.062A pdb=" N THR E 82 " --> pdb=" O SER E 74 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 62 through 63 removed outlier: 6.590A pdb=" N TRP E 37 " --> pdb=" O ILE E 49 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N CYS E 51 " --> pdb=" O ARG E 35 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ARG E 35 " --> pdb=" O CYS E 51 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N TRP E 34 " --> pdb=" O ALA E 101 " (cutoff:3.500A) removed outlier: 11.174A pdb=" N CYS E 98 " --> pdb=" O ASN E 113 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N ASN E 113 " --> pdb=" O CYS E 98 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ARG E 100 " --> pdb=" O PHE E 111 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N PHE E 111 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY E 102 " --> pdb=" O ALA E 109 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 62 through 63 removed outlier: 6.590A pdb=" N TRP E 37 " --> pdb=" O ILE E 49 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N CYS E 51 " --> pdb=" O ARG E 35 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ARG E 35 " --> pdb=" O CYS E 51 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N TRP E 34 " --> pdb=" O ALA E 101 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 4 through 5 Processing sheet with id=AD6, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.516A pdb=" N VAL D 11 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.516A pdb=" N VAL D 11 " --> pdb=" O VAL D 109 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 19 through 22 removed outlier: 3.603A pdb=" N GLU D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 4 through 5 removed outlier: 3.565A pdb=" N TYR F 71 " --> pdb=" O CYS F 23 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.716A pdb=" N VAL F 11 " --> pdb=" O VAL F 109 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'W' and resid 546 through 547 Processing sheet with id=AE3, first strand: chain 'W' and resid 580 through 581 removed outlier: 3.536A pdb=" N ASN T 98 " --> pdb=" O THR W 581 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'X' and resid 546 through 547 Processing sheet with id=AE5, first strand: chain 'X' and resid 580 through 581 removed outlier: 3.579A pdb=" N ASN U 98 " --> pdb=" O THR X 581 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU U 165 " --> pdb=" O TYR U 162 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE U 38 " --> pdb=" O ILE U 185 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'X' and resid 580 through 581 removed outlier: 3.579A pdb=" N ASN U 98 " --> pdb=" O THR X 581 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU U 165 " --> pdb=" O TYR U 162 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'T' and resid 42 through 45 removed outlier: 3.896A pdb=" N ILE T 38 " --> pdb=" O ILE T 185 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'T' and resid 42 through 45 removed outlier: 3.896A pdb=" N ILE T 38 " --> pdb=" O ILE T 185 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'T' and resid 86 through 89 Processing sheet with id=AF1, first strand: chain 'T' and resid 105 through 114 removed outlier: 6.376A pdb=" N GLU T 106 " --> pdb=" O TYR T 137 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N HIS T 139 " --> pdb=" O GLU T 106 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N CYS T 108 " --> pdb=" O HIS T 139 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N VAL T 141 " --> pdb=" O CYS T 108 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ASN T 110 " --> pdb=" O VAL T 141 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N GLY T 143 " --> pdb=" O ASN T 110 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLU T 112 " --> pdb=" O GLY T 143 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ARG T 136 " --> pdb=" O THR T 216 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ILE T 218 " --> pdb=" O ARG T 136 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL T 138 " --> pdb=" O ILE T 218 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N TYR T 220 " --> pdb=" O VAL T 138 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LYS T 140 " --> pdb=" O TYR T 220 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ALA T 222 " --> pdb=" O LYS T 140 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N SER T 142 " --> pdb=" O ALA T 222 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ARG T 219 " --> pdb=" O GLU T 235 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N VAL T 277 " --> pdb=" O GLN T 243 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'U' and resid 86 through 89 Processing sheet with id=AF3, first strand: chain 'U' and resid 105 through 114 removed outlier: 6.415A pdb=" N GLU U 106 " --> pdb=" O TYR U 137 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N HIS U 139 " --> pdb=" O GLU U 106 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N CYS U 108 " --> pdb=" O HIS U 139 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL U 141 " --> pdb=" O CYS U 108 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ASN U 110 " --> pdb=" O VAL U 141 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N GLY U 143 " --> pdb=" O ASN U 110 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLU U 112 " --> pdb=" O GLY U 143 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ARG U 136 " --> pdb=" O THR U 216 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ILE U 218 " --> pdb=" O ARG U 136 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL U 138 " --> pdb=" O ILE U 218 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'U' and resid 105 through 114 removed outlier: 6.415A pdb=" N GLU U 106 " --> pdb=" O TYR U 137 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N HIS U 139 " --> pdb=" O GLU U 106 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N CYS U 108 " --> pdb=" O HIS U 139 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL U 141 " --> pdb=" O CYS U 108 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ASN U 110 " --> pdb=" O VAL U 141 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N GLY U 143 " --> pdb=" O ASN U 110 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLU U 112 " --> pdb=" O GLY U 143 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR U 241 " --> pdb=" O TRP U 275 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N VAL U 277 " --> pdb=" O TYR U 241 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N GLN U 243 " --> pdb=" O VAL U 277 " (cutoff:3.500A) 601 hydrogen bonds defined for protein. 1506 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: 3.00 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5313 1.34 - 1.46: 4468 1.46 - 1.58: 7388 1.58 - 1.70: 0 1.70 - 1.82: 88 Bond restraints: 17257 Sorted by residual: bond pdb=" C3 BMA I 3 " pdb=" O3 BMA I 3 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.45e+00 bond pdb=" C3 BMA H 3 " pdb=" O3 BMA H 3 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.45e+00 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.551 -0.032 2.00e-02 2.50e+03 2.58e+00 bond pdb=" C1 MAN G 4 " pdb=" C2 MAN G 4 " ideal model delta sigma weight residual 1.526 1.557 -0.031 2.00e-02 2.50e+03 2.40e+00 bond pdb=" C1 NAG T 402 " pdb=" O5 NAG T 402 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.26e+00 ... (remaining 17252 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 22792 1.27 - 2.53: 532 2.53 - 3.80: 136 3.80 - 5.07: 36 5.07 - 6.34: 16 Bond angle restraints: 23512 Sorted by residual: angle pdb=" C ALA M 72 " pdb=" CA ALA M 72 " pdb=" CB ALA M 72 " ideal model delta sigma weight residual 115.89 110.77 5.12 1.32e+00 5.74e-01 1.50e+01 angle pdb=" CA GLY N 66 " pdb=" C GLY N 66 " pdb=" O GLY N 66 " ideal model delta sigma weight residual 122.45 120.38 2.07 7.20e-01 1.93e+00 8.27e+00 angle pdb=" C HIS U 39 " pdb=" N ASN U 40 " pdb=" CA ASN U 40 " ideal model delta sigma weight residual 122.46 125.63 -3.17 1.41e+00 5.03e-01 5.06e+00 angle pdb=" CA PRO M 111 " pdb=" C PRO M 111 " pdb=" O PRO M 111 " ideal model delta sigma weight residual 123.07 120.13 2.94 1.38e+00 5.25e-01 4.53e+00 angle pdb=" C SER B 50 " pdb=" N ALA B 51 " pdb=" CA ALA B 51 " ideal model delta sigma weight residual 121.54 125.59 -4.05 1.91e+00 2.74e-01 4.49e+00 ... (remaining 23507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.07: 9839 22.07 - 44.14: 434 44.14 - 66.21: 42 66.21 - 88.28: 34 88.28 - 110.35: 14 Dihedral angle restraints: 10363 sinusoidal: 4225 harmonic: 6138 Sorted by residual: dihedral pdb=" CB CYS V 601 " pdb=" SG CYS V 601 " pdb=" SG CYS V 608 " pdb=" CB CYS V 608 " ideal model delta sinusoidal sigma weight residual -86.00 -175.65 89.65 1 1.00e+01 1.00e-02 9.54e+01 dihedral pdb=" CB CYS W 601 " pdb=" SG CYS W 601 " pdb=" SG CYS W 608 " pdb=" CB CYS W 608 " ideal model delta sinusoidal sigma weight residual 93.00 178.91 -85.91 1 1.00e+01 1.00e-02 8.92e+01 dihedral pdb=" CB CYS X 601 " pdb=" SG CYS X 601 " pdb=" SG CYS X 608 " pdb=" CB CYS X 608 " ideal model delta sinusoidal sigma weight residual -86.00 -169.03 83.03 1 1.00e+01 1.00e-02 8.43e+01 ... (remaining 10360 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.155: 2697 0.155 - 0.311: 8 0.311 - 0.466: 0 0.466 - 0.621: 1 0.621 - 0.777: 2 Chirality restraints: 2708 Sorted by residual: chirality pdb=" C1 NAG S 401 " pdb=" ND2 ASN S 257 " pdb=" C2 NAG S 401 " pdb=" O5 NAG S 401 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-01 2.50e+01 1.51e+01 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN W 563 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 9.93e+00 chirality pdb=" C1 NAG U 401 " pdb=" ND2 ASN U 257 " pdb=" C2 NAG U 401 " pdb=" O5 NAG U 401 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.41e+00 ... (remaining 2705 not shown) Planarity restraints: 2971 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU V 611 " -0.027 5.00e-02 4.00e+02 4.01e-02 2.58e+00 pdb=" N PRO V 612 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO V 612 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO V 612 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL M 39 " -0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO M 40 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO M 40 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO M 40 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN E 13 " -0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO E 14 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO E 14 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 14 " -0.017 5.00e-02 4.00e+02 ... (remaining 2968 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 284 2.68 - 3.24: 15395 3.24 - 3.79: 24703 3.79 - 4.35: 33856 4.35 - 4.90: 57542 Nonbonded interactions: 131780 Sorted by model distance: nonbonded pdb=" O VAL S 236 " pdb=" OH TYR S 261 " model vdw 2.131 3.040 nonbonded pdb=" OG1 THR O 71 " pdb=" OG1 THR O 75 " model vdw 2.157 3.040 nonbonded pdb=" O HIS U 39 " pdb=" OG1 THR U 42 " model vdw 2.237 3.040 nonbonded pdb=" OD1 ASP N 1 " pdb=" OH TYR N 97 " model vdw 2.242 3.040 nonbonded pdb=" OG SER C 30 " pdb=" OE2 GLU T 287 " model vdw 2.258 3.040 ... (remaining 131775 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = (chain 'M' and (resid 1 through 39 or resid 44 through 120)) selection = chain 'O' } ncs_group { reference = (chain 'N' and (resid 1 through 15 or resid 19 through 55 or resid 61 through 75 \ or resid 82 through 109)) selection = chain 'P' } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.230 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: 0.500 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.630 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 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 : 0.003 0.051 17306 Z= 0.138 Angle : 0.562 14.340 23634 Z= 0.276 Chirality : 0.048 0.777 2708 Planarity : 0.003 0.040 2962 Dihedral : 13.074 110.355 6400 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.18), residues: 2110 helix: 2.98 (0.38), residues: 165 sheet: 0.33 (0.22), residues: 641 loop : -0.78 (0.16), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 70 TYR 0.018 0.001 TYR S 261 PHE 0.009 0.001 PHE W 592 TRP 0.011 0.001 TRP M 52 HIS 0.002 0.001 HIS S 139 Details of bonding type rmsd covalent geometry : bond 0.00274 (17257) covalent geometry : angle 0.53341 (23512) SS BOND : bond 0.00257 ( 25) SS BOND : angle 0.47671 ( 50) hydrogen bonds : bond 0.16189 ( 527) hydrogen bonds : angle 6.60201 ( 1506) link_ALPHA1-3 : bond 0.00731 ( 3) link_ALPHA1-3 : angle 2.92646 ( 9) link_ALPHA1-6 : bond 0.00399 ( 3) link_ALPHA1-6 : angle 1.71711 ( 9) link_BETA1-4 : bond 0.00585 ( 9) link_BETA1-4 : angle 1.68571 ( 27) link_NAG-ASN : bond 0.00130 ( 9) link_NAG-ASN : angle 4.68515 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 646 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 VAL cc_start: 0.7487 (t) cc_final: 0.7285 (m) REVERT: N 19 VAL cc_start: 0.6467 (t) cc_final: 0.5987 (m) REVERT: N 78 LEU cc_start: 0.7617 (tt) cc_final: 0.6999 (tt) REVERT: O 18 THR cc_start: 0.8872 (m) cc_final: 0.8647 (m) REVERT: O 107 ASP cc_start: 0.7075 (m-30) cc_final: 0.6785 (m-30) REVERT: P 39 LYS cc_start: 0.8130 (mttm) cc_final: 0.7479 (mmtm) REVERT: P 75 ILE cc_start: 0.6736 (mt) cc_final: 0.6013 (mt) REVERT: S 239 LEU cc_start: 0.8374 (mt) cc_final: 0.8119 (mm) REVERT: V 552 ASP cc_start: 0.6418 (t0) cc_final: 0.5983 (t0) REVERT: C 52 VAL cc_start: 0.7575 (p) cc_final: 0.7235 (p) REVERT: C 61 THR cc_start: 0.7600 (p) cc_final: 0.7335 (m) REVERT: C 71 PHE cc_start: 0.5751 (m-80) cc_final: 0.4781 (m-10) REVERT: E 18 LEU cc_start: 0.8205 (tp) cc_final: 0.7816 (tm) REVERT: D 59 PRO cc_start: 0.8179 (Cg_exo) cc_final: 0.7975 (Cg_endo) REVERT: F 62 PHE cc_start: 0.7587 (m-80) cc_final: 0.6986 (m-80) REVERT: W 591 ASP cc_start: 0.8026 (t0) cc_final: 0.7621 (m-30) REVERT: W 612 PRO cc_start: 0.8301 (Cg_exo) cc_final: 0.7895 (Cg_endo) REVERT: X 545 GLU cc_start: 0.6121 (tm-30) cc_final: 0.5780 (tp30) REVERT: T 50 LYS cc_start: 0.7807 (tptt) cc_final: 0.7556 (tmtt) REVERT: T 187 PRO cc_start: 0.7507 (Cg_exo) cc_final: 0.7183 (Cg_endo) REVERT: T 214 TYR cc_start: 0.7813 (m-10) cc_final: 0.7410 (m-10) REVERT: T 229 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7400 (pp20) REVERT: T 233 LEU cc_start: 0.7790 (mt) cc_final: 0.7512 (mm) REVERT: T 261 TYR cc_start: 0.7226 (m-80) cc_final: 0.5183 (m-10) REVERT: U 187 PRO cc_start: 0.5916 (Cg_exo) cc_final: 0.5661 (Cg_endo) REVERT: U 237 ASP cc_start: 0.6945 (t0) cc_final: 0.6720 (t0) outliers start: 0 outliers final: 5 residues processed: 646 average time/residue: 0.5665 time to fit residues: 410.3357 Evaluate side-chains 340 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 335 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 129 ILE Chi-restraints excluded: chain X residue 547 LEU Chi-restraints excluded: chain T residue 63 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN N 32 ASN N 42 GLN O 1 GLN ** P 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 89 GLN S 40 ASN S 44 GLN ** S 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN F 89 GLN W 508 GLN W 549 HIS X 516 HIS X 521 GLN X 551 GLN X 613 HIS T 62 GLN U 107 ASN U 255 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.087507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.061697 restraints weight = 42826.520| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.46 r_work: 0.2825 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.5470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 17306 Z= 0.254 Angle : 0.899 13.926 23634 Z= 0.456 Chirality : 0.053 0.289 2708 Planarity : 0.007 0.140 2962 Dihedral : 7.540 58.158 2828 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.55 % Favored : 95.40 % Rotamer: Outliers : 5.78 % Allowed : 15.37 % Favored : 78.86 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.17), residues: 2110 helix: 2.19 (0.37), residues: 165 sheet: 0.17 (0.21), residues: 646 loop : -0.91 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG T 247 TYR 0.032 0.003 TYR N 97 PHE 0.023 0.003 PHE C 27 TRP 0.051 0.003 TRP E 66 HIS 0.013 0.002 HIS V 549 Details of bonding type rmsd covalent geometry : bond 0.00570 (17257) covalent geometry : angle 0.87955 (23512) SS BOND : bond 0.00919 ( 25) SS BOND : angle 1.44094 ( 50) hydrogen bonds : bond 0.04522 ( 527) hydrogen bonds : angle 5.25201 ( 1506) link_ALPHA1-3 : bond 0.01522 ( 3) link_ALPHA1-3 : angle 4.15422 ( 9) link_ALPHA1-6 : bond 0.01098 ( 3) link_ALPHA1-6 : angle 1.91071 ( 9) link_BETA1-4 : bond 0.00693 ( 9) link_BETA1-4 : angle 2.64358 ( 27) link_NAG-ASN : bond 0.00576 ( 9) link_NAG-ASN : angle 4.05557 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 376 time to evaluate : 0.626 Fit side-chains REVERT: A 6 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7930 (pm20) REVERT: A 18 LEU cc_start: 0.7784 (tp) cc_final: 0.7313 (tp) REVERT: A 47 GLU cc_start: 0.8004 (tt0) cc_final: 0.7649 (tt0) REVERT: B 22 LYS cc_start: 0.8931 (tttt) cc_final: 0.8685 (tptm) REVERT: B 24 GLN cc_start: 0.8522 (tp40) cc_final: 0.7964 (tm-30) REVERT: B 109 VAL cc_start: 0.7965 (t) cc_final: 0.7699 (m) REVERT: M 79 LYS cc_start: 0.8336 (ttmm) cc_final: 0.8133 (mtpp) REVERT: N 73 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8134 (tp) REVERT: N 78 LEU cc_start: 0.8317 (tt) cc_final: 0.8076 (tt) REVERT: N 79 GLU cc_start: 0.6829 (mp0) cc_final: 0.6460 (mp0) REVERT: O 58 TYR cc_start: 0.6324 (m-80) cc_final: 0.6094 (m-80) REVERT: O 79 LYS cc_start: 0.8674 (tmtm) cc_final: 0.8452 (tptt) REVERT: P 2 VAL cc_start: 0.8229 (m) cc_final: 0.7991 (t) REVERT: P 24 GLN cc_start: 0.6079 (tm-30) cc_final: 0.5676 (tm-30) REVERT: P 91 THR cc_start: 0.7559 (p) cc_final: 0.7033 (p) REVERT: S 56 LYS cc_start: 0.8692 (mtpp) cc_final: 0.8036 (mmtp) REVERT: S 227 THR cc_start: 0.8185 (OUTLIER) cc_final: 0.7949 (m) REVERT: S 261 TYR cc_start: 0.8819 (m-80) cc_final: 0.8595 (m-80) REVERT: S 282 ASP cc_start: 0.6601 (p0) cc_final: 0.6299 (p0) REVERT: V 552 ASP cc_start: 0.7102 (t0) cc_final: 0.6281 (t0) REVERT: C 56 ARG cc_start: 0.8064 (ptp-110) cc_final: 0.7610 (ptp-170) REVERT: E 68 LYS cc_start: 0.9024 (mmmm) cc_final: 0.8796 (tppp) REVERT: D 59 PRO cc_start: 0.8551 (Cg_exo) cc_final: 0.8141 (Cg_endo) REVERT: D 63 LYS cc_start: 0.7348 (tppp) cc_final: 0.7122 (tppp) REVERT: F 45 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7555 (tmmm) REVERT: F 54 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8988 (mm) REVERT: F 61 ARG cc_start: 0.7985 (mtm110) cc_final: 0.7722 (mtm110) REVERT: W 591 ASP cc_start: 0.8346 (t0) cc_final: 0.7963 (m-30) REVERT: X 550 ASN cc_start: 0.7545 (m110) cc_final: 0.7234 (m-40) REVERT: X 611 GLU cc_start: 0.5463 (pm20) cc_final: 0.5262 (pm20) REVERT: T 38 ILE cc_start: 0.6905 (OUTLIER) cc_final: 0.6464 (pp) REVERT: T 214 TYR cc_start: 0.7954 (m-10) cc_final: 0.7610 (m-10) REVERT: T 227 THR cc_start: 0.8210 (p) cc_final: 0.7335 (p) REVERT: T 229 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7767 (pp20) REVERT: T 231 GLU cc_start: 0.8276 (tt0) cc_final: 0.7977 (tt0) REVERT: T 276 LYS cc_start: 0.6526 (mtmm) cc_final: 0.6281 (mttp) REVERT: U 47 ASP cc_start: 0.7335 (t0) cc_final: 0.6891 (t0) REVERT: U 49 ASP cc_start: 0.7047 (p0) cc_final: 0.6719 (p0) REVERT: U 56 LYS cc_start: 0.7853 (tttm) cc_final: 0.7564 (ttmt) outliers start: 103 outliers final: 29 residues processed: 436 average time/residue: 0.5519 time to fit residues: 270.7331 Evaluate side-chains 302 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 267 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain O residue 80 ILE Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain P residue 82 ASP Chi-restraints excluded: chain P residue 95 SER Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 221 GLN Chi-restraints excluded: chain S residue 227 THR Chi-restraints excluded: chain V residue 540 GLU Chi-restraints excluded: chain V residue 577 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain W residue 504 ILE Chi-restraints excluded: chain W residue 545 GLU Chi-restraints excluded: chain W residue 609 CYS Chi-restraints excluded: chain T residue 38 ILE Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain T residue 167 SER Chi-restraints excluded: chain T residue 235 GLU Chi-restraints excluded: chain T residue 239 LEU Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 107 ASN Chi-restraints excluded: chain U residue 144 THR Chi-restraints excluded: chain U residue 242 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 28 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 165 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 186 optimal weight: 8.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 89 GLN O 30 ASN O 38 GLN P 24 GLN P 27 GLN P 38 GLN V 549 HIS V 613 HIS F 6 GLN F 37 GLN U 39 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.084707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.058350 restraints weight = 42765.895| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 3.40 r_work: 0.2771 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.7524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 17306 Z= 0.200 Angle : 0.717 11.371 23634 Z= 0.362 Chirality : 0.049 0.411 2708 Planarity : 0.005 0.043 2962 Dihedral : 6.898 55.018 2820 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 5.44 % Allowed : 19.46 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.18), residues: 2110 helix: 2.46 (0.37), residues: 165 sheet: 0.03 (0.20), residues: 678 loop : -0.80 (0.16), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 39 TYR 0.019 0.002 TYR U 261 PHE 0.020 0.002 PHE A 71 TRP 0.041 0.002 TRP A 66 HIS 0.008 0.001 HIS V 613 Details of bonding type rmsd covalent geometry : bond 0.00462 (17257) covalent geometry : angle 0.70030 (23512) SS BOND : bond 0.00986 ( 25) SS BOND : angle 2.03378 ( 50) hydrogen bonds : bond 0.04273 ( 527) hydrogen bonds : angle 4.85299 ( 1506) link_ALPHA1-3 : bond 0.00645 ( 3) link_ALPHA1-3 : angle 3.22419 ( 9) link_ALPHA1-6 : bond 0.00502 ( 3) link_ALPHA1-6 : angle 1.78257 ( 9) link_BETA1-4 : bond 0.00903 ( 9) link_BETA1-4 : angle 2.30008 ( 27) link_NAG-ASN : bond 0.00905 ( 9) link_NAG-ASN : angle 2.35605 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 285 time to evaluate : 0.696 Fit side-chains REVERT: A 6 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8060 (mp0) REVERT: B 22 LYS cc_start: 0.9178 (tttt) cc_final: 0.8976 (mtpt) REVERT: B 24 GLN cc_start: 0.8607 (tp40) cc_final: 0.8028 (tm-30) REVERT: B 29 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8494 (pp) REVERT: B 63 LYS cc_start: 0.8129 (tppp) cc_final: 0.7799 (ttmm) REVERT: B 109 VAL cc_start: 0.8331 (t) cc_final: 0.8038 (m) REVERT: M 4 GLU cc_start: 0.7776 (tp30) cc_final: 0.7554 (tp30) REVERT: M 87 ASP cc_start: 0.8333 (m-30) cc_final: 0.7942 (m-30) REVERT: N 61 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7716 (ttm110) REVERT: N 73 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8498 (tp) REVERT: N 77 ASP cc_start: 0.8921 (m-30) cc_final: 0.8154 (m-30) REVERT: N 78 LEU cc_start: 0.8360 (tt) cc_final: 0.8119 (tt) REVERT: N 79 GLU cc_start: 0.6805 (mp0) cc_final: 0.6260 (mp0) REVERT: O 70 LYS cc_start: 0.7563 (ptmt) cc_final: 0.7299 (ptmm) REVERT: P 22 LYS cc_start: 0.5709 (ptmm) cc_final: 0.5487 (pptt) REVERT: S 214 TYR cc_start: 0.7998 (OUTLIER) cc_final: 0.7750 (p90) REVERT: S 221 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8653 (tm-30) REVERT: S 260 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7899 (mp) REVERT: S 261 TYR cc_start: 0.8961 (m-80) cc_final: 0.8689 (m-80) REVERT: V 521 GLN cc_start: 0.8220 (pp30) cc_final: 0.7923 (pp30) REVERT: V 552 ASP cc_start: 0.7678 (t0) cc_final: 0.7047 (OUTLIER) REVERT: V 591 ASP cc_start: 0.8869 (t0) cc_final: 0.8529 (m-30) REVERT: V 613 HIS cc_start: 0.5514 (OUTLIER) cc_final: 0.5297 (t-170) REVERT: C 56 ARG cc_start: 0.8026 (ptp-110) cc_final: 0.7558 (ptp-170) REVERT: E 66 TRP cc_start: 0.8059 (p-90) cc_final: 0.7704 (p-90) REVERT: E 68 LYS cc_start: 0.9012 (mmmm) cc_final: 0.8787 (tppp) REVERT: D 59 PRO cc_start: 0.8844 (Cg_exo) cc_final: 0.8567 (Cg_endo) REVERT: D 63 LYS cc_start: 0.8003 (tppp) cc_final: 0.7752 (ttpp) REVERT: D 107 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8321 (pm20) REVERT: F 24 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8076 (tm-30) REVERT: F 54 LEU cc_start: 0.9338 (mm) cc_final: 0.9073 (mm) REVERT: F 61 ARG cc_start: 0.7885 (mtm110) cc_final: 0.7625 (mtm110) REVERT: F 77 ASP cc_start: 0.8414 (p0) cc_final: 0.7171 (p0) REVERT: F 79 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8170 (mm-30) REVERT: X 545 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7814 (tm-30) REVERT: T 214 TYR cc_start: 0.7822 (m-10) cc_final: 0.7403 (m-80) REVERT: T 229 GLU cc_start: 0.8405 (mt-10) cc_final: 0.7840 (pp20) REVERT: T 237 ASP cc_start: 0.8001 (m-30) cc_final: 0.7704 (m-30) REVERT: U 47 ASP cc_start: 0.7529 (t0) cc_final: 0.7260 (t0) REVERT: U 107 ASN cc_start: 0.8640 (OUTLIER) cc_final: 0.8319 (m-40) outliers start: 97 outliers final: 32 residues processed: 355 average time/residue: 0.5402 time to fit residues: 216.9393 Evaluate side-chains 284 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 243 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 61 ARG Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain O residue 80 ILE Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain P residue 82 ASP Chi-restraints excluded: chain S residue 214 TYR Chi-restraints excluded: chain S residue 221 GLN Chi-restraints excluded: chain S residue 260 ILE Chi-restraints excluded: chain S residue 277 VAL Chi-restraints excluded: chain V residue 613 HIS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain X residue 545 GLU Chi-restraints excluded: chain T residue 38 ILE Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 239 LEU Chi-restraints excluded: chain T residue 277 VAL Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 83 THR Chi-restraints excluded: chain U residue 107 ASN Chi-restraints excluded: chain U residue 144 THR Chi-restraints excluded: chain U residue 172 ARG Chi-restraints excluded: chain U residue 223 THR Chi-restraints excluded: chain U residue 242 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 202 optimal weight: 0.0870 chunk 147 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 205 optimal weight: 0.1980 chunk 38 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 186 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.6564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN B 42 GLN P 38 GLN P 89 GLN S 188 GLN ** S 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 549 HIS E 13 GLN F 37 GLN X 508 GLN X 516 HIS T 221 GLN U 39 HIS U 107 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.082747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.056163 restraints weight = 42648.746| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.39 r_work: 0.2759 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.8735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 17306 Z= 0.190 Angle : 0.714 15.978 23634 Z= 0.356 Chirality : 0.048 0.386 2708 Planarity : 0.005 0.095 2962 Dihedral : 6.290 57.709 2818 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 5.16 % Allowed : 21.09 % Favored : 73.75 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.17), residues: 2110 helix: 2.60 (0.37), residues: 165 sheet: 0.01 (0.20), residues: 670 loop : -0.82 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 39 TYR 0.017 0.001 TYR D 87 PHE 0.021 0.002 PHE N 71 TRP 0.032 0.002 TRP O 35 HIS 0.034 0.002 HIS V 613 Details of bonding type rmsd covalent geometry : bond 0.00448 (17257) covalent geometry : angle 0.70222 (23512) SS BOND : bond 0.00351 ( 25) SS BOND : angle 1.08683 ( 50) hydrogen bonds : bond 0.03568 ( 527) hydrogen bonds : angle 4.73574 ( 1506) link_ALPHA1-3 : bond 0.00638 ( 3) link_ALPHA1-3 : angle 3.81603 ( 9) link_ALPHA1-6 : bond 0.00418 ( 3) link_ALPHA1-6 : angle 1.58941 ( 9) link_BETA1-4 : bond 0.00503 ( 9) link_BETA1-4 : angle 2.49907 ( 27) link_NAG-ASN : bond 0.00427 ( 9) link_NAG-ASN : angle 1.49640 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 278 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: A 6 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8407 (pm20) REVERT: B 24 GLN cc_start: 0.8778 (tp40) cc_final: 0.8306 (tm-30) REVERT: B 42 GLN cc_start: 0.8530 (mm-40) cc_final: 0.8271 (mp10) REVERT: B 63 LYS cc_start: 0.8467 (tppp) cc_final: 0.8163 (ttmm) REVERT: M 45 GLU cc_start: 0.8498 (mp0) cc_final: 0.8232 (mp0) REVERT: M 70 LYS cc_start: 0.8780 (ttmt) cc_final: 0.8568 (tttm) REVERT: M 87 ASP cc_start: 0.8391 (m-30) cc_final: 0.8002 (m-30) REVERT: N 61 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.8017 (ttm110) REVERT: N 77 ASP cc_start: 0.9075 (m-30) cc_final: 0.8721 (m-30) REVERT: N 79 GLU cc_start: 0.7295 (mp0) cc_final: 0.6907 (mp0) REVERT: O 17 LEU cc_start: 0.7435 (mt) cc_final: 0.7060 (mp) REVERT: S 56 LYS cc_start: 0.8824 (mtpp) cc_final: 0.8347 (mmmm) REVERT: S 69 ASN cc_start: 0.8819 (OUTLIER) cc_final: 0.8473 (m-40) REVERT: S 261 TYR cc_start: 0.9044 (m-80) cc_final: 0.8788 (m-80) REVERT: S 282 ASP cc_start: 0.6975 (p0) cc_final: 0.6702 (p0) REVERT: V 521 GLN cc_start: 0.8395 (pp30) cc_final: 0.8083 (pp30) REVERT: V 552 ASP cc_start: 0.8037 (t0) cc_final: 0.7465 (t0) REVERT: V 591 ASP cc_start: 0.9015 (t0) cc_final: 0.8741 (m-30) REVERT: C 47 GLU cc_start: 0.8215 (tp30) cc_final: 0.7931 (tm-30) REVERT: C 56 ARG cc_start: 0.8012 (ptp-110) cc_final: 0.7695 (ptp-170) REVERT: E 47 GLU cc_start: 0.8122 (tp30) cc_final: 0.7764 (tm-30) REVERT: E 68 LYS cc_start: 0.8958 (mmmm) cc_final: 0.8665 (tppp) REVERT: D 59 PRO cc_start: 0.9049 (Cg_exo) cc_final: 0.8802 (Cg_endo) REVERT: D 107 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8354 (pm20) REVERT: F 22 LYS cc_start: 0.8780 (ttmm) cc_final: 0.8569 (mtpp) REVERT: F 24 GLN cc_start: 0.8567 (tm-30) cc_final: 0.8155 (tm-30) REVERT: F 45 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7425 (tmmm) REVERT: F 54 LEU cc_start: 0.9450 (mm) cc_final: 0.9231 (mm) REVERT: F 77 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8155 (p0) REVERT: X 595 GLN cc_start: 0.8448 (tp40) cc_final: 0.8003 (tt0) REVERT: T 44 GLN cc_start: 0.6727 (mp10) cc_final: 0.6497 (mp10) REVERT: T 136 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8297 (mmm160) REVERT: T 214 TYR cc_start: 0.7865 (m-10) cc_final: 0.7599 (m-80) REVERT: T 229 GLU cc_start: 0.8472 (mt-10) cc_final: 0.7855 (pp20) REVERT: T 237 ASP cc_start: 0.8174 (m-30) cc_final: 0.7697 (m-30) REVERT: U 47 ASP cc_start: 0.7761 (t0) cc_final: 0.7067 (t0) REVERT: U 49 ASP cc_start: 0.7492 (p0) cc_final: 0.6965 (p0) REVERT: U 50 LYS cc_start: 0.8171 (mmmm) cc_final: 0.7368 (mmpt) REVERT: U 57 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8688 (tt) outliers start: 92 outliers final: 38 residues processed: 339 average time/residue: 0.5219 time to fit residues: 200.1479 Evaluate side-chains 289 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 244 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 61 ARG Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 80 ILE Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain P residue 22 LYS Chi-restraints excluded: chain P residue 38 GLN Chi-restraints excluded: chain S residue 69 ASN Chi-restraints excluded: chain V residue 558 LEU Chi-restraints excluded: chain V residue 594 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain W residue 504 ILE Chi-restraints excluded: chain X residue 514 ASN Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 110 ASN Chi-restraints excluded: chain T residue 136 ARG Chi-restraints excluded: chain T residue 223 THR Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 53 CYS Chi-restraints excluded: chain U residue 57 LEU Chi-restraints excluded: chain U residue 144 THR Chi-restraints excluded: chain U residue 172 ARG Chi-restraints excluded: chain U residue 229 GLU Chi-restraints excluded: chain U residue 242 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 12 optimal weight: 9.9990 chunk 112 optimal weight: 7.9990 chunk 129 optimal weight: 7.9990 chunk 117 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 70 optimal weight: 0.4980 chunk 157 optimal weight: 1.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN N 42 GLN P 27 GLN P 100 ASN S 188 GLN V 549 HIS C 32 ASN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 39 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.080850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.053586 restraints weight = 42805.320| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 3.49 r_work: 0.2710 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.9671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17306 Z= 0.212 Angle : 0.689 10.746 23634 Z= 0.344 Chirality : 0.047 0.276 2708 Planarity : 0.004 0.043 2962 Dihedral : 6.156 56.002 2818 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.16 % Allowed : 22.99 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.18), residues: 2110 helix: 2.57 (0.38), residues: 165 sheet: 0.01 (0.20), residues: 680 loop : -0.81 (0.16), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 65 TYR 0.026 0.002 TYR P 87 PHE 0.017 0.002 PHE A 71 TRP 0.029 0.002 TRP E 66 HIS 0.006 0.001 HIS V 613 Details of bonding type rmsd covalent geometry : bond 0.00511 (17257) covalent geometry : angle 0.67559 (23512) SS BOND : bond 0.00499 ( 25) SS BOND : angle 1.62081 ( 50) hydrogen bonds : bond 0.03815 ( 527) hydrogen bonds : angle 4.74565 ( 1506) link_ALPHA1-3 : bond 0.00871 ( 3) link_ALPHA1-3 : angle 3.34204 ( 9) link_ALPHA1-6 : bond 0.00255 ( 3) link_ALPHA1-6 : angle 1.91992 ( 9) link_BETA1-4 : bond 0.00681 ( 9) link_BETA1-4 : angle 2.42939 ( 27) link_NAG-ASN : bond 0.00467 ( 9) link_NAG-ASN : angle 1.58858 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 262 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8647 (pm20) cc_final: 0.8076 (pm20) REVERT: B 24 GLN cc_start: 0.8797 (tp40) cc_final: 0.8361 (tm-30) REVERT: B 42 GLN cc_start: 0.8587 (mm-40) cc_final: 0.8364 (mp10) REVERT: B 63 LYS cc_start: 0.8591 (tppp) cc_final: 0.8359 (ttmm) REVERT: M 4 GLU cc_start: 0.8115 (tp30) cc_final: 0.7880 (tm-30) REVERT: M 5 GLU cc_start: 0.8583 (pm20) cc_final: 0.8075 (pm20) REVERT: M 87 ASP cc_start: 0.8487 (m-30) cc_final: 0.8080 (m-30) REVERT: N 22 LYS cc_start: 0.9262 (mtpp) cc_final: 0.9040 (mmmm) REVERT: N 61 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7857 (ttp80) REVERT: N 77 ASP cc_start: 0.9295 (m-30) cc_final: 0.8209 (m-30) REVERT: N 79 GLU cc_start: 0.7532 (mp0) cc_final: 0.6338 (mp0) REVERT: O 33 MET cc_start: 0.9014 (tpp) cc_final: 0.8667 (tpt) REVERT: O 70 LYS cc_start: 0.7677 (ptmt) cc_final: 0.7437 (ptmm) REVERT: O 71 THR cc_start: 0.5427 (OUTLIER) cc_final: 0.5200 (p) REVERT: P 27 GLN cc_start: 0.6923 (mp10) cc_final: 0.6665 (mp10) REVERT: P 28 SER cc_start: 0.8758 (p) cc_final: 0.8454 (t) REVERT: P 38 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.7178 (OUTLIER) REVERT: S 56 LYS cc_start: 0.8849 (mtpp) cc_final: 0.8301 (mmmm) REVERT: S 69 ASN cc_start: 0.8901 (OUTLIER) cc_final: 0.8484 (m-40) REVERT: S 282 ASP cc_start: 0.7201 (p0) cc_final: 0.6926 (p0) REVERT: V 521 GLN cc_start: 0.8492 (pp30) cc_final: 0.8159 (pp30) REVERT: V 552 ASP cc_start: 0.8217 (t0) cc_final: 0.7691 (t0) REVERT: V 591 ASP cc_start: 0.9021 (t0) cc_final: 0.8799 (m-30) REVERT: C 47 GLU cc_start: 0.8276 (tp30) cc_final: 0.8023 (tt0) REVERT: C 56 ARG cc_start: 0.8043 (ptp-110) cc_final: 0.7578 (ptp-170) REVERT: E 47 GLU cc_start: 0.8177 (tp30) cc_final: 0.7828 (tm-30) REVERT: E 74 SER cc_start: 0.8245 (OUTLIER) cc_final: 0.8026 (p) REVERT: D 59 PRO cc_start: 0.9149 (Cg_exo) cc_final: 0.8906 (Cg_endo) REVERT: D 107 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8303 (pm20) REVERT: F 24 GLN cc_start: 0.8580 (tm-30) cc_final: 0.8091 (tm-30) REVERT: F 45 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7843 (tmmm) REVERT: X 595 GLN cc_start: 0.8684 (tp40) cc_final: 0.8338 (tt0) REVERT: X 604 LEU cc_start: 0.7359 (mm) cc_final: 0.7056 (tm) REVERT: T 136 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8430 (mmm160) REVERT: T 237 ASP cc_start: 0.8147 (m-30) cc_final: 0.7724 (m-30) REVERT: U 47 ASP cc_start: 0.7847 (t0) cc_final: 0.7489 (t0) REVERT: U 229 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7628 (mp0) outliers start: 92 outliers final: 42 residues processed: 324 average time/residue: 0.5526 time to fit residues: 202.2270 Evaluate side-chains 284 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 235 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 61 ARG Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain O residue 22 ILE Chi-restraints excluded: chain O residue 71 THR Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 80 ILE Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain P residue 22 LYS Chi-restraints excluded: chain P residue 38 GLN Chi-restraints excluded: chain S residue 69 ASN Chi-restraints excluded: chain S residue 150 ASP Chi-restraints excluded: chain S residue 240 THR Chi-restraints excluded: chain S residue 277 VAL Chi-restraints excluded: chain V residue 545 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain X residue 505 VAL Chi-restraints excluded: chain X residue 514 ASN Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 136 ARG Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain T residue 277 VAL Chi-restraints excluded: chain T residue 285 ILE Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 83 THR Chi-restraints excluded: chain U residue 144 THR Chi-restraints excluded: chain U residue 223 THR Chi-restraints excluded: chain U residue 229 GLU Chi-restraints excluded: chain U residue 242 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 168 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 176 optimal weight: 0.6980 chunk 188 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN N 42 GLN P 38 GLN P 100 ASN V 549 HIS W 516 HIS T 44 GLN U 39 HIS U 40 ASN U 107 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.082217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.055063 restraints weight = 42595.319| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 3.48 r_work: 0.2746 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.9850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17306 Z= 0.119 Angle : 0.634 10.460 23634 Z= 0.314 Chirality : 0.045 0.252 2708 Planarity : 0.004 0.043 2962 Dihedral : 5.804 56.359 2818 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.76 % Allowed : 24.85 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.18), residues: 2110 helix: 2.92 (0.38), residues: 165 sheet: 0.16 (0.21), residues: 671 loop : -0.72 (0.16), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 56 TYR 0.016 0.001 TYR F 87 PHE 0.016 0.001 PHE A 71 TRP 0.033 0.001 TRP O 61 HIS 0.003 0.001 HIS X 549 Details of bonding type rmsd covalent geometry : bond 0.00284 (17257) covalent geometry : angle 0.62344 (23512) SS BOND : bond 0.00260 ( 25) SS BOND : angle 1.28660 ( 50) hydrogen bonds : bond 0.03111 ( 527) hydrogen bonds : angle 4.49238 ( 1506) link_ALPHA1-3 : bond 0.00678 ( 3) link_ALPHA1-3 : angle 3.22213 ( 9) link_ALPHA1-6 : bond 0.00294 ( 3) link_ALPHA1-6 : angle 1.66105 ( 9) link_BETA1-4 : bond 0.00554 ( 9) link_BETA1-4 : angle 2.12996 ( 27) link_NAG-ASN : bond 0.00419 ( 9) link_NAG-ASN : angle 1.39290 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 247 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8605 (pm20) cc_final: 0.8037 (pm20) REVERT: B 24 GLN cc_start: 0.8734 (tp40) cc_final: 0.8351 (tm-30) REVERT: B 37 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8287 (tt0) REVERT: B 63 LYS cc_start: 0.8611 (tppp) cc_final: 0.8410 (ttmm) REVERT: M 4 GLU cc_start: 0.8080 (tp30) cc_final: 0.7851 (tm-30) REVERT: M 5 GLU cc_start: 0.8567 (pm20) cc_final: 0.8217 (pm20) REVERT: M 45 GLU cc_start: 0.8407 (mp0) cc_final: 0.8203 (mp0) REVERT: M 87 ASP cc_start: 0.8413 (m-30) cc_final: 0.8038 (m-30) REVERT: M 107 ASP cc_start: 0.9091 (m-30) cc_final: 0.8869 (m-30) REVERT: N 61 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7913 (ttp80) REVERT: N 77 ASP cc_start: 0.9279 (m-30) cc_final: 0.8321 (m-30) REVERT: N 78 LEU cc_start: 0.8658 (tt) cc_final: 0.8328 (tt) REVERT: N 79 GLU cc_start: 0.7501 (mp0) cc_final: 0.6410 (mp0) REVERT: O 33 MET cc_start: 0.9053 (tpp) cc_final: 0.8746 (tpt) REVERT: O 65 ARG cc_start: 0.8496 (mmp80) cc_final: 0.7331 (mtm-85) REVERT: P 22 LYS cc_start: 0.6035 (OUTLIER) cc_final: 0.5687 (pptt) REVERT: P 24 GLN cc_start: 0.7618 (pp30) cc_final: 0.7281 (pp30) REVERT: P 27 GLN cc_start: 0.6990 (mp10) cc_final: 0.6730 (mp10) REVERT: P 28 SER cc_start: 0.8799 (p) cc_final: 0.8526 (t) REVERT: P 37 GLN cc_start: 0.7850 (tt0) cc_final: 0.7648 (tm-30) REVERT: S 56 LYS cc_start: 0.8845 (mtpp) cc_final: 0.8336 (mmmm) REVERT: S 282 ASP cc_start: 0.7159 (p0) cc_final: 0.6884 (p0) REVERT: V 544 THR cc_start: 0.9426 (OUTLIER) cc_final: 0.9171 (p) REVERT: V 552 ASP cc_start: 0.8276 (t0) cc_final: 0.7765 (t0) REVERT: C 56 ARG cc_start: 0.8064 (ptp-110) cc_final: 0.7800 (ptp-170) REVERT: E 47 GLU cc_start: 0.8110 (tp30) cc_final: 0.7824 (tm-30) REVERT: D 59 PRO cc_start: 0.9162 (Cg_exo) cc_final: 0.8936 (Cg_endo) REVERT: D 107 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8241 (pm20) REVERT: F 77 ASP cc_start: 0.8563 (p0) cc_final: 0.7582 (p0) REVERT: F 79 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8314 (mm-30) REVERT: W 540 GLU cc_start: 0.8704 (pp20) cc_final: 0.8415 (pp20) REVERT: W 552 ASP cc_start: 0.8385 (m-30) cc_final: 0.7498 (t0) REVERT: W 591 ASP cc_start: 0.8738 (t0) cc_final: 0.8482 (m-30) REVERT: X 604 LEU cc_start: 0.7570 (mm) cc_final: 0.7230 (tm) REVERT: T 44 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7386 (mp10) REVERT: T 136 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8453 (mmm160) REVERT: U 47 ASP cc_start: 0.7847 (t0) cc_final: 0.7508 (t0) REVERT: U 229 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7619 (mp0) outliers start: 67 outliers final: 33 residues processed: 293 average time/residue: 0.5716 time to fit residues: 186.7325 Evaluate side-chains 267 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 227 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 61 ARG Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain O residue 22 ILE Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 80 ILE Chi-restraints excluded: chain O residue 96 VAL Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain P residue 22 LYS Chi-restraints excluded: chain S residue 150 ASP Chi-restraints excluded: chain S residue 240 THR Chi-restraints excluded: chain S residue 277 VAL Chi-restraints excluded: chain V residue 544 THR Chi-restraints excluded: chain V residue 545 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain X residue 505 VAL Chi-restraints excluded: chain T residue 44 GLN Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 136 ARG Chi-restraints excluded: chain T residue 277 VAL Chi-restraints excluded: chain T residue 285 ILE Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 107 ASN Chi-restraints excluded: chain U residue 229 GLU Chi-restraints excluded: chain U residue 242 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 157 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN O 38 GLN V 549 HIS V 602 HIS E 13 GLN E 32 ASN F 24 GLN U 39 HIS U 107 ASN U 188 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.080237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.052850 restraints weight = 42787.937| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 3.48 r_work: 0.2694 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 1.0222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17306 Z= 0.215 Angle : 0.688 10.833 23634 Z= 0.341 Chirality : 0.046 0.260 2708 Planarity : 0.004 0.039 2962 Dihedral : 5.807 57.114 2818 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.53 % Allowed : 25.35 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.18), residues: 2110 helix: 2.85 (0.39), residues: 165 sheet: 0.13 (0.21), residues: 673 loop : -0.78 (0.16), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 61 TYR 0.017 0.001 TYR N 49 PHE 0.015 0.002 PHE C 111 TRP 0.033 0.002 TRP O 61 HIS 0.004 0.001 HIS S 139 Details of bonding type rmsd covalent geometry : bond 0.00522 (17257) covalent geometry : angle 0.67614 (23512) SS BOND : bond 0.00394 ( 25) SS BOND : angle 1.44665 ( 50) hydrogen bonds : bond 0.03654 ( 527) hydrogen bonds : angle 4.61261 ( 1506) link_ALPHA1-3 : bond 0.00712 ( 3) link_ALPHA1-3 : angle 3.28520 ( 9) link_ALPHA1-6 : bond 0.00373 ( 3) link_ALPHA1-6 : angle 1.86511 ( 9) link_BETA1-4 : bond 0.00498 ( 9) link_BETA1-4 : angle 2.36561 ( 27) link_NAG-ASN : bond 0.00286 ( 9) link_NAG-ASN : angle 1.49410 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 233 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8696 (pm20) cc_final: 0.8110 (pm20) REVERT: B 24 GLN cc_start: 0.8729 (tp40) cc_final: 0.8406 (tm-30) REVERT: B 79 GLU cc_start: 0.7610 (pm20) cc_final: 0.7174 (mp0) REVERT: M 4 GLU cc_start: 0.8134 (tp30) cc_final: 0.7894 (tm-30) REVERT: M 5 GLU cc_start: 0.8596 (pm20) cc_final: 0.8123 (pm20) REVERT: M 42 LYS cc_start: 0.7919 (mmmm) cc_final: 0.7590 (mmmt) REVERT: M 45 GLU cc_start: 0.8439 (mp0) cc_final: 0.8237 (mp0) REVERT: M 87 ASP cc_start: 0.8547 (m-30) cc_final: 0.8115 (m-30) REVERT: M 107 ASP cc_start: 0.9147 (m-30) cc_final: 0.8926 (m-30) REVERT: N 77 ASP cc_start: 0.9327 (m-30) cc_final: 0.8723 (m-30) REVERT: N 78 LEU cc_start: 0.8676 (tt) cc_final: 0.8356 (tt) REVERT: N 79 GLU cc_start: 0.7492 (mp0) cc_final: 0.6924 (mp0) REVERT: O 33 MET cc_start: 0.9185 (tpp) cc_final: 0.8870 (tpt) REVERT: O 65 ARG cc_start: 0.8639 (mmp80) cc_final: 0.7641 (mpp80) REVERT: P 27 GLN cc_start: 0.7073 (mp10) cc_final: 0.6779 (mp10) REVERT: P 28 SER cc_start: 0.8874 (p) cc_final: 0.8607 (t) REVERT: P 37 GLN cc_start: 0.7858 (tt0) cc_final: 0.7542 (tt0) REVERT: S 69 ASN cc_start: 0.8890 (OUTLIER) cc_final: 0.8510 (m-40) REVERT: S 282 ASP cc_start: 0.7295 (p0) cc_final: 0.7012 (p0) REVERT: V 544 THR cc_start: 0.9415 (OUTLIER) cc_final: 0.9162 (p) REVERT: V 552 ASP cc_start: 0.8326 (t0) cc_final: 0.7822 (t0) REVERT: C 56 ARG cc_start: 0.8055 (ptp-110) cc_final: 0.7580 (ptp-170) REVERT: E 47 GLU cc_start: 0.8159 (tp30) cc_final: 0.7877 (tm-30) REVERT: D 59 PRO cc_start: 0.9247 (Cg_exo) cc_final: 0.9023 (Cg_endo) REVERT: D 107 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8233 (pm20) REVERT: F 77 ASP cc_start: 0.8510 (p0) cc_final: 0.7528 (p0) REVERT: F 79 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8293 (mm-30) REVERT: W 540 GLU cc_start: 0.8776 (pp20) cc_final: 0.8517 (pp20) REVERT: W 552 ASP cc_start: 0.8417 (m-30) cc_final: 0.7379 (t0) REVERT: T 136 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8451 (mmm160) REVERT: U 47 ASP cc_start: 0.7858 (t0) cc_final: 0.7479 (t0) REVERT: U 229 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7570 (mp0) outliers start: 63 outliers final: 38 residues processed: 279 average time/residue: 0.5940 time to fit residues: 185.1889 Evaluate side-chains 263 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 221 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 80 ILE Chi-restraints excluded: chain O residue 96 VAL Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain P residue 22 LYS Chi-restraints excluded: chain S residue 69 ASN Chi-restraints excluded: chain S residue 150 ASP Chi-restraints excluded: chain S residue 240 THR Chi-restraints excluded: chain S residue 277 VAL Chi-restraints excluded: chain V residue 544 THR Chi-restraints excluded: chain V residue 545 GLU Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain E residue 66 TRP Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain X residue 505 VAL Chi-restraints excluded: chain X residue 514 ASN Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 136 ARG Chi-restraints excluded: chain T residue 277 VAL Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 83 THR Chi-restraints excluded: chain U residue 144 THR Chi-restraints excluded: chain U residue 229 GLU Chi-restraints excluded: chain U residue 242 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 85 optimal weight: 7.9990 chunk 180 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 154 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN O 38 GLN V 549 HIS F 24 GLN U 107 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.080637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.053903 restraints weight = 41697.193| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 3.48 r_work: 0.2674 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 1.0486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17306 Z= 0.173 Angle : 0.671 10.270 23634 Z= 0.333 Chirality : 0.046 0.257 2708 Planarity : 0.004 0.039 2962 Dihedral : 5.674 56.556 2818 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.37 % Allowed : 26.02 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.18), residues: 2110 helix: 2.94 (0.38), residues: 165 sheet: 0.21 (0.21), residues: 663 loop : -0.75 (0.16), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 61 TYR 0.017 0.001 TYR F 87 PHE 0.014 0.001 PHE W 592 TRP 0.043 0.002 TRP O 61 HIS 0.004 0.001 HIS V 602 Details of bonding type rmsd covalent geometry : bond 0.00419 (17257) covalent geometry : angle 0.66020 (23512) SS BOND : bond 0.00434 ( 25) SS BOND : angle 1.30061 ( 50) hydrogen bonds : bond 0.03380 ( 527) hydrogen bonds : angle 4.48857 ( 1506) link_ALPHA1-3 : bond 0.00737 ( 3) link_ALPHA1-3 : angle 3.12712 ( 9) link_ALPHA1-6 : bond 0.00318 ( 3) link_ALPHA1-6 : angle 1.73641 ( 9) link_BETA1-4 : bond 0.00507 ( 9) link_BETA1-4 : angle 2.17828 ( 27) link_NAG-ASN : bond 0.00288 ( 9) link_NAG-ASN : angle 1.40599 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 233 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8636 (pm20) cc_final: 0.8038 (pm20) REVERT: B 24 GLN cc_start: 0.8711 (tp40) cc_final: 0.8358 (tm-30) REVERT: B 79 GLU cc_start: 0.7517 (pm20) cc_final: 0.7175 (mp0) REVERT: M 4 GLU cc_start: 0.8133 (tp30) cc_final: 0.7774 (tm-30) REVERT: M 5 GLU cc_start: 0.8504 (pm20) cc_final: 0.8136 (pm20) REVERT: M 45 GLU cc_start: 0.8353 (mp0) cc_final: 0.8097 (mp0) REVERT: M 87 ASP cc_start: 0.8519 (m-30) cc_final: 0.8094 (m-30) REVERT: M 107 ASP cc_start: 0.9163 (m-30) cc_final: 0.8930 (m-30) REVERT: N 61 ARG cc_start: 0.8419 (ttm110) cc_final: 0.7367 (ttp80) REVERT: N 77 ASP cc_start: 0.9394 (m-30) cc_final: 0.8622 (m-30) REVERT: N 78 LEU cc_start: 0.8644 (tt) cc_final: 0.8392 (tt) REVERT: N 79 GLU cc_start: 0.7654 (mp0) cc_final: 0.6715 (mp0) REVERT: O 33 MET cc_start: 0.9185 (tpp) cc_final: 0.8899 (tpt) REVERT: O 65 ARG cc_start: 0.8667 (mmp80) cc_final: 0.7885 (mpp80) REVERT: P 27 GLN cc_start: 0.7125 (mp10) cc_final: 0.6827 (mp10) REVERT: P 28 SER cc_start: 0.8934 (p) cc_final: 0.8667 (t) REVERT: P 37 GLN cc_start: 0.7922 (tt0) cc_final: 0.7593 (tm-30) REVERT: S 56 LYS cc_start: 0.8782 (mtpp) cc_final: 0.8013 (mmmm) REVERT: S 69 ASN cc_start: 0.8857 (OUTLIER) cc_final: 0.8490 (m-40) REVERT: S 260 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.7991 (mp) REVERT: S 282 ASP cc_start: 0.7324 (p0) cc_final: 0.7044 (p0) REVERT: V 544 THR cc_start: 0.9404 (OUTLIER) cc_final: 0.9139 (p) REVERT: V 552 ASP cc_start: 0.8402 (t0) cc_final: 0.7917 (t0) REVERT: V 611 GLU cc_start: 0.7675 (pt0) cc_final: 0.6777 (pm20) REVERT: C 56 ARG cc_start: 0.8091 (ptp-110) cc_final: 0.7604 (ptp-170) REVERT: E 47 GLU cc_start: 0.8086 (tp30) cc_final: 0.7814 (tm-30) REVERT: D 59 PRO cc_start: 0.9250 (Cg_exo) cc_final: 0.9034 (Cg_endo) REVERT: D 107 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8138 (pm20) REVERT: F 77 ASP cc_start: 0.8442 (p0) cc_final: 0.7516 (p0) REVERT: W 540 GLU cc_start: 0.8776 (pp20) cc_final: 0.8459 (pp20) REVERT: W 552 ASP cc_start: 0.8453 (m-30) cc_final: 0.7431 (t0) REVERT: T 136 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8406 (mmm160) REVERT: T 237 ASP cc_start: 0.8412 (t0) cc_final: 0.8204 (t0) REVERT: U 47 ASP cc_start: 0.7785 (t0) cc_final: 0.7407 (t0) REVERT: U 229 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7516 (mp0) REVERT: U 266 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8309 (mtp180) outliers start: 60 outliers final: 36 residues processed: 278 average time/residue: 0.5806 time to fit residues: 180.6093 Evaluate side-chains 263 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 221 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 96 VAL Chi-restraints excluded: chain P residue 22 LYS Chi-restraints excluded: chain S residue 69 ASN Chi-restraints excluded: chain S residue 150 ASP Chi-restraints excluded: chain S residue 240 THR Chi-restraints excluded: chain S residue 260 ILE Chi-restraints excluded: chain S residue 277 VAL Chi-restraints excluded: chain V residue 544 THR Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain X residue 505 VAL Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 136 ARG Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain T residue 277 VAL Chi-restraints excluded: chain T residue 285 ILE Chi-restraints excluded: chain U residue 35 LEU Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 229 GLU Chi-restraints excluded: chain U residue 242 VAL Chi-restraints excluded: chain U residue 266 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 191 optimal weight: 4.9990 chunk 167 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 179 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN P 89 GLN V 549 HIS F 24 GLN U 188 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.080552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.053599 restraints weight = 41537.641| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 3.50 r_work: 0.2688 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 1.0592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17306 Z= 0.144 Angle : 0.668 10.273 23634 Z= 0.331 Chirality : 0.045 0.251 2708 Planarity : 0.004 0.038 2962 Dihedral : 5.547 56.577 2818 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.20 % Allowed : 26.25 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.18), residues: 2110 helix: 3.06 (0.38), residues: 165 sheet: 0.23 (0.21), residues: 662 loop : -0.70 (0.16), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 61 TYR 0.018 0.001 TYR C 96 PHE 0.014 0.001 PHE W 592 TRP 0.045 0.001 TRP O 61 HIS 0.002 0.001 HIS X 549 Details of bonding type rmsd covalent geometry : bond 0.00352 (17257) covalent geometry : angle 0.65821 (23512) SS BOND : bond 0.00356 ( 25) SS BOND : angle 1.20438 ( 50) hydrogen bonds : bond 0.03210 ( 527) hydrogen bonds : angle 4.43918 ( 1506) link_ALPHA1-3 : bond 0.00671 ( 3) link_ALPHA1-3 : angle 3.04648 ( 9) link_ALPHA1-6 : bond 0.00284 ( 3) link_ALPHA1-6 : angle 1.70162 ( 9) link_BETA1-4 : bond 0.00496 ( 9) link_BETA1-4 : angle 2.06829 ( 27) link_NAG-ASN : bond 0.00290 ( 9) link_NAG-ASN : angle 1.37903 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 232 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8620 (pm20) cc_final: 0.8096 (pp30) REVERT: B 24 GLN cc_start: 0.8765 (tp40) cc_final: 0.8360 (tm-30) REVERT: B 79 GLU cc_start: 0.7516 (pm20) cc_final: 0.7200 (mp0) REVERT: M 4 GLU cc_start: 0.8174 (tp30) cc_final: 0.7921 (tm-30) REVERT: M 5 GLU cc_start: 0.8487 (pm20) cc_final: 0.8168 (pm20) REVERT: M 87 ASP cc_start: 0.8505 (m-30) cc_final: 0.8063 (m-30) REVERT: M 107 ASP cc_start: 0.9149 (m-30) cc_final: 0.8930 (m-30) REVERT: N 61 ARG cc_start: 0.8435 (ttm110) cc_final: 0.7918 (ttp80) REVERT: N 77 ASP cc_start: 0.9419 (m-30) cc_final: 0.9102 (m-30) REVERT: N 79 GLU cc_start: 0.7682 (mp0) cc_final: 0.7411 (mp0) REVERT: O 33 MET cc_start: 0.9234 (tpp) cc_final: 0.8941 (tpt) REVERT: O 65 ARG cc_start: 0.8686 (mmp80) cc_final: 0.7982 (mpp80) REVERT: P 27 GLN cc_start: 0.7133 (mp10) cc_final: 0.6851 (mp10) REVERT: P 28 SER cc_start: 0.8966 (p) cc_final: 0.8704 (t) REVERT: P 87 TYR cc_start: 0.7150 (m-10) cc_final: 0.6905 (m-10) REVERT: S 260 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.8004 (mp) REVERT: S 282 ASP cc_start: 0.7316 (p0) cc_final: 0.7036 (p0) REVERT: V 544 THR cc_start: 0.9414 (OUTLIER) cc_final: 0.9166 (p) REVERT: V 552 ASP cc_start: 0.8431 (t0) cc_final: 0.7947 (t0) REVERT: V 611 GLU cc_start: 0.7727 (pt0) cc_final: 0.6830 (pm20) REVERT: C 56 ARG cc_start: 0.8095 (ptp-110) cc_final: 0.7763 (ptp-170) REVERT: E 15 GLU cc_start: 0.8107 (tp30) cc_final: 0.7827 (tp30) REVERT: E 47 GLU cc_start: 0.8070 (tp30) cc_final: 0.7834 (tm-30) REVERT: E 56 ARG cc_start: 0.7675 (tmm-80) cc_final: 0.7332 (tmm-80) REVERT: D 59 PRO cc_start: 0.9248 (Cg_exo) cc_final: 0.9038 (Cg_endo) REVERT: D 107 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8124 (pm20) REVERT: F 45 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8158 (tmmm) REVERT: F 77 ASP cc_start: 0.8517 (p0) cc_final: 0.7444 (p0) REVERT: W 540 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8508 (pp20) REVERT: W 552 ASP cc_start: 0.8418 (m-30) cc_final: 0.7447 (t0) REVERT: T 136 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8429 (mmm160) REVERT: T 237 ASP cc_start: 0.8419 (t0) cc_final: 0.8161 (t0) REVERT: U 47 ASP cc_start: 0.7765 (t0) cc_final: 0.7395 (t0) REVERT: U 229 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7511 (mp0) outliers start: 57 outliers final: 36 residues processed: 273 average time/residue: 0.5842 time to fit residues: 178.3814 Evaluate side-chains 265 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 223 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 80 ILE Chi-restraints excluded: chain O residue 96 VAL Chi-restraints excluded: chain S residue 150 ASP Chi-restraints excluded: chain S residue 240 THR Chi-restraints excluded: chain S residue 260 ILE Chi-restraints excluded: chain S residue 277 VAL Chi-restraints excluded: chain V residue 544 THR Chi-restraints excluded: chain V residue 545 GLU Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain W residue 540 GLU Chi-restraints excluded: chain X residue 505 VAL Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 136 ARG Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain T residue 277 VAL Chi-restraints excluded: chain U residue 35 LEU Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 229 GLU Chi-restraints excluded: chain U residue 242 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 120 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 185 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN P 37 GLN V 549 HIS C 3 GLN C 84 GLN E 13 GLN F 6 GLN F 24 GLN F 42 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.079726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.052963 restraints weight = 41730.610| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 3.47 r_work: 0.2648 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 1.0844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17306 Z= 0.214 Angle : 0.706 10.341 23634 Z= 0.352 Chirality : 0.046 0.257 2708 Planarity : 0.004 0.041 2962 Dihedral : 5.605 57.245 2818 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.97 % Allowed : 26.47 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.18), residues: 2110 helix: 2.92 (0.38), residues: 165 sheet: 0.18 (0.21), residues: 662 loop : -0.76 (0.16), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 61 TYR 0.019 0.001 TYR C 96 PHE 0.014 0.002 PHE A 71 TRP 0.044 0.002 TRP O 61 HIS 0.003 0.001 HIS V 516 Details of bonding type rmsd covalent geometry : bond 0.00522 (17257) covalent geometry : angle 0.69589 (23512) SS BOND : bond 0.00415 ( 25) SS BOND : angle 1.35711 ( 50) hydrogen bonds : bond 0.03668 ( 527) hydrogen bonds : angle 4.53668 ( 1506) link_ALPHA1-3 : bond 0.00643 ( 3) link_ALPHA1-3 : angle 3.08891 ( 9) link_ALPHA1-6 : bond 0.00364 ( 3) link_ALPHA1-6 : angle 1.84902 ( 9) link_BETA1-4 : bond 0.00444 ( 9) link_BETA1-4 : angle 2.24678 ( 27) link_NAG-ASN : bond 0.00198 ( 9) link_NAG-ASN : angle 1.53956 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 227 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: B 24 GLN cc_start: 0.8766 (tp40) cc_final: 0.8419 (tm-30) REVERT: B 79 GLU cc_start: 0.7620 (pm20) cc_final: 0.7290 (mp0) REVERT: M 4 GLU cc_start: 0.8193 (tp30) cc_final: 0.7901 (tm-30) REVERT: M 5 GLU cc_start: 0.8518 (pm20) cc_final: 0.8193 (pm20) REVERT: M 87 ASP cc_start: 0.8564 (m-30) cc_final: 0.8127 (m-30) REVERT: N 61 ARG cc_start: 0.8513 (ttm110) cc_final: 0.7915 (ttp80) REVERT: N 77 ASP cc_start: 0.9433 (m-30) cc_final: 0.9042 (m-30) REVERT: N 79 GLU cc_start: 0.7743 (mp0) cc_final: 0.7526 (mp0) REVERT: O 33 MET cc_start: 0.9307 (tpp) cc_final: 0.9048 (tpt) REVERT: O 65 ARG cc_start: 0.8734 (mmp80) cc_final: 0.8061 (mpp80) REVERT: O 87 ASP cc_start: 0.8154 (m-30) cc_final: 0.7714 (m-30) REVERT: P 27 GLN cc_start: 0.7240 (mp10) cc_final: 0.6949 (mp10) REVERT: P 28 SER cc_start: 0.9010 (p) cc_final: 0.8763 (t) REVERT: P 37 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7874 (tt0) REVERT: P 87 TYR cc_start: 0.7303 (m-10) cc_final: 0.7092 (m-10) REVERT: S 69 ASN cc_start: 0.8889 (OUTLIER) cc_final: 0.8496 (m-40) REVERT: S 260 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.8006 (mp) REVERT: S 282 ASP cc_start: 0.7420 (p0) cc_final: 0.7131 (p0) REVERT: V 544 THR cc_start: 0.9388 (OUTLIER) cc_final: 0.9134 (p) REVERT: V 552 ASP cc_start: 0.8463 (t0) cc_final: 0.7979 (t0) REVERT: V 611 GLU cc_start: 0.7738 (pt0) cc_final: 0.6951 (pm20) REVERT: C 47 GLU cc_start: 0.8168 (tt0) cc_final: 0.7951 (tt0) REVERT: C 56 ARG cc_start: 0.8089 (ptp-110) cc_final: 0.7704 (ptp-170) REVERT: C 84 GLN cc_start: 0.8717 (pt0) cc_final: 0.8107 (pm20) REVERT: E 47 GLU cc_start: 0.8071 (tp30) cc_final: 0.7844 (tm-30) REVERT: E 56 ARG cc_start: 0.7662 (tmm-80) cc_final: 0.7329 (tmm-80) REVERT: D 59 PRO cc_start: 0.9278 (Cg_exo) cc_final: 0.9072 (Cg_endo) REVERT: D 107 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8110 (pm20) REVERT: F 77 ASP cc_start: 0.8495 (p0) cc_final: 0.7373 (p0) REVERT: F 79 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8043 (mm-30) REVERT: W 540 GLU cc_start: 0.8803 (pp20) cc_final: 0.8522 (pp20) REVERT: W 552 ASP cc_start: 0.8456 (m-30) cc_final: 0.7508 (t0) REVERT: T 136 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8403 (mmm160) REVERT: T 237 ASP cc_start: 0.8454 (t0) cc_final: 0.8244 (t0) REVERT: U 47 ASP cc_start: 0.7792 (t0) cc_final: 0.7426 (t0) REVERT: U 229 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7505 (mp0) outliers start: 53 outliers final: 33 residues processed: 268 average time/residue: 0.5778 time to fit residues: 173.3211 Evaluate side-chains 256 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 217 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain O residue 96 VAL Chi-restraints excluded: chain P residue 22 LYS Chi-restraints excluded: chain P residue 37 GLN Chi-restraints excluded: chain S residue 69 ASN Chi-restraints excluded: chain S residue 150 ASP Chi-restraints excluded: chain S residue 260 ILE Chi-restraints excluded: chain S residue 277 VAL Chi-restraints excluded: chain V residue 544 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain X residue 505 VAL Chi-restraints excluded: chain X residue 514 ASN Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 136 ARG Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain T residue 277 VAL Chi-restraints excluded: chain T residue 285 ILE Chi-restraints excluded: chain U residue 35 LEU Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 229 GLU Chi-restraints excluded: chain U residue 242 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 25 optimal weight: 4.9990 chunk 118 optimal weight: 10.0000 chunk 164 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN P 37 GLN P 89 GLN V 549 HIS C 3 GLN F 24 GLN F 27 GLN F 42 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.078566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.051819 restraints weight = 41740.453| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 3.46 r_work: 0.2623 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 1.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 17306 Z= 0.312 Angle : 0.749 10.255 23634 Z= 0.374 Chirality : 0.049 0.268 2708 Planarity : 0.005 0.050 2962 Dihedral : 5.749 57.567 2818 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.03 % Allowed : 26.86 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.18), residues: 2110 helix: 2.72 (0.38), residues: 165 sheet: 0.07 (0.20), residues: 683 loop : -0.85 (0.16), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 61 TYR 0.018 0.002 TYR C 96 PHE 0.018 0.002 PHE C 111 TRP 0.048 0.002 TRP O 61 HIS 0.005 0.001 HIS V 516 Details of bonding type rmsd covalent geometry : bond 0.00756 (17257) covalent geometry : angle 0.73728 (23512) SS BOND : bond 0.00481 ( 25) SS BOND : angle 1.52036 ( 50) hydrogen bonds : bond 0.04108 ( 527) hydrogen bonds : angle 4.69807 ( 1506) link_ALPHA1-3 : bond 0.00656 ( 3) link_ALPHA1-3 : angle 3.13065 ( 9) link_ALPHA1-6 : bond 0.00458 ( 3) link_ALPHA1-6 : angle 2.02976 ( 9) link_BETA1-4 : bond 0.00412 ( 9) link_BETA1-4 : angle 2.44434 ( 27) link_NAG-ASN : bond 0.00214 ( 9) link_NAG-ASN : angle 1.69390 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6196.86 seconds wall clock time: 106 minutes 27.19 seconds (6387.19 seconds total)