Starting phenix.real_space_refine on Tue Aug 26 14:13:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h9v_34583/08_2025/8h9v_34583.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h9v_34583/08_2025/8h9v_34583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8h9v_34583/08_2025/8h9v_34583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h9v_34583/08_2025/8h9v_34583.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h9v_34583/08_2025/8h9v_34583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h9v_34583/08_2025/8h9v_34583.map" } resolution = 3.02 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= 0.009 sd= 1.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 158 5.16 5 C 24212 2.51 5 N 6427 2.21 5 O 7106 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 264 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37921 Number of models: 1 Model: "" Number of chains: 32 Chain: "4" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "5" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "6" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "7" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "8" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "1" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "2" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "3" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "H" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 975 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "I" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 354 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "K" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1573 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1259 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 144} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "N" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1718 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 208} Chain: "P" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 344 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "Q" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 422 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 8, 'TRANS': 42} Chain: "R" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 621 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 605 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "T" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 346 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 39} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 549 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 62} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 3706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3706 Classifications: {'peptide': 486} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 467} Chain: "B" Number of atoms: 3639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3639 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 458} Chain breaks: 1 Chain: "C" Number of atoms: 3587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3587 Classifications: {'peptide': 470} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 451} Chain breaks: 1 Chain: "E" Number of atoms: 3458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3458 Classifications: {'peptide': 456} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 430} Chain breaks: 1 Chain: "F" Number of atoms: 3529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3529 Classifications: {'peptide': 466} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 440} Chain: "D" Number of atoms: 3272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3272 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 410} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 2103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2103 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 5, 'TRANS': 265} Chain: "O" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1437 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 8, 'TRANS': 178} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.97, per 1000 atoms: 0.21 Number of scatterers: 37921 At special positions: 0 Unit cell: (150.38, 141.62, 249.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 158 16.00 P 13 15.00 Mg 5 11.99 O 7106 8.00 N 6427 7.00 C 24212 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 3.41 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 715.3 nanoseconds 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9036 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 28 sheets defined 58.9% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain '4' and resid 1 through 17 removed outlier: 3.868A pdb=" N GLY 4 17 " --> pdb=" O ALA 4 13 " (cutoff:3.500A) Processing helix chain '4' and resid 17 through 39 removed outlier: 4.407A pdb=" N SER 4 21 " --> pdb=" O GLY 4 17 " (cutoff:3.500A) Processing helix chain '4' and resid 42 through 73 removed outlier: 3.588A pdb=" N ALA 4 59 " --> pdb=" O ALA 4 55 " (cutoff:3.500A) Processing helix chain '5' and resid 2 through 17 removed outlier: 3.868A pdb=" N GLY 5 17 " --> pdb=" O ALA 5 13 " (cutoff:3.500A) Processing helix chain '5' and resid 17 through 39 removed outlier: 4.408A pdb=" N SER 5 21 " --> pdb=" O GLY 5 17 " (cutoff:3.500A) Processing helix chain '5' and resid 42 through 73 removed outlier: 3.588A pdb=" N ALA 5 59 " --> pdb=" O ALA 5 55 " (cutoff:3.500A) Processing helix chain '6' and resid 2 through 17 removed outlier: 3.868A pdb=" N GLY 6 17 " --> pdb=" O ALA 6 13 " (cutoff:3.500A) Processing helix chain '6' and resid 17 through 39 removed outlier: 4.406A pdb=" N SER 6 21 " --> pdb=" O GLY 6 17 " (cutoff:3.500A) Processing helix chain '6' and resid 42 through 73 removed outlier: 3.588A pdb=" N ALA 6 59 " --> pdb=" O ALA 6 55 " (cutoff:3.500A) Processing helix chain '7' and resid 2 through 17 removed outlier: 3.868A pdb=" N GLY 7 17 " --> pdb=" O ALA 7 13 " (cutoff:3.500A) Processing helix chain '7' and resid 17 through 39 removed outlier: 4.408A pdb=" N SER 7 21 " --> pdb=" O GLY 7 17 " (cutoff:3.500A) Processing helix chain '7' and resid 42 through 73 removed outlier: 3.587A pdb=" N ALA 7 59 " --> pdb=" O ALA 7 55 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 17 removed outlier: 3.868A pdb=" N GLY 8 17 " --> pdb=" O ALA 8 13 " (cutoff:3.500A) Processing helix chain '8' and resid 17 through 39 removed outlier: 4.407A pdb=" N SER 8 21 " --> pdb=" O GLY 8 17 " (cutoff:3.500A) Processing helix chain '8' and resid 42 through 73 removed outlier: 3.588A pdb=" N ALA 8 59 " --> pdb=" O ALA 8 55 " (cutoff:3.500A) Processing helix chain '1' and resid 2 through 17 removed outlier: 3.868A pdb=" N GLY 1 17 " --> pdb=" O ALA 1 13 " (cutoff:3.500A) Processing helix chain '1' and resid 17 through 39 removed outlier: 4.408A pdb=" N SER 1 21 " --> pdb=" O GLY 1 17 " (cutoff:3.500A) Processing helix chain '1' and resid 42 through 73 removed outlier: 3.588A pdb=" N ALA 1 59 " --> pdb=" O ALA 1 55 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 17 removed outlier: 3.868A pdb=" N GLY 2 17 " --> pdb=" O ALA 2 13 " (cutoff:3.500A) Processing helix chain '2' and resid 17 through 39 removed outlier: 4.406A pdb=" N SER 2 21 " --> pdb=" O GLY 2 17 " (cutoff:3.500A) Processing helix chain '2' and resid 42 through 73 removed outlier: 3.587A pdb=" N ALA 2 59 " --> pdb=" O ALA 2 55 " (cutoff:3.500A) Processing helix chain '3' and resid 2 through 17 removed outlier: 3.867A pdb=" N GLY 3 17 " --> pdb=" O ALA 3 13 " (cutoff:3.500A) Processing helix chain '3' and resid 17 through 39 removed outlier: 4.407A pdb=" N SER 3 21 " --> pdb=" O GLY 3 17 " (cutoff:3.500A) Processing helix chain '3' and resid 42 through 73 removed outlier: 3.588A pdb=" N ALA 3 59 " --> pdb=" O ALA 3 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 103 No H-bonds generated for 'chain 'H' and resid 101 through 103' Processing helix chain 'H' and resid 104 through 122 removed outlier: 3.697A pdb=" N ALA H 108 " --> pdb=" O ASP H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 146 Processing helix chain 'I' and resid 3 through 9 Processing helix chain 'I' and resid 11 through 26 Processing helix chain 'I' and resid 28 through 38 removed outlier: 4.643A pdb=" N ALA I 33 " --> pdb=" O THR I 29 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ASN I 34 " --> pdb=" O GLU I 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 30 Proline residue: K 27 - end of helix Processing helix chain 'K' and resid 32 through 48 Processing helix chain 'K' and resid 54 through 97 removed outlier: 3.614A pdb=" N PHE K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) Proline residue: K 76 - end of helix Processing helix chain 'K' and resid 98 through 120 removed outlier: 3.853A pdb=" N GLN K 102 " --> pdb=" O GLN K 98 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS K 103 " --> pdb=" O ALA K 99 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 182 removed outlier: 3.653A pdb=" N ASP K 126 " --> pdb=" O HIS K 122 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN K 175 " --> pdb=" O GLU K 171 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL K 177 " --> pdb=" O MET K 173 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU K 178 " --> pdb=" O ILE K 174 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL K 182 " --> pdb=" O GLU K 178 " (cutoff:3.500A) Processing helix chain 'K' and resid 194 through 206 Processing helix chain 'M' and resid 12 through 18 removed outlier: 3.639A pdb=" N ILE M 18 " --> pdb=" O ALA M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 19 through 22 removed outlier: 5.957A pdb=" N ASN M 22 " --> pdb=" O ILE M 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 19 through 22' Processing helix chain 'M' and resid 23 through 43 removed outlier: 3.671A pdb=" N ALA M 27 " --> pdb=" O GLN M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 58 Processing helix chain 'M' and resid 64 through 75 Processing helix chain 'M' and resid 85 through 123 removed outlier: 3.775A pdb=" N VAL M 89 " --> pdb=" O TYR M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 130 Processing helix chain 'M' and resid 131 through 139 Processing helix chain 'N' and resid 6 through 10 removed outlier: 3.710A pdb=" N ILE N 10 " --> pdb=" O ALA N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 26 removed outlier: 3.548A pdb=" N ILE N 23 " --> pdb=" O ALA N 19 " (cutoff:3.500A) Processing helix chain 'N' and resid 27 through 31 Processing helix chain 'N' and resid 40 through 59 removed outlier: 3.591A pdb=" N THR N 59 " --> pdb=" O LYS N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 64 through 67 Processing helix chain 'N' and resid 68 through 87 removed outlier: 3.654A pdb=" N ALA N 80 " --> pdb=" O ILE N 76 " (cutoff:3.500A) Processing helix chain 'N' and resid 93 through 96 Processing helix chain 'N' and resid 97 through 119 removed outlier: 3.591A pdb=" N ASN N 101 " --> pdb=" O GLN N 97 " (cutoff:3.500A) Proline residue: N 107 - end of helix removed outlier: 3.617A pdb=" N SER N 119 " --> pdb=" O MET N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 127 Processing helix chain 'N' and resid 134 through 136 No H-bonds generated for 'chain 'N' and resid 134 through 136' Processing helix chain 'N' and resid 137 through 181 removed outlier: 4.137A pdb=" N LEU N 141 " --> pdb=" O LEU N 137 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL N 142 " --> pdb=" O ILE N 138 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU N 145 " --> pdb=" O LEU N 141 " (cutoff:3.500A) Proline residue: N 153 - end of helix removed outlier: 3.646A pdb=" N ASN N 163 " --> pdb=" O ARG N 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 185 through 225 Processing helix chain 'P' and resid 4 through 9 Processing helix chain 'P' and resid 9 through 19 removed outlier: 3.699A pdb=" N MET P 13 " --> pdb=" O ILE P 9 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS P 14 " --> pdb=" O TRP P 10 " (cutoff:3.500A) Proline residue: P 15 - end of helix Processing helix chain 'P' and resid 21 through 41 Processing helix chain 'Q' and resid 1 through 8 removed outlier: 5.286A pdb=" N THR Q 6 " --> pdb=" O GLN Q 3 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N THR Q 7 " --> pdb=" O LEU Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 22 Proline residue: Q 15 - end of helix removed outlier: 3.524A pdb=" N PHE Q 21 " --> pdb=" O LEU Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 30 Processing helix chain 'R' and resid 26 through 32 removed outlier: 3.799A pdb=" N LEU R 30 " --> pdb=" O PRO R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 35 through 55 Processing helix chain 'R' and resid 62 through 85 removed outlier: 4.761A pdb=" N VAL R 68 " --> pdb=" O GLY R 64 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE R 79 " --> pdb=" O PHE R 75 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LYS R 82 " --> pdb=" O SER R 78 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N HIS R 83 " --> pdb=" O PHE R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 88 No H-bonds generated for 'chain 'R' and resid 86 through 88' Processing helix chain 'S' and resid 27 through 37 removed outlier: 4.229A pdb=" N VAL S 35 " --> pdb=" O TYR S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 61 Processing helix chain 'S' and resid 62 through 67 Processing helix chain 'S' and resid 68 through 94 Processing helix chain 'T' and resid 8 through 45 Proline residue: T 35 - end of helix removed outlier: 4.004A pdb=" N ALA T 45 " --> pdb=" O ARG T 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 54 Processing helix chain 'L' and resid 67 through 83 removed outlier: 4.379A pdb=" N ARG L 73 " --> pdb=" O GLN L 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.809A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 191 Processing helix chain 'A' and resid 209 through 222 Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 239 through 260 Proline residue: A 247 - end of helix removed outlier: 3.775A pdb=" N PHE A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN A 260 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 285 removed outlier: 3.794A pdb=" N GLN A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 353 through 359 Processing helix chain 'A' and resid 374 through 379 Processing helix chain 'A' and resid 380 through 399 removed outlier: 4.260A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 404 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 411 through 429 Processing helix chain 'A' and resid 437 through 450 Processing helix chain 'A' and resid 457 through 459 No H-bonds generated for 'chain 'A' and resid 457 through 459' Processing helix chain 'A' and resid 460 through 476 removed outlier: 3.587A pdb=" N LEU A 469 " --> pdb=" O GLU A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 487 Processing helix chain 'A' and resid 490 through 508 Processing helix chain 'B' and resid 78 through 82 Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 187 through 189 No H-bonds generated for 'chain 'B' and resid 187 through 189' Processing helix chain 'B' and resid 209 through 223 Processing helix chain 'B' and resid 239 through 259 Proline residue: B 247 - end of helix removed outlier: 3.976A pdb=" N PHE B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 284 removed outlier: 3.691A pdb=" N GLN B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 297 through 307 removed outlier: 4.014A pdb=" N HIS B 302 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 336 through 346 removed outlier: 3.609A pdb=" N THR B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 380 through 401 removed outlier: 4.404A pdb=" N THR B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 429 removed outlier: 3.851A pdb=" N GLN B 416 " --> pdb=" O ALA B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 450 Processing helix chain 'B' and resid 457 through 476 removed outlier: 4.405A pdb=" N THR B 462 " --> pdb=" O PRO B 458 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LYS B 463 " --> pdb=" O SER B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 487 Processing helix chain 'B' and resid 490 through 507 Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.755A pdb=" N ILE C 82 " --> pdb=" O ASP C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.705A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 191 Processing helix chain 'C' and resid 209 through 223 Processing helix chain 'C' and resid 239 through 260 Proline residue: C 247 - end of helix removed outlier: 4.152A pdb=" N PHE C 257 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 285 removed outlier: 3.977A pdb=" N GLN C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 294 Processing helix chain 'C' and resid 297 through 307 removed outlier: 3.940A pdb=" N LEU C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 346 Processing helix chain 'C' and resid 354 through 359 Processing helix chain 'C' and resid 374 through 379 removed outlier: 4.001A pdb=" N ALA C 377 " --> pdb=" O VAL C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 401 removed outlier: 4.254A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 429 removed outlier: 3.590A pdb=" N LYS C 429 " --> pdb=" O THR C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 450 Processing helix chain 'C' and resid 460 through 476 Processing helix chain 'C' and resid 476 through 487 Processing helix chain 'C' and resid 490 through 507 Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'E' and resid 125 through 129 removed outlier: 3.546A pdb=" N MET E 129 " --> pdb=" O PHE E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 147 removed outlier: 3.500A pdb=" N ALA E 147 " --> pdb=" O VAL E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 180 Processing helix chain 'E' and resid 192 through 206 Processing helix chain 'E' and resid 228 through 249 removed outlier: 4.930A pdb=" N ALA E 236 " --> pdb=" O ARG E 232 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LEU E 237 " --> pdb=" O ALA E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 275 Processing helix chain 'E' and resid 287 through 297 Processing helix chain 'E' and resid 315 through 319 Processing helix chain 'E' and resid 322 through 330 removed outlier: 3.982A pdb=" N ALA E 330 " --> pdb=" O ALA E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 345 Processing helix chain 'E' and resid 362 through 391 removed outlier: 7.399A pdb=" N SER E 368 " --> pdb=" O ASN E 364 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N GLU E 369 " --> pdb=" O ILE E 365 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N HIS E 370 " --> pdb=" O VAL E 366 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE E 390 " --> pdb=" O SER E 386 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE E 391 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 418 removed outlier: 3.828A pdb=" N SER E 418 " --> pdb=" O GLN E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 423 No H-bonds generated for 'chain 'E' and resid 421 through 423' Processing helix chain 'E' and resid 424 through 429 Processing helix chain 'E' and resid 436 through 449 Processing helix chain 'E' and resid 456 through 461 removed outlier: 3.527A pdb=" N TYR E 461 " --> pdb=" O GLN E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 465 through 475 removed outlier: 3.519A pdb=" N ALA E 469 " --> pdb=" O PRO E 465 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS E 475 " --> pdb=" O ALA E 471 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 140 through 147 Processing helix chain 'F' and resid 164 through 176 Processing helix chain 'F' and resid 192 through 206 Processing helix chain 'F' and resid 228 through 249 removed outlier: 4.797A pdb=" N ALA F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 273 removed outlier: 3.952A pdb=" N THR F 265 " --> pdb=" O ILE F 261 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA F 273 " --> pdb=" O SER F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 297 Processing helix chain 'F' and resid 316 through 319 Processing helix chain 'F' and resid 322 through 329 Processing helix chain 'F' and resid 330 through 332 No H-bonds generated for 'chain 'F' and resid 330 through 332' Processing helix chain 'F' and resid 339 through 344 Processing helix chain 'F' and resid 362 through 394 removed outlier: 7.297A pdb=" N SER F 368 " --> pdb=" O ASN F 364 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N GLU F 369 " --> pdb=" O ILE F 365 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N HIS F 370 " --> pdb=" O VAL F 366 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASP F 389 " --> pdb=" O LYS F 385 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ILE F 390 " --> pdb=" O SER F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 418 removed outlier: 3.800A pdb=" N SER F 418 " --> pdb=" O GLN F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 436 through 449 Processing helix chain 'F' and resid 456 through 460 Processing helix chain 'F' and resid 465 through 476 Processing helix chain 'D' and resid 90 through 94 removed outlier: 3.539A pdb=" N LEU D 94 " --> pdb=" O PRO D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 129 Processing helix chain 'D' and resid 165 through 179 Processing helix chain 'D' and resid 192 through 205 Processing helix chain 'D' and resid 228 through 251 removed outlier: 5.268A pdb=" N ALA D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU D 237 " --> pdb=" O ALA D 233 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY D 239 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE D 246 " --> pdb=" O VAL D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 276 removed outlier: 3.559A pdb=" N PHE D 264 " --> pdb=" O ASN D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 297 Processing helix chain 'D' and resid 339 through 345 removed outlier: 3.597A pdb=" N ALA D 343 " --> pdb=" O SER D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 388 removed outlier: 3.587A pdb=" N TYR D 371 " --> pdb=" O GLY D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 417 Processing helix chain 'D' and resid 421 through 425 Processing helix chain 'D' and resid 436 through 448 Processing helix chain 'D' and resid 456 through 460 removed outlier: 3.682A pdb=" N ALA D 459 " --> pdb=" O PRO D 456 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE D 460 " --> pdb=" O GLU D 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 456 through 460' Processing helix chain 'D' and resid 465 through 475 removed outlier: 3.677A pdb=" N ALA D 469 " --> pdb=" O PRO D 465 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 32 Processing helix chain 'G' and resid 37 through 56 removed outlier: 3.800A pdb=" N ALA G 41 " --> pdb=" O GLU G 37 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N TYR G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 99 removed outlier: 3.654A pdb=" N ALA G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 118 removed outlier: 4.574A pdb=" N ARG G 118 " --> pdb=" O GLY G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 150 removed outlier: 3.537A pdb=" N ALA G 141 " --> pdb=" O THR G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 187 Processing helix chain 'G' and resid 188 through 193 removed outlier: 3.952A pdb=" N ILE G 192 " --> pdb=" O SER G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 270 removed outlier: 3.791A pdb=" N THR G 222 " --> pdb=" O LYS G 218 " (cutoff:3.500A) Processing helix chain 'O' and resid 12 through 28 Processing helix chain 'O' and resid 31 through 46 Processing helix chain 'O' and resid 48 through 55 Processing helix chain 'O' and resid 61 through 75 removed outlier: 4.039A pdb=" N LYS O 75 " --> pdb=" O ASP O 71 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 91 removed outlier: 3.566A pdb=" N THR O 83 " --> pdb=" O SER O 79 " (cutoff:3.500A) Processing helix chain 'O' and resid 97 through 113 Processing helix chain 'O' and resid 127 through 141 removed outlier: 4.003A pdb=" N PHE O 141 " --> pdb=" O VAL O 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 155 through 159 Processing helix chain 'O' and resid 174 through 187 Processing sheet with id=AA1, first strand: chain 'H' and resid 25 through 26 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 31 through 40 current: chain 'H' and resid 80 through 84 Processing sheet with id=AA2, first strand: chain 'H' and resid 43 through 48 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 17 through 22 current: chain 'H' and resid 72 through 77 Processing sheet with id=AA3, first strand: chain 'I' and resid 44 through 46 removed outlier: 3.500A pdb=" N LYS I 44 " --> pdb=" O LYS G 129 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA G 127 " --> pdb=" O VAL I 46 " (cutoff:3.500A) removed outlier: 10.200A pdb=" N VAL G 126 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU G 105 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N PHE G 128 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLY G 107 " --> pdb=" O PHE G 128 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N HIS G 66 " --> pdb=" O MET G 104 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N VAL G 106 " --> pdb=" O HIS G 66 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU G 68 " --> pdb=" O VAL G 106 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE G 108 " --> pdb=" O LEU G 68 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLY G 70 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ASN G 163 " --> pdb=" O VAL G 71 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 12 through 13 Processing sheet with id=AA5, first strand: chain 'A' and resid 26 through 27 removed outlier: 6.226A pdb=" N VAL O 116 " --> pdb=" O LYS O 149 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 29 through 33 removed outlier: 5.426A pdb=" N VAL A 31 " --> pdb=" O HIS A 42 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N HIS A 42 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER A 33 " --> pdb=" O ARG A 40 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 29 through 33 removed outlier: 5.426A pdb=" N VAL A 31 " --> pdb=" O HIS A 42 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N HIS A 42 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER A 33 " --> pdb=" O ARG A 40 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 60 through 66 current: chain 'E' and resid 38 through 41 removed outlier: 6.693A pdb=" N ARG E 62 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N HIS E 55 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR E 60 " --> pdb=" O HIS E 55 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL E 23 " --> pdb=" O VAL E 19 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL E 19 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ASP E 25 " --> pdb=" O VAL E 17 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.165A pdb=" N THR A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.695A pdb=" N VAL A 108 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N CYS A 201 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N VAL A 232 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR A 203 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ALA A 234 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ALA A 205 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N TYR A 200 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ILE A 267 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE A 202 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ASP A 269 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL A 204 " --> pdb=" O ASP A 269 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 326 through 328 removed outlier: 6.522A pdb=" N ILE A 167 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU A 166 " --> pdb=" O GLY A 348 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 60 through 66 removed outlier: 4.027A pdb=" N GLU B 51 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N MET B 52 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG B 40 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE B 38 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ASN B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LEU B 66 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ARG F 62 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N HIS F 55 " --> pdb=" O THR F 60 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR F 60 " --> pdb=" O HIS F 55 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLN F 27 " --> pdb=" O ILE F 16 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ILE F 16 " --> pdb=" O GLN F 27 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.355A pdb=" N THR B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.860A pdb=" N VAL B 108 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR B 200 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ILE B 267 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE B 202 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ASP B 269 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL B 204 " --> pdb=" O ASP B 269 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA B 264 " --> pdb=" O THR B 322 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 326 through 328 removed outlier: 6.460A pdb=" N ILE B 167 " --> pdb=" O ILE B 327 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU B 166 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU B 352 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE B 168 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 60 through 66 removed outlier: 3.933A pdb=" N GLU C 51 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ARG C 40 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL C 74 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N SER C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ARG D 62 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N HIS D 55 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N THR D 60 " --> pdb=" O HIS D 55 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLN D 27 " --> pdb=" O ILE D 16 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE D 16 " --> pdb=" O GLN D 27 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.349A pdb=" N THR C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 107 through 108 removed outlier: 6.361A pdb=" N VAL C 108 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N ILE C 230 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N CYS C 201 " --> pdb=" O ILE C 230 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N VAL C 232 " --> pdb=" O CYS C 201 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TYR C 203 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ALA C 234 " --> pdb=" O TYR C 203 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ALA C 205 " --> pdb=" O ALA C 234 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 326 through 328 removed outlier: 6.453A pdb=" N ILE C 167 " --> pdb=" O ILE C 327 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE C 168 " --> pdb=" O LEU C 352 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 86 through 89 removed outlier: 4.124A pdb=" N GLN E 115 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 97 through 98 removed outlier: 6.100A pdb=" N MET E 98 " --> pdb=" O TYR E 222 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N GLN E 224 " --> pdb=" O MET E 98 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL E 185 " --> pdb=" O PHE E 257 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL E 254 " --> pdb=" O THR E 308 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL E 310 " --> pdb=" O VAL E 254 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU E 256 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ALA E 312 " --> pdb=" O LEU E 256 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ILE E 258 " --> pdb=" O ALA E 312 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ILE E 155 " --> pdb=" O GLN E 311 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LYS E 154 " --> pdb=" O ASP E 333 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N THR E 335 " --> pdb=" O LYS E 154 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLY E 156 " --> pdb=" O THR E 335 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 135 through 136 removed outlier: 4.297A pdb=" N TYR E 149 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 86 through 89 removed outlier: 4.282A pdb=" N GLN F 115 " --> pdb=" O VAL F 89 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 97 through 98 removed outlier: 6.621A pdb=" N VAL F 185 " --> pdb=" O PHE F 257 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ASP F 259 " --> pdb=" O VAL F 185 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ALA F 187 " --> pdb=" O ASP F 259 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL F 254 " --> pdb=" O THR F 308 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N VAL F 310 " --> pdb=" O VAL F 254 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU F 256 " --> pdb=" O VAL F 310 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ALA F 312 " --> pdb=" O LEU F 256 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE F 258 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N TYR F 314 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LYS F 154 " --> pdb=" O ALA F 334 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N THR F 336 " --> pdb=" O LYS F 154 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLY F 156 " --> pdb=" O THR F 336 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 135 through 136 removed outlier: 4.272A pdb=" N TYR F 149 " --> pdb=" O LEU F 136 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 86 through 89 removed outlier: 3.966A pdb=" N GLN D 115 " --> pdb=" O VAL D 89 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 97 through 98 removed outlier: 5.907A pdb=" N MET D 98 " --> pdb=" O TYR D 222 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N GLN D 224 " --> pdb=" O MET D 98 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY D 223 " --> pdb=" O GLY D 188 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE D 155 " --> pdb=" O GLN D 311 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 135 through 136 removed outlier: 4.646A pdb=" N TYR D 149 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 334 through 335 2231 hydrogen bonds defined for protein. 6459 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: 8.79 Time building geometry restraints manager: 4.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11867 1.33 - 1.46: 6263 1.46 - 1.58: 20098 1.58 - 1.70: 21 1.70 - 1.82: 297 Bond restraints: 38546 Sorted by residual: bond pdb=" C6 ATP A 601 " pdb=" N6 ATP A 601 " ideal model delta sigma weight residual 1.337 1.461 -0.124 1.10e-02 8.26e+03 1.27e+02 bond pdb=" C6 ATP C 601 " pdb=" N6 ATP C 601 " ideal model delta sigma weight residual 1.337 1.456 -0.119 1.10e-02 8.26e+03 1.18e+02 bond pdb=" C6 ATP B 601 " pdb=" N6 ATP B 601 " ideal model delta sigma weight residual 1.337 1.455 -0.118 1.10e-02 8.26e+03 1.15e+02 bond pdb=" C4 ATP C 601 " pdb=" N9 ATP C 601 " ideal model delta sigma weight residual 1.374 1.279 0.095 1.00e-02 1.00e+04 9.02e+01 bond pdb=" C4 ATP B 601 " pdb=" N9 ATP B 601 " ideal model delta sigma weight residual 1.374 1.280 0.094 1.00e-02 1.00e+04 8.92e+01 ... (remaining 38541 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.61: 51849 3.61 - 7.23: 265 7.23 - 10.84: 31 10.84 - 14.45: 3 14.45 - 18.06: 3 Bond angle restraints: 52151 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 121.81 18.06 1.00e+00 1.00e+00 3.26e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 121.85 18.02 1.00e+00 1.00e+00 3.25e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 121.14 15.69 1.00e+00 1.00e+00 2.46e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 125.69 14.18 1.00e+00 1.00e+00 2.01e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 122.90 13.93 1.00e+00 1.00e+00 1.94e+02 ... (remaining 52146 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.05: 22519 29.05 - 58.10: 731 58.10 - 87.16: 104 87.16 - 116.21: 6 116.21 - 145.26: 2 Dihedral angle restraints: 23362 sinusoidal: 9242 harmonic: 14120 Sorted by residual: dihedral pdb=" O1B ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PB ADP D 501 " pdb=" PA ADP D 501 " ideal model delta sinusoidal sigma weight residual 300.00 154.74 145.26 1 2.00e+01 2.50e-03 4.37e+01 dihedral pdb=" O2A ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PA ADP D 501 " pdb=" PB ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 59.26 -119.25 1 2.00e+01 2.50e-03 3.57e+01 dihedral pdb=" C5' ADP D 501 " pdb=" O5' ADP D 501 " pdb=" PA ADP D 501 " pdb=" O2A ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 47.78 -107.77 1 2.00e+01 2.50e-03 3.13e+01 ... (remaining 23359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 4345 0.048 - 0.096: 1373 0.096 - 0.143: 339 0.143 - 0.191: 17 0.191 - 0.239: 4 Chirality restraints: 6078 Sorted by residual: chirality pdb=" C2' ATP B 601 " pdb=" C1' ATP B 601 " pdb=" C3' ATP B 601 " pdb=" O2' ATP B 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.44 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" C2' ATP C 601 " pdb=" C1' ATP C 601 " pdb=" C3' ATP C 601 " pdb=" O2' ATP C 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.45 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" C2' ATP A 601 " pdb=" C1' ATP A 601 " pdb=" C3' ATP A 601 " pdb=" O2' ATP A 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.46 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 6075 not shown) Planarity restraints: 6644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP Q 51 " -0.013 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" CG TRP Q 51 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP Q 51 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP Q 51 " -0.022 2.00e-02 2.50e+03 pdb=" NE1 TRP Q 51 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP Q 51 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP Q 51 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP Q 51 " 0.026 2.00e-02 2.50e+03 pdb=" CZ3 TRP Q 51 " 0.027 2.00e-02 2.50e+03 pdb=" CH2 TRP Q 51 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS Q 49 " -0.041 5.00e-02 4.00e+02 6.19e-02 6.13e+00 pdb=" N PRO Q 50 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO Q 50 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO Q 50 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 140 " -0.011 2.00e-02 2.50e+03 2.12e-02 4.48e+00 pdb=" C ILE E 140 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE E 140 " -0.014 2.00e-02 2.50e+03 pdb=" N LYS E 141 " -0.012 2.00e-02 2.50e+03 ... (remaining 6641 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4765 2.74 - 3.28: 41111 3.28 - 3.82: 63143 3.82 - 4.36: 77924 4.36 - 4.90: 130492 Nonbonded interactions: 317435 Sorted by model distance: nonbonded pdb=" O THR H 122 " pdb=" NH2 ARG H 128 " model vdw 2.196 3.120 nonbonded pdb=" OE1 GLU B 307 " pdb=" OG1 THR F 193 " model vdw 2.203 3.040 nonbonded pdb=" O ARG H 134 " pdb=" ND2 ASN H 138 " model vdw 2.206 3.120 nonbonded pdb=" O VAL G 168 " pdb=" OG SER G 226 " model vdw 2.210 3.040 nonbonded pdb=" NE ARG D 411 " pdb=" OE2 GLU D 457 " model vdw 2.212 3.120 ... (remaining 317430 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 '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' } ncs_group { reference = (chain 'A' and (resid 24 through 401 or resid 417 through 508 or resid 601 throu \ gh 602)) selection = (chain 'B' and (resid 24 through 401 or resid 417 through 508 or resid 601 throu \ gh 602)) selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 12 through 475) selection = (chain 'E' and (resid 12 through 160 or resid 162 through 312 or resid 332 throu \ gh 389 or (resid 404 and (name N or name CA or name C or name O or name CB )) or \ resid 405 through 475)) selection = (chain 'F' and (resid 12 through 160 or resid 162 through 312 or resid 332 throu \ gh 389 or (resid 404 and (name N or name CA or name C or name O or name CB )) or \ resid 405 through 475)) } 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: 9.370 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: 0.790 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 34.450 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 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 : 0.009 0.145 38546 Z= 0.442 Angle : 0.785 18.063 52151 Z= 0.476 Chirality : 0.047 0.239 6078 Planarity : 0.004 0.065 6644 Dihedral : 14.502 145.261 14326 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.02 % Favored : 93.96 % Rotamer: Outliers : 0.08 % Allowed : 5.16 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.11 % 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 aren not related in a simple way. whole: -3.18 (0.10), residues: 4885 helix: -1.70 (0.09), residues: 2624 sheet: -2.50 (0.18), residues: 575 loop : -2.33 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 30 TYR 0.024 0.002 TYR D 284 PHE 0.021 0.002 PHE H 45 TRP 0.033 0.002 TRP Q 51 HIS 0.005 0.001 HIS K 172 Details of bonding type rmsd covalent geometry : bond 0.00884 (38546) covalent geometry : angle 0.78457 (52151) hydrogen bonds : bond 0.15249 ( 2221) hydrogen bonds : angle 7.06523 ( 6459) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 4012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 892 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 39 ASN cc_start: 0.7811 (t0) cc_final: 0.7601 (t0) REVERT: 2 60 MET cc_start: 0.7962 (mmm) cc_final: 0.7704 (mmm) REVERT: H 111 ASN cc_start: 0.8382 (m110) cc_final: 0.8179 (m-40) REVERT: I 13 ILE cc_start: 0.8701 (mm) cc_final: 0.8438 (mm) REVERT: I 28 LYS cc_start: 0.6946 (mtpp) cc_final: 0.6705 (mttt) REVERT: K 164 MET cc_start: 0.8550 (tpp) cc_final: 0.7853 (tpp) REVERT: M 51 ILE cc_start: 0.8219 (pt) cc_final: 0.7920 (mt) REVERT: N 145 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7833 (tp30) REVERT: S 70 LYS cc_start: 0.7077 (tptt) cc_final: 0.6841 (tptt) REVERT: T 16 TYR cc_start: 0.7287 (m-80) cc_final: 0.7008 (m-80) REVERT: A 416 GLN cc_start: 0.8116 (tm-30) cc_final: 0.7893 (tm-30) REVERT: A 463 LYS cc_start: 0.8854 (mtpt) cc_final: 0.8558 (mtpt) REVERT: B 226 MET cc_start: 0.8212 (mmm) cc_final: 0.7801 (tpt) REVERT: C 373 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7757 (mtt90) REVERT: E 347 ILE cc_start: 0.9213 (mm) cc_final: 0.8896 (mm) REVERT: E 458 GLN cc_start: 0.7938 (mm110) cc_final: 0.7496 (tp40) REVERT: D 62 ARG cc_start: 0.7928 (ttm170) cc_final: 0.7665 (ttm-80) REVERT: D 296 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7917 (tt0) REVERT: D 297 GLU cc_start: 0.8246 (tp30) cc_final: 0.8042 (tp30) REVERT: D 433 LYS cc_start: 0.6790 (mmtm) cc_final: 0.6275 (mptt) REVERT: D 460 PHE cc_start: 0.6993 (m-10) cc_final: 0.6720 (m-10) REVERT: D 467 GLU cc_start: 0.7216 (tt0) cc_final: 0.6702 (mp0) REVERT: G 75 ARG cc_start: 0.7949 (mtp85) cc_final: 0.7653 (ttt180) REVERT: G 104 MET cc_start: 0.6501 (tpp) cc_final: 0.5925 (tpt) REVERT: O 163 ILE cc_start: 0.8444 (mm) cc_final: 0.8206 (tp) outliers start: 3 outliers final: 0 residues processed: 894 average time/residue: 0.2588 time to fit residues: 363.7209 Evaluate side-chains 639 residues out of total 4012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 638 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 373 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 1.9990 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 470 optimal weight: 50.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 45 GLN 8 44 GLN H 111 ASN H 138 ASN K 102 GLN ** K 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 130 ASN K 180 HIS M 34 ASN N 46 GLN N 47 GLN N 61 HIS N 185 ASN ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 32 ASN R 83 HIS S 57 ASN T 31 ASN L 84 ASN A 208 GLN A 349 GLN A 385 GLN ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN B 471 HIS B 475 GLN C 78 ASN C 208 GLN C 385 GLN E 210 ASN E 370 HIS E 388 GLN F 133 GLN F 175 ASN F 197 ASN F 249 GLN F 252 GLN F 296 GLN D 378 GLN D 382 GLN D 419 GLN G 120 HIS G 163 ASN G 202 GLN O 57 ASN O 84 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.133472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.103900 restraints weight = 73760.450| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.59 r_work: 0.3277 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 38546 Z= 0.195 Angle : 0.648 12.416 52151 Z= 0.330 Chirality : 0.045 0.210 6078 Planarity : 0.004 0.065 6644 Dihedral : 6.994 124.829 5440 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.03 % Allowed : 12.67 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.11 % 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 aren not related in a simple way. whole: -1.20 (0.12), residues: 4885 helix: 0.13 (0.10), residues: 2605 sheet: -2.01 (0.19), residues: 579 loop : -1.66 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 113 TYR 0.025 0.002 TYR S 100 PHE 0.033 0.002 PHE T 20 TRP 0.013 0.002 TRP M 53 HIS 0.006 0.001 HIS C 476 Details of bonding type rmsd covalent geometry : bond 0.00441 (38546) covalent geometry : angle 0.64797 (52151) hydrogen bonds : bond 0.05751 ( 2221) hydrogen bonds : angle 5.00939 ( 6459) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 4012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 739 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 75 MET cc_start: 0.7977 (mtp) cc_final: 0.6643 (mmt) REVERT: 7 45 GLN cc_start: 0.8313 (tp40) cc_final: 0.8054 (tp40) REVERT: 7 58 GLU cc_start: 0.8254 (tp30) cc_final: 0.8049 (tp30) REVERT: 1 75 MET cc_start: 0.5576 (mmt) cc_final: 0.5308 (mmm) REVERT: 2 39 ASN cc_start: 0.8461 (t0) cc_final: 0.8102 (t0) REVERT: H 59 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7334 (ptt90) REVERT: H 130 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8082 (tp30) REVERT: H 136 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8630 (mt-10) REVERT: K 134 MET cc_start: 0.8710 (ttm) cc_final: 0.8398 (ttm) REVERT: K 166 ARG cc_start: 0.8792 (ttm110) cc_final: 0.8584 (ptp-170) REVERT: M 51 ILE cc_start: 0.8330 (pt) cc_final: 0.7962 (mt) REVERT: M 151 TYR cc_start: 0.8442 (m-80) cc_final: 0.8224 (m-10) REVERT: N 41 ARG cc_start: 0.8478 (mtt180) cc_final: 0.8241 (mtm-85) REVERT: N 56 GLN cc_start: 0.8623 (tt0) cc_final: 0.8124 (tt0) REVERT: N 145 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8364 (tp30) REVERT: N 152 GLN cc_start: 0.8827 (mt0) cc_final: 0.8346 (mp10) REVERT: P 5 ILE cc_start: 0.7461 (OUTLIER) cc_final: 0.7139 (mm) REVERT: P 39 ARG cc_start: 0.8647 (mtp180) cc_final: 0.8261 (mtp180) REVERT: Q 30 ASN cc_start: 0.8917 (t0) cc_final: 0.8669 (t0) REVERT: S 70 LYS cc_start: 0.7172 (tptt) cc_final: 0.6785 (tptt) REVERT: L 71 LEU cc_start: 0.7680 (pp) cc_final: 0.7436 (pp) REVERT: L 74 GLU cc_start: 0.8459 (tm-30) cc_final: 0.7943 (pp20) REVERT: A 416 GLN cc_start: 0.8155 (tm-30) cc_final: 0.7873 (tm-30) REVERT: A 460 LYS cc_start: 0.8045 (ttmt) cc_final: 0.7741 (ttmt) REVERT: A 463 LYS cc_start: 0.8860 (mtpt) cc_final: 0.8550 (mtpp) REVERT: B 226 MET cc_start: 0.8301 (mmm) cc_final: 0.8021 (tpt) REVERT: B 397 TYR cc_start: 0.8483 (t80) cc_final: 0.8206 (t80) REVERT: B 477 GLN cc_start: 0.7595 (mm-40) cc_final: 0.6934 (tm-30) REVERT: C 45 ARG cc_start: 0.8227 (mmm160) cc_final: 0.7904 (mmm160) REVERT: C 353 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8498 (mt-10) REVERT: E 263 ARG cc_start: 0.7487 (mtt180) cc_final: 0.7167 (mtm-85) REVERT: E 266 GLN cc_start: 0.7869 (mm110) cc_final: 0.7531 (mt0) REVERT: E 347 ILE cc_start: 0.9160 (mm) cc_final: 0.8793 (mm) REVERT: E 384 TYR cc_start: 0.8416 (t80) cc_final: 0.7888 (t80) REVERT: E 458 GLN cc_start: 0.7958 (mm110) cc_final: 0.7466 (tp40) REVERT: D 62 ARG cc_start: 0.8123 (ttm170) cc_final: 0.7741 (ttm-80) REVERT: D 263 ARG cc_start: 0.8391 (mmt-90) cc_final: 0.7867 (mpt180) REVERT: D 297 GLU cc_start: 0.8619 (tp30) cc_final: 0.8254 (tp30) REVERT: D 371 TYR cc_start: 0.7855 (t80) cc_final: 0.7508 (t80) REVERT: D 375 ARG cc_start: 0.8128 (tpp80) cc_final: 0.7825 (tpm170) REVERT: D 433 LYS cc_start: 0.6431 (mmtm) cc_final: 0.5912 (mptt) REVERT: D 460 PHE cc_start: 0.6941 (m-10) cc_final: 0.6631 (m-10) REVERT: D 467 GLU cc_start: 0.7162 (tt0) cc_final: 0.6613 (mp0) REVERT: G 21 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7815 (mtmm) REVERT: G 37 GLU cc_start: 0.7504 (mp0) cc_final: 0.7250 (mp0) REVERT: G 104 MET cc_start: 0.6545 (tpp) cc_final: 0.5794 (tpt) REVERT: O 163 ILE cc_start: 0.8421 (mm) cc_final: 0.8112 (tp) outliers start: 81 outliers final: 44 residues processed: 773 average time/residue: 0.2386 time to fit residues: 295.1081 Evaluate side-chains 689 residues out of total 4012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 642 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 18 VAL Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 62 LEU Chi-restraints excluded: chain 5 residue 21 SER Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 54 PHE Chi-restraints excluded: chain 6 residue 16 VAL Chi-restraints excluded: chain 6 residue 62 LEU Chi-restraints excluded: chain 7 residue 1 ASP Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 7 residue 33 ILE Chi-restraints excluded: chain 8 residue 65 LEU Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 33 ILE Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 3 residue 9 ILE Chi-restraints excluded: chain H residue 59 ARG Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 14 LYS Chi-restraints excluded: chain P residue 25 TRP Chi-restraints excluded: chain Q residue 42 MET Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain S residue 50 GLN Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain G residue 21 LYS Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain O residue 120 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 449 optimal weight: 8.9990 chunk 193 optimal weight: 0.9990 chunk 283 optimal weight: 4.9990 chunk 440 optimal weight: 0.8980 chunk 265 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 321 optimal weight: 7.9990 chunk 474 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 359 optimal weight: 4.9990 chunk 153 optimal weight: 10.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 45 GLN 8 45 GLN ** K 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 122 HIS ** K 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 30 ASN R 83 HIS T 31 ASN A 46 ASN A 208 GLN A 432 GLN ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.131781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.102157 restraints weight = 74063.314| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.58 r_work: 0.3249 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 38546 Z= 0.238 Angle : 0.649 10.830 52151 Z= 0.328 Chirality : 0.045 0.184 6078 Planarity : 0.004 0.047 6644 Dihedral : 6.698 113.127 5436 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.88 % Allowed : 14.73 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.11 % 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 aren not related in a simple way. whole: -0.45 (0.12), residues: 4885 helix: 0.77 (0.10), residues: 2604 sheet: -1.72 (0.20), residues: 578 loop : -1.36 (0.15), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 133 TYR 0.027 0.002 TYR T 32 PHE 0.020 0.002 PHE 4 29 TRP 0.013 0.001 TRP Q 51 HIS 0.013 0.001 HIS K 158 Details of bonding type rmsd covalent geometry : bond 0.00559 (38546) covalent geometry : angle 0.64893 (52151) hydrogen bonds : bond 0.05448 ( 2221) hydrogen bonds : angle 4.78868 ( 6459) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 4012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 675 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 75 MET cc_start: 0.7919 (mtp) cc_final: 0.6879 (mmt) REVERT: 5 60 MET cc_start: 0.8772 (mmp) cc_final: 0.8531 (mmm) REVERT: 6 66 MET cc_start: 0.7938 (ttp) cc_final: 0.6370 (tpt) REVERT: 8 39 ASN cc_start: 0.7986 (t0) cc_final: 0.7767 (t0) REVERT: 1 73 PHE cc_start: 0.8163 (m-10) cc_final: 0.7932 (m-80) REVERT: 1 75 MET cc_start: 0.5402 (mmt) cc_final: 0.5122 (mmm) REVERT: 2 39 ASN cc_start: 0.8490 (t0) cc_final: 0.8118 (t0) REVERT: 2 66 MET cc_start: 0.8821 (tmm) cc_final: 0.8466 (tmm) REVERT: 3 15 THR cc_start: 0.8959 (m) cc_final: 0.8587 (p) REVERT: 3 21 SER cc_start: 0.8350 (t) cc_final: 0.8015 (m) REVERT: H 59 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7370 (ptt90) REVERT: H 139 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8704 (mt-10) REVERT: K 134 MET cc_start: 0.8806 (ttm) cc_final: 0.8415 (ttt) REVERT: M 51 ILE cc_start: 0.8452 (pt) cc_final: 0.8017 (mt) REVERT: M 118 MET cc_start: 0.8646 (tpp) cc_final: 0.8442 (tpp) REVERT: M 151 TYR cc_start: 0.8445 (m-80) cc_final: 0.8224 (m-10) REVERT: N 56 GLN cc_start: 0.8670 (tt0) cc_final: 0.8192 (tt0) REVERT: N 71 MET cc_start: 0.8616 (tpt) cc_final: 0.8110 (tpt) REVERT: N 145 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8303 (mm-30) REVERT: N 152 GLN cc_start: 0.8838 (mt0) cc_final: 0.8388 (mp-120) REVERT: S 53 LYS cc_start: 0.9420 (mttp) cc_final: 0.9109 (mmtp) REVERT: S 70 LYS cc_start: 0.7209 (tptt) cc_final: 0.6808 (tptt) REVERT: S 90 GLU cc_start: 0.8323 (tm-30) cc_final: 0.8120 (tm-30) REVERT: T 41 ARG cc_start: 0.9112 (mtm110) cc_final: 0.8654 (ptt-90) REVERT: A 399 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7671 (pp20) REVERT: A 416 GLN cc_start: 0.8200 (tm-30) cc_final: 0.7892 (tm-30) REVERT: A 460 LYS cc_start: 0.8036 (ttmt) cc_final: 0.7653 (ttmt) REVERT: A 463 LYS cc_start: 0.8858 (mtpt) cc_final: 0.8546 (mtpp) REVERT: B 224 ASP cc_start: 0.8732 (t0) cc_final: 0.8516 (t0) REVERT: B 226 MET cc_start: 0.8410 (mmm) cc_final: 0.8122 (tpt) REVERT: B 397 TYR cc_start: 0.8456 (t80) cc_final: 0.8223 (t80) REVERT: B 477 GLN cc_start: 0.7590 (mm-40) cc_final: 0.6957 (tm-30) REVERT: C 353 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8483 (mt-10) REVERT: E 263 ARG cc_start: 0.7536 (mtt180) cc_final: 0.7283 (mtm-85) REVERT: E 347 ILE cc_start: 0.9205 (mm) cc_final: 0.8839 (mm) REVERT: E 384 TYR cc_start: 0.8396 (t80) cc_final: 0.7890 (t80) REVERT: E 427 PHE cc_start: 0.8216 (t80) cc_final: 0.7992 (t80) REVERT: E 458 GLN cc_start: 0.7877 (mm110) cc_final: 0.7352 (tp40) REVERT: D 62 ARG cc_start: 0.8125 (ttm170) cc_final: 0.7730 (ttm-80) REVERT: D 297 GLU cc_start: 0.8646 (tp30) cc_final: 0.8284 (tp30) REVERT: D 433 LYS cc_start: 0.6424 (mmtm) cc_final: 0.5901 (mptt) REVERT: D 460 PHE cc_start: 0.6871 (m-10) cc_final: 0.6591 (m-10) REVERT: D 467 GLU cc_start: 0.7166 (tt0) cc_final: 0.6597 (mp0) REVERT: G 37 GLU cc_start: 0.7444 (mp0) cc_final: 0.7192 (mp0) REVERT: G 104 MET cc_start: 0.6671 (tpp) cc_final: 0.5943 (tpt) REVERT: G 113 ARG cc_start: 0.8631 (ttp80) cc_final: 0.7835 (ttp80) REVERT: O 163 ILE cc_start: 0.8432 (mm) cc_final: 0.8116 (tp) outliers start: 115 outliers final: 78 residues processed: 737 average time/residue: 0.2529 time to fit residues: 299.1895 Evaluate side-chains 711 residues out of total 4012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 632 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 18 VAL Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 5 residue 16 VAL Chi-restraints excluded: chain 5 residue 21 SER Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 6 residue 18 VAL Chi-restraints excluded: chain 6 residue 62 LEU Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 1 ASP Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 7 residue 33 ILE Chi-restraints excluded: chain 8 residue 27 THR Chi-restraints excluded: chain 8 residue 33 ILE Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 65 LEU Chi-restraints excluded: chain 8 residue 69 PHE Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 33 ILE Chi-restraints excluded: chain 1 residue 67 VAL Chi-restraints excluded: chain 1 residue 72 LEU Chi-restraints excluded: chain 2 residue 16 VAL Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 2 residue 34 ILE Chi-restraints excluded: chain 2 residue 72 LEU Chi-restraints excluded: chain 3 residue 9 ILE Chi-restraints excluded: chain H residue 59 ARG Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain N residue 10 ILE Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 197 ILE Chi-restraints excluded: chain N residue 200 THR Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 25 TRP Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain Q residue 42 MET Chi-restraints excluded: chain Q residue 47 TYR Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain S residue 50 GLN Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain T residue 8 SER Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 284 TYR Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 155 ASP Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 7 optimal weight: 2.9990 chunk 354 optimal weight: 3.9990 chunk 359 optimal weight: 6.9990 chunk 466 optimal weight: 3.9990 chunk 325 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 196 optimal weight: 7.9990 chunk 277 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 433 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 GLN ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 HIS T 31 ASN F 331 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.133070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.103836 restraints weight = 72543.833| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.56 r_work: 0.3264 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 38546 Z= 0.197 Angle : 0.616 11.991 52151 Z= 0.308 Chirality : 0.044 0.154 6078 Planarity : 0.004 0.056 6644 Dihedral : 6.401 108.244 5436 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.65 % Allowed : 16.95 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.11 % 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 aren not related in a simple way. whole: -0.07 (0.12), residues: 4885 helix: 1.07 (0.10), residues: 2616 sheet: -1.55 (0.21), residues: 558 loop : -1.20 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 133 TYR 0.023 0.001 TYR T 32 PHE 0.018 0.001 PHE H 45 TRP 0.010 0.001 TRP K 176 HIS 0.012 0.001 HIS K 158 Details of bonding type rmsd covalent geometry : bond 0.00458 (38546) covalent geometry : angle 0.61579 (52151) hydrogen bonds : bond 0.05056 ( 2221) hydrogen bonds : angle 4.62100 ( 6459) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 4012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 686 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 75 MET cc_start: 0.7942 (mtp) cc_final: 0.6828 (mmt) REVERT: 6 66 MET cc_start: 0.7583 (ttp) cc_final: 0.6096 (tpt) REVERT: 8 39 ASN cc_start: 0.8086 (t0) cc_final: 0.7864 (t0) REVERT: 1 75 MET cc_start: 0.5446 (mmt) cc_final: 0.5116 (mmm) REVERT: 2 39 ASN cc_start: 0.8456 (t0) cc_final: 0.8139 (t0) REVERT: 2 66 MET cc_start: 0.8791 (tmm) cc_final: 0.8400 (tmm) REVERT: H 59 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7383 (ptt90) REVERT: H 130 GLU cc_start: 0.8326 (tm-30) cc_final: 0.8104 (tp30) REVERT: H 136 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8529 (mt-10) REVERT: H 139 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8653 (mt-10) REVERT: M 51 ILE cc_start: 0.8475 (pt) cc_final: 0.8003 (mt) REVERT: M 118 MET cc_start: 0.8606 (tpp) cc_final: 0.8366 (tpp) REVERT: M 151 TYR cc_start: 0.8414 (m-80) cc_final: 0.8186 (m-10) REVERT: N 56 GLN cc_start: 0.8634 (tt0) cc_final: 0.8123 (tt0) REVERT: N 115 MET cc_start: 0.8806 (ppp) cc_final: 0.8595 (ppp) REVERT: N 145 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8293 (mm-30) REVERT: N 152 GLN cc_start: 0.8731 (mt0) cc_final: 0.8380 (mp10) REVERT: S 70 LYS cc_start: 0.7117 (tptt) cc_final: 0.6714 (tptt) REVERT: L 87 MET cc_start: 0.6628 (tpt) cc_final: 0.6399 (mmm) REVERT: A 416 GLN cc_start: 0.8229 (tm-30) cc_final: 0.7909 (tm-30) REVERT: A 463 LYS cc_start: 0.8826 (mtpt) cc_final: 0.8530 (mtpp) REVERT: B 224 ASP cc_start: 0.8768 (t0) cc_final: 0.8535 (t0) REVERT: B 226 MET cc_start: 0.8429 (mmm) cc_final: 0.8168 (tpt) REVERT: B 397 TYR cc_start: 0.8476 (t80) cc_final: 0.8242 (t80) REVERT: B 477 GLN cc_start: 0.7561 (mm-40) cc_final: 0.6960 (tm-30) REVERT: C 45 ARG cc_start: 0.8287 (mmm160) cc_final: 0.7901 (mmm-85) REVERT: C 353 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8442 (mt-10) REVERT: E 263 ARG cc_start: 0.7549 (mtt180) cc_final: 0.7156 (mtm-85) REVERT: E 266 GLN cc_start: 0.7941 (mm110) cc_final: 0.7622 (mt0) REVERT: E 347 ILE cc_start: 0.9208 (mm) cc_final: 0.8816 (mm) REVERT: E 384 TYR cc_start: 0.8399 (t80) cc_final: 0.7908 (t80) REVERT: E 458 GLN cc_start: 0.7846 (mm110) cc_final: 0.7310 (tp40) REVERT: F 398 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7019 (mp0) REVERT: F 430 HIS cc_start: 0.8040 (m-70) cc_final: 0.7821 (m90) REVERT: D 62 ARG cc_start: 0.8091 (ttm170) cc_final: 0.7705 (ttm-80) REVERT: D 297 GLU cc_start: 0.8611 (tp30) cc_final: 0.8247 (tp30) REVERT: D 433 LYS cc_start: 0.6514 (mmtm) cc_final: 0.5962 (mptt) REVERT: D 460 PHE cc_start: 0.6818 (m-10) cc_final: 0.6593 (m-10) REVERT: D 467 GLU cc_start: 0.7199 (tt0) cc_final: 0.6607 (mp0) REVERT: G 37 GLU cc_start: 0.7484 (mp0) cc_final: 0.7227 (mp0) REVERT: O 162 MET cc_start: 0.8411 (ptp) cc_final: 0.8207 (ptp) REVERT: O 163 ILE cc_start: 0.8453 (mm) cc_final: 0.8125 (tp) outliers start: 106 outliers final: 73 residues processed: 742 average time/residue: 0.2141 time to fit residues: 256.0444 Evaluate side-chains 711 residues out of total 4012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 636 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 18 VAL Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 5 residue 16 VAL Chi-restraints excluded: chain 5 residue 21 SER Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 69 PHE Chi-restraints excluded: chain 6 residue 62 LEU Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 1 ASP Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 7 residue 33 ILE Chi-restraints excluded: chain 8 residue 27 THR Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 65 LEU Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain 8 residue 69 PHE Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 32 LEU Chi-restraints excluded: chain 1 residue 33 ILE Chi-restraints excluded: chain 1 residue 67 VAL Chi-restraints excluded: chain 1 residue 72 LEU Chi-restraints excluded: chain 2 residue 16 VAL Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 2 residue 72 LEU Chi-restraints excluded: chain 3 residue 33 ILE Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 3 residue 65 LEU Chi-restraints excluded: chain H residue 59 ARG Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain Q residue 42 MET Chi-restraints excluded: chain Q residue 47 TYR Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 91 LYS Chi-restraints excluded: chain S residue 50 GLN Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 398 GLU Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 284 TYR Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 111 optimal weight: 0.6980 chunk 163 optimal weight: 10.0000 chunk 482 optimal weight: 0.0030 chunk 350 optimal weight: 0.8980 chunk 342 optimal weight: 5.9990 chunk 299 optimal weight: 4.9990 chunk 169 optimal weight: 9.9990 chunk 373 optimal weight: 6.9990 chunk 139 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 390 optimal weight: 0.3980 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 44 GLN K 163 ASN ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 HIS T 31 ASN B 379 GLN D 285 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.134426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.104995 restraints weight = 72747.999| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.58 r_work: 0.3288 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 38546 Z= 0.142 Angle : 0.588 10.795 52151 Z= 0.293 Chirality : 0.043 0.193 6078 Planarity : 0.004 0.048 6644 Dihedral : 6.070 109.141 5436 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.33 % Allowed : 18.53 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.11 % 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 aren not related in a simple way. whole: 0.28 (0.12), residues: 4885 helix: 1.33 (0.10), residues: 2614 sheet: -1.32 (0.21), residues: 577 loop : -1.02 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 133 TYR 0.027 0.001 TYR C 397 PHE 0.020 0.001 PHE T 20 TRP 0.009 0.001 TRP K 176 HIS 0.008 0.001 HIS K 158 Details of bonding type rmsd covalent geometry : bond 0.00317 (38546) covalent geometry : angle 0.58813 (52151) hydrogen bonds : bond 0.04700 ( 2221) hydrogen bonds : angle 4.45700 ( 6459) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 4012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 701 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 66 MET cc_start: 0.7244 (ttp) cc_final: 0.5898 (tpt) REVERT: 8 66 MET cc_start: 0.8010 (ttp) cc_final: 0.7290 (mmt) REVERT: 1 69 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8289 (t80) REVERT: 1 75 MET cc_start: 0.5351 (mmt) cc_final: 0.4986 (mmm) REVERT: 2 39 ASN cc_start: 0.8335 (t0) cc_final: 0.8017 (t0) REVERT: 2 47 PHE cc_start: 0.8513 (t80) cc_final: 0.8195 (t80) REVERT: 2 66 MET cc_start: 0.8731 (tmm) cc_final: 0.8348 (tmm) REVERT: H 25 GLN cc_start: 0.7862 (tm-30) cc_final: 0.7252 (tm-30) REVERT: H 59 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7349 (ptt90) REVERT: H 136 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8512 (mt-10) REVERT: H 139 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8593 (mt-10) REVERT: K 134 MET cc_start: 0.8607 (ttm) cc_final: 0.8271 (ttt) REVERT: K 156 ASP cc_start: 0.9252 (m-30) cc_final: 0.8788 (p0) REVERT: M 51 ILE cc_start: 0.8488 (pt) cc_final: 0.8022 (mt) REVERT: M 151 TYR cc_start: 0.8416 (m-80) cc_final: 0.8181 (m-10) REVERT: N 56 GLN cc_start: 0.8606 (tt0) cc_final: 0.8118 (tt0) REVERT: N 145 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8259 (mm-30) REVERT: N 152 GLN cc_start: 0.8689 (mt0) cc_final: 0.8403 (mp10) REVERT: P 7 LYS cc_start: 0.8690 (tttt) cc_final: 0.8370 (mttt) REVERT: P 19 LYS cc_start: 0.9127 (mptt) cc_final: 0.8885 (mmtm) REVERT: Q 43 LYS cc_start: 0.7787 (tmtt) cc_final: 0.7561 (mtmt) REVERT: S 57 ASN cc_start: 0.9291 (m110) cc_final: 0.8920 (p0) REVERT: S 70 LYS cc_start: 0.6971 (tptt) cc_final: 0.6581 (tptt) REVERT: L 41 LYS cc_start: 0.8461 (tptt) cc_final: 0.8122 (tptp) REVERT: L 74 GLU cc_start: 0.8286 (pp20) cc_final: 0.7879 (pp20) REVERT: L 87 MET cc_start: 0.6666 (tpt) cc_final: 0.6098 (mmm) REVERT: A 399 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7551 (pp20) REVERT: A 416 GLN cc_start: 0.8205 (tm-30) cc_final: 0.7879 (tm-30) REVERT: A 463 LYS cc_start: 0.8838 (mtpt) cc_final: 0.8554 (mtpp) REVERT: B 224 ASP cc_start: 0.8751 (t0) cc_final: 0.8505 (t0) REVERT: B 397 TYR cc_start: 0.8498 (t80) cc_final: 0.8261 (t80) REVERT: B 415 GLN cc_start: 0.7368 (mt0) cc_final: 0.6823 (mm-40) REVERT: B 477 GLN cc_start: 0.7578 (mm-40) cc_final: 0.6956 (tm-30) REVERT: C 45 ARG cc_start: 0.8263 (mmm160) cc_final: 0.7882 (mmm-85) REVERT: C 143 ARG cc_start: 0.7513 (mtm110) cc_final: 0.7185 (mtm180) REVERT: C 353 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8411 (mt-10) REVERT: E 263 ARG cc_start: 0.7466 (mtt180) cc_final: 0.6952 (mtm-85) REVERT: E 266 GLN cc_start: 0.7846 (mm110) cc_final: 0.7558 (mt0) REVERT: E 347 ILE cc_start: 0.9202 (mm) cc_final: 0.8793 (mm) REVERT: E 384 TYR cc_start: 0.8400 (t80) cc_final: 0.7833 (t80) REVERT: E 458 GLN cc_start: 0.7886 (mm110) cc_final: 0.7305 (tp40) REVERT: E 462 MET cc_start: 0.8574 (mmt) cc_final: 0.8328 (mmm) REVERT: F 398 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.6994 (mp0) REVERT: F 430 HIS cc_start: 0.8015 (m-70) cc_final: 0.7776 (m90) REVERT: D 62 ARG cc_start: 0.8029 (ttm170) cc_final: 0.7660 (ttm-80) REVERT: D 284 TYR cc_start: 0.7903 (OUTLIER) cc_final: 0.7271 (m-10) REVERT: D 297 GLU cc_start: 0.8566 (tp30) cc_final: 0.8213 (tp30) REVERT: D 460 PHE cc_start: 0.6812 (m-10) cc_final: 0.6569 (m-10) REVERT: D 467 GLU cc_start: 0.7141 (tt0) cc_final: 0.6583 (mp0) REVERT: G 37 GLU cc_start: 0.7463 (mp0) cc_final: 0.7181 (mp0) REVERT: G 113 ARG cc_start: 0.8642 (ttp80) cc_final: 0.7817 (ttp80) REVERT: O 163 ILE cc_start: 0.8452 (mm) cc_final: 0.8127 (tp) outliers start: 93 outliers final: 68 residues processed: 751 average time/residue: 0.2121 time to fit residues: 258.4390 Evaluate side-chains 716 residues out of total 4012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 644 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 18 VAL Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 62 LEU Chi-restraints excluded: chain 5 residue 16 VAL Chi-restraints excluded: chain 5 residue 21 SER Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 54 PHE Chi-restraints excluded: chain 5 residue 69 PHE Chi-restraints excluded: chain 5 residue 71 ILE Chi-restraints excluded: chain 6 residue 62 LEU Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 1 ASP Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 65 LEU Chi-restraints excluded: chain 8 residue 69 PHE Chi-restraints excluded: chain 1 residue 32 LEU Chi-restraints excluded: chain 1 residue 33 ILE Chi-restraints excluded: chain 1 residue 69 PHE Chi-restraints excluded: chain 1 residue 72 LEU Chi-restraints excluded: chain 2 residue 16 VAL Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 2 residue 72 LEU Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain H residue 59 ARG Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain Q residue 42 MET Chi-restraints excluded: chain Q residue 47 TYR Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 91 LYS Chi-restraints excluded: chain S residue 50 GLN Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 379 GLN Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 398 GLU Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 284 TYR Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 155 ASP Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 80 optimal weight: 1.9990 chunk 431 optimal weight: 2.9990 chunk 253 optimal weight: 1.9990 chunk 355 optimal weight: 8.9990 chunk 221 optimal weight: 0.9980 chunk 281 optimal weight: 3.9990 chunk 191 optimal weight: 10.0000 chunk 277 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 chunk 478 optimal weight: 20.0000 chunk 293 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 46 ASN R 83 HIS A 208 GLN E 174 ASN D 260 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.133801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.104384 restraints weight = 73041.336| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.58 r_work: 0.3278 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 38546 Z= 0.168 Angle : 0.608 12.963 52151 Z= 0.301 Chirality : 0.044 0.204 6078 Planarity : 0.004 0.054 6644 Dihedral : 5.985 107.153 5436 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.48 % Favored : 97.50 % Rotamer: Outliers : 3.01 % Allowed : 18.66 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.11 % 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 aren not related in a simple way. whole: 0.39 (0.12), residues: 4885 helix: 1.41 (0.10), residues: 2608 sheet: -1.25 (0.21), residues: 557 loop : -0.95 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 133 TYR 0.027 0.001 TYR C 397 PHE 0.019 0.001 PHE 4 29 TRP 0.012 0.001 TRP P 10 HIS 0.007 0.001 HIS C 476 Details of bonding type rmsd covalent geometry : bond 0.00388 (38546) covalent geometry : angle 0.60847 (52151) hydrogen bonds : bond 0.04710 ( 2221) hydrogen bonds : angle 4.44659 ( 6459) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 4012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 677 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 66 MET cc_start: 0.7192 (ttp) cc_final: 0.5916 (tpt) REVERT: 7 58 GLU cc_start: 0.8137 (tp30) cc_final: 0.7889 (tp30) REVERT: 8 39 ASN cc_start: 0.8179 (t0) cc_final: 0.7942 (t0) REVERT: 8 66 MET cc_start: 0.8048 (ttp) cc_final: 0.7194 (mmt) REVERT: 1 69 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.8283 (t80) REVERT: 1 75 MET cc_start: 0.5434 (mmt) cc_final: 0.5048 (mmm) REVERT: 2 39 ASN cc_start: 0.8365 (t0) cc_final: 0.8068 (t0) REVERT: 2 47 PHE cc_start: 0.8548 (t80) cc_final: 0.8226 (t80) REVERT: 3 21 SER cc_start: 0.8463 (t) cc_final: 0.8157 (m) REVERT: H 25 GLN cc_start: 0.7887 (tm-30) cc_final: 0.7422 (tm-30) REVERT: H 59 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7350 (ptt90) REVERT: H 130 GLU cc_start: 0.8298 (tm-30) cc_final: 0.8037 (tp30) REVERT: H 136 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8536 (mt-10) REVERT: H 139 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8607 (mt-10) REVERT: K 134 MET cc_start: 0.8772 (ttm) cc_final: 0.8388 (ttt) REVERT: K 156 ASP cc_start: 0.9240 (m-30) cc_final: 0.8796 (p0) REVERT: M 151 TYR cc_start: 0.8432 (m-80) cc_final: 0.8190 (m-10) REVERT: N 56 GLN cc_start: 0.8612 (tt0) cc_final: 0.8101 (tt0) REVERT: N 145 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8260 (mm-30) REVERT: N 152 GLN cc_start: 0.8709 (mt0) cc_final: 0.8491 (mp10) REVERT: P 7 LYS cc_start: 0.8720 (tttt) cc_final: 0.8363 (mttt) REVERT: P 19 LYS cc_start: 0.9125 (mptt) cc_final: 0.8866 (mmtt) REVERT: S 50 GLN cc_start: 0.9260 (OUTLIER) cc_final: 0.8399 (mp10) REVERT: T 41 ARG cc_start: 0.8683 (ptp-170) cc_final: 0.8063 (ptt-90) REVERT: L 87 MET cc_start: 0.6669 (tpt) cc_final: 0.6120 (tmm) REVERT: A 416 GLN cc_start: 0.8256 (tm-30) cc_final: 0.7932 (tm-30) REVERT: A 463 LYS cc_start: 0.8835 (mtpt) cc_final: 0.8553 (mtpp) REVERT: B 224 ASP cc_start: 0.8754 (t0) cc_final: 0.8497 (t0) REVERT: B 397 TYR cc_start: 0.8489 (t80) cc_final: 0.8253 (t80) REVERT: B 415 GLN cc_start: 0.7423 (mt0) cc_final: 0.6860 (mm-40) REVERT: B 477 GLN cc_start: 0.7592 (mm-40) cc_final: 0.6975 (tm-30) REVERT: C 45 ARG cc_start: 0.8256 (mmm160) cc_final: 0.7870 (mmm-85) REVERT: C 353 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8421 (mt-10) REVERT: E 263 ARG cc_start: 0.7265 (mtt180) cc_final: 0.6959 (mtm-85) REVERT: E 266 GLN cc_start: 0.7838 (mm110) cc_final: 0.7542 (mt0) REVERT: E 347 ILE cc_start: 0.9215 (mm) cc_final: 0.8811 (mm) REVERT: E 384 TYR cc_start: 0.8398 (t80) cc_final: 0.7826 (t80) REVERT: E 458 GLN cc_start: 0.7893 (mm110) cc_final: 0.7291 (tp40) REVERT: F 70 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8287 (pt0) REVERT: F 129 MET cc_start: 0.9203 (mmt) cc_final: 0.8774 (mmt) REVERT: F 398 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.6922 (mp0) REVERT: F 430 HIS cc_start: 0.8000 (m-70) cc_final: 0.7783 (m90) REVERT: D 62 ARG cc_start: 0.8047 (ttm170) cc_final: 0.7664 (ttm-80) REVERT: D 128 GLU cc_start: 0.8373 (tt0) cc_final: 0.7993 (mt-10) REVERT: D 284 TYR cc_start: 0.8134 (OUTLIER) cc_final: 0.7423 (m-10) REVERT: D 297 GLU cc_start: 0.8531 (tp30) cc_final: 0.8175 (tp30) REVERT: D 433 LYS cc_start: 0.6464 (mmtt) cc_final: 0.5748 (mppt) REVERT: D 460 PHE cc_start: 0.6810 (m-10) cc_final: 0.6558 (m-10) REVERT: D 467 GLU cc_start: 0.7168 (tt0) cc_final: 0.6588 (mp0) REVERT: G 37 GLU cc_start: 0.7451 (mp0) cc_final: 0.7158 (mp0) REVERT: O 108 MET cc_start: 0.5603 (mtp) cc_final: 0.5403 (mtp) REVERT: O 113 ARG cc_start: 0.6328 (ptp-170) cc_final: 0.5982 (ptp-110) REVERT: O 163 ILE cc_start: 0.8464 (mm) cc_final: 0.8131 (tp) outliers start: 120 outliers final: 91 residues processed: 746 average time/residue: 0.2188 time to fit residues: 265.0903 Evaluate side-chains 736 residues out of total 4012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 639 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 18 VAL Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 71 ILE Chi-restraints excluded: chain 5 residue 16 VAL Chi-restraints excluded: chain 5 residue 21 SER Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 69 PHE Chi-restraints excluded: chain 5 residue 71 ILE Chi-restraints excluded: chain 6 residue 33 ILE Chi-restraints excluded: chain 6 residue 62 LEU Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 1 ASP Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 7 residue 33 ILE Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 65 LEU Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 32 LEU Chi-restraints excluded: chain 1 residue 33 ILE Chi-restraints excluded: chain 1 residue 69 PHE Chi-restraints excluded: chain 1 residue 72 LEU Chi-restraints excluded: chain 2 residue 16 VAL Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 2 residue 72 LEU Chi-restraints excluded: chain 3 residue 33 ILE Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 3 residue 65 LEU Chi-restraints excluded: chain H residue 59 ARG Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain N residue 174 ILE Chi-restraints excluded: chain N residue 197 ILE Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain Q residue 42 MET Chi-restraints excluded: chain Q residue 47 TYR Chi-restraints excluded: chain Q residue 51 TRP Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 91 LYS Chi-restraints excluded: chain S residue 50 GLN Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain T residue 38 GLU Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 398 GLU Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 284 TYR Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 134 LEU Chi-restraints excluded: chain O residue 155 ASP Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 178 optimal weight: 0.9980 chunk 337 optimal weight: 1.9990 chunk 242 optimal weight: 5.9990 chunk 300 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 327 optimal weight: 0.7980 chunk 370 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 134 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 103 HIS ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 HIS O 87 ASN O 112 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.135303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.105867 restraints weight = 72763.013| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.58 r_work: 0.3302 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 38546 Z= 0.132 Angle : 0.601 12.639 52151 Z= 0.295 Chirality : 0.043 0.179 6078 Planarity : 0.004 0.079 6644 Dihedral : 5.779 100.582 5436 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.31 % Favored : 97.67 % Rotamer: Outliers : 2.70 % Allowed : 19.71 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.11 % 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 aren not related in a simple way. whole: 0.56 (0.12), residues: 4885 helix: 1.52 (0.10), residues: 2612 sheet: -1.14 (0.22), residues: 548 loop : -0.83 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG L 73 TYR 0.024 0.001 TYR C 397 PHE 0.019 0.001 PHE M 15 TRP 0.010 0.001 TRP P 10 HIS 0.006 0.001 HIS C 476 Details of bonding type rmsd covalent geometry : bond 0.00293 (38546) covalent geometry : angle 0.60108 (52151) hydrogen bonds : bond 0.04445 ( 2221) hydrogen bonds : angle 4.35821 ( 6459) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 4012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 689 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 63 PHE cc_start: 0.7152 (m-80) cc_final: 0.6946 (m-80) REVERT: 6 66 MET cc_start: 0.6997 (ttp) cc_final: 0.5813 (tpt) REVERT: 7 58 GLU cc_start: 0.8110 (tp30) cc_final: 0.7877 (tp30) REVERT: 8 66 MET cc_start: 0.8039 (ttp) cc_final: 0.7187 (mmt) REVERT: 1 69 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8214 (t80) REVERT: 1 75 MET cc_start: 0.5431 (mmt) cc_final: 0.5025 (mmm) REVERT: 2 39 ASN cc_start: 0.8291 (t0) cc_final: 0.7988 (t0) REVERT: 2 47 PHE cc_start: 0.8527 (t80) cc_final: 0.8201 (t80) REVERT: 2 66 MET cc_start: 0.8738 (tmm) cc_final: 0.8432 (tmm) REVERT: 3 21 SER cc_start: 0.8438 (t) cc_final: 0.8123 (m) REVERT: H 25 GLN cc_start: 0.7871 (tm-30) cc_final: 0.7406 (tm-30) REVERT: H 59 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7334 (ptt90) REVERT: H 130 GLU cc_start: 0.8300 (tm-30) cc_final: 0.8063 (tp30) REVERT: H 136 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8534 (mt-10) REVERT: H 139 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8601 (mt-10) REVERT: K 134 MET cc_start: 0.8752 (ttm) cc_final: 0.8506 (ttm) REVERT: K 156 ASP cc_start: 0.9229 (m-30) cc_final: 0.8763 (p0) REVERT: M 151 TYR cc_start: 0.8409 (m-80) cc_final: 0.8182 (m-10) REVERT: N 56 GLN cc_start: 0.8575 (tt0) cc_final: 0.8082 (tt0) REVERT: N 140 MET cc_start: 0.8315 (pmm) cc_final: 0.8065 (pmm) REVERT: N 145 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8208 (mm-30) REVERT: N 152 GLN cc_start: 0.8802 (mt0) cc_final: 0.8411 (mp10) REVERT: P 7 LYS cc_start: 0.8742 (tttt) cc_final: 0.8323 (mttt) REVERT: P 19 LYS cc_start: 0.9094 (mptt) cc_final: 0.8823 (mmtt) REVERT: Q 12 MET cc_start: 0.9136 (mmt) cc_final: 0.8600 (mmt) REVERT: R 88 ARG cc_start: 0.8545 (ptp-110) cc_final: 0.8300 (mtt-85) REVERT: L 41 LYS cc_start: 0.8318 (tptt) cc_final: 0.7876 (tptp) REVERT: L 87 MET cc_start: 0.6784 (tpt) cc_final: 0.6335 (mmm) REVERT: A 399 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7554 (pp20) REVERT: A 416 GLN cc_start: 0.8216 (tm-30) cc_final: 0.7892 (tm-30) REVERT: A 463 LYS cc_start: 0.8835 (mtpt) cc_final: 0.8553 (mtpp) REVERT: B 224 ASP cc_start: 0.8750 (t0) cc_final: 0.8490 (t0) REVERT: B 397 TYR cc_start: 0.8499 (t80) cc_final: 0.8271 (t80) REVERT: B 415 GLN cc_start: 0.7512 (mt0) cc_final: 0.6926 (mm-40) REVERT: B 475 GLN cc_start: 0.7408 (mp10) cc_final: 0.6916 (mp10) REVERT: B 477 GLN cc_start: 0.7608 (mm-40) cc_final: 0.6969 (tm-30) REVERT: C 45 ARG cc_start: 0.8233 (mmm160) cc_final: 0.7843 (mmm-85) REVERT: C 143 ARG cc_start: 0.7533 (mtm110) cc_final: 0.7231 (mtm180) REVERT: C 353 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8410 (mt-10) REVERT: E 263 ARG cc_start: 0.7237 (mtt180) cc_final: 0.6958 (mtm-85) REVERT: E 266 GLN cc_start: 0.7844 (mm110) cc_final: 0.7567 (mt0) REVERT: E 347 ILE cc_start: 0.9217 (mm) cc_final: 0.8810 (mm) REVERT: E 384 TYR cc_start: 0.8426 (t80) cc_final: 0.7861 (t80) REVERT: E 458 GLN cc_start: 0.7931 (mm110) cc_final: 0.7293 (tp40) REVERT: E 462 MET cc_start: 0.8554 (mmt) cc_final: 0.8275 (mmm) REVERT: F 70 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8294 (pt0) REVERT: F 129 MET cc_start: 0.9162 (mmt) cc_final: 0.8729 (mmt) REVERT: F 398 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.6946 (mp0) REVERT: F 430 HIS cc_start: 0.8000 (m-70) cc_final: 0.7780 (m90) REVERT: D 129 MET cc_start: 0.8776 (mmt) cc_final: 0.8387 (mmm) REVERT: D 263 ARG cc_start: 0.8211 (mmt-90) cc_final: 0.7841 (mpt180) REVERT: D 284 TYR cc_start: 0.8254 (OUTLIER) cc_final: 0.7445 (m-10) REVERT: D 297 GLU cc_start: 0.8482 (tp30) cc_final: 0.8134 (tp30) REVERT: D 433 LYS cc_start: 0.6499 (mmtt) cc_final: 0.5823 (mppt) REVERT: D 460 PHE cc_start: 0.6785 (m-10) cc_final: 0.6533 (m-10) REVERT: D 467 GLU cc_start: 0.7149 (tt0) cc_final: 0.6599 (mp0) REVERT: G 37 GLU cc_start: 0.7534 (mp0) cc_final: 0.7255 (mp0) REVERT: G 113 ARG cc_start: 0.8619 (ttp80) cc_final: 0.7877 (ttp80) REVERT: O 113 ARG cc_start: 0.6316 (ptp-170) cc_final: 0.5983 (ptp-110) REVERT: O 163 ILE cc_start: 0.8449 (mm) cc_final: 0.8110 (tp) REVERT: O 180 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8880 (mm-40) outliers start: 108 outliers final: 84 residues processed: 750 average time/residue: 0.2301 time to fit residues: 279.6203 Evaluate side-chains 735 residues out of total 4012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 646 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 18 VAL Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 5 residue 15 THR Chi-restraints excluded: chain 5 residue 16 VAL Chi-restraints excluded: chain 5 residue 21 SER Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 54 PHE Chi-restraints excluded: chain 5 residue 69 PHE Chi-restraints excluded: chain 5 residue 71 ILE Chi-restraints excluded: chain 6 residue 62 LEU Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 1 ASP Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 8 residue 16 VAL Chi-restraints excluded: chain 8 residue 33 ILE Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 65 LEU Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain 8 residue 69 PHE Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 32 LEU Chi-restraints excluded: chain 1 residue 33 ILE Chi-restraints excluded: chain 1 residue 69 PHE Chi-restraints excluded: chain 1 residue 72 LEU Chi-restraints excluded: chain 2 residue 16 VAL Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 2 residue 72 LEU Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 3 residue 70 LEU Chi-restraints excluded: chain H residue 59 ARG Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 68 ASP Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 91 LYS Chi-restraints excluded: chain S residue 50 GLN Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain T residue 38 GLU Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 398 GLU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 284 TYR Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 134 LEU Chi-restraints excluded: chain O residue 155 ASP Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 466 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 323 optimal weight: 4.9990 chunk 193 optimal weight: 0.7980 chunk 267 optimal weight: 3.9990 chunk 238 optimal weight: 0.7980 chunk 177 optimal weight: 0.9980 chunk 232 optimal weight: 3.9990 chunk 138 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 44 GLN ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 HIS F 174 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.135616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.105917 restraints weight = 72622.260| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.57 r_work: 0.3318 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 38546 Z= 0.125 Angle : 0.600 13.975 52151 Z= 0.294 Chirality : 0.043 0.280 6078 Planarity : 0.004 0.058 6644 Dihedral : 5.585 88.578 5436 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.15 % Favored : 97.83 % Rotamer: Outliers : 2.60 % Allowed : 20.46 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.11 % 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 aren not related in a simple way. whole: 0.72 (0.12), residues: 4885 helix: 1.61 (0.10), residues: 2605 sheet: -1.02 (0.22), residues: 559 loop : -0.71 (0.15), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG T 41 TYR 0.023 0.001 TYR C 397 PHE 0.039 0.001 PHE 4 54 TRP 0.009 0.001 TRP P 10 HIS 0.006 0.001 HIS C 476 Details of bonding type rmsd covalent geometry : bond 0.00272 (38546) covalent geometry : angle 0.59954 (52151) hydrogen bonds : bond 0.04318 ( 2221) hydrogen bonds : angle 4.30535 ( 6459) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 4012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 696 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 63 PHE cc_start: 0.7188 (m-80) cc_final: 0.6913 (m-80) REVERT: 6 66 MET cc_start: 0.6781 (ttp) cc_final: 0.5636 (tpt) REVERT: 7 58 GLU cc_start: 0.8051 (tp30) cc_final: 0.7826 (mm-30) REVERT: 8 45 GLN cc_start: 0.6820 (tp40) cc_final: 0.6375 (tp-100) REVERT: 8 66 MET cc_start: 0.8025 (ttp) cc_final: 0.7227 (mmt) REVERT: 1 69 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.8212 (t80) REVERT: 1 75 MET cc_start: 0.5431 (mmt) cc_final: 0.5151 (mmm) REVERT: 2 39 ASN cc_start: 0.8243 (t0) cc_final: 0.7938 (t0) REVERT: 2 44 GLN cc_start: 0.8119 (pm20) cc_final: 0.7838 (tm-30) REVERT: 2 47 PHE cc_start: 0.8523 (t80) cc_final: 0.8192 (t80) REVERT: 2 66 MET cc_start: 0.8749 (tmm) cc_final: 0.8454 (tmm) REVERT: 3 21 SER cc_start: 0.8443 (t) cc_final: 0.8121 (m) REVERT: 3 65 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8512 (mm) REVERT: H 25 GLN cc_start: 0.7871 (tm-30) cc_final: 0.7395 (tm-30) REVERT: H 59 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7314 (ptt90) REVERT: H 130 GLU cc_start: 0.8288 (tm-30) cc_final: 0.8047 (tp30) REVERT: H 136 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8546 (mt-10) REVERT: H 139 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8638 (mt-10) REVERT: K 134 MET cc_start: 0.8764 (ttm) cc_final: 0.8376 (ttt) REVERT: K 146 ARG cc_start: 0.8063 (ttp80) cc_final: 0.7829 (ttp80) REVERT: M 151 TYR cc_start: 0.8376 (m-80) cc_final: 0.8173 (m-10) REVERT: N 56 GLN cc_start: 0.8593 (tt0) cc_final: 0.8121 (tt0) REVERT: N 145 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8179 (mm-30) REVERT: N 152 GLN cc_start: 0.8730 (mt0) cc_final: 0.8449 (mp10) REVERT: P 19 LYS cc_start: 0.9096 (mptt) cc_final: 0.8813 (mmtt) REVERT: Q 12 MET cc_start: 0.9117 (mmt) cc_final: 0.8569 (mmt) REVERT: L 87 MET cc_start: 0.6804 (tpt) cc_final: 0.6377 (mmm) REVERT: A 52 MET cc_start: 0.8525 (ttp) cc_final: 0.8255 (ttp) REVERT: A 54 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7101 (tm-30) REVERT: A 399 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7537 (pp20) REVERT: A 416 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7900 (tm-30) REVERT: A 463 LYS cc_start: 0.8890 (mtpt) cc_final: 0.8636 (mtpp) REVERT: B 224 ASP cc_start: 0.8751 (t0) cc_final: 0.8489 (t0) REVERT: B 397 TYR cc_start: 0.8515 (t80) cc_final: 0.8305 (t80) REVERT: B 415 GLN cc_start: 0.7555 (mt0) cc_final: 0.6959 (mm-40) REVERT: B 475 GLN cc_start: 0.7377 (mp10) cc_final: 0.6890 (mp10) REVERT: B 477 GLN cc_start: 0.7626 (mm-40) cc_final: 0.6989 (tm-30) REVERT: C 45 ARG cc_start: 0.8227 (mmm160) cc_final: 0.7847 (mmm-85) REVERT: C 353 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8453 (mt-10) REVERT: E 263 ARG cc_start: 0.7189 (mtt180) cc_final: 0.6957 (mtm-85) REVERT: E 266 GLN cc_start: 0.7857 (mm110) cc_final: 0.7588 (mt0) REVERT: E 291 ASP cc_start: 0.7715 (m-30) cc_final: 0.7292 (m-30) REVERT: E 347 ILE cc_start: 0.9221 (mm) cc_final: 0.8815 (mm) REVERT: E 384 TYR cc_start: 0.8474 (t80) cc_final: 0.7938 (t80) REVERT: E 458 GLN cc_start: 0.7920 (mm110) cc_final: 0.7253 (tp40) REVERT: E 462 MET cc_start: 0.8491 (mmt) cc_final: 0.8258 (mmm) REVERT: F 70 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8282 (pt0) REVERT: F 129 MET cc_start: 0.9128 (mmt) cc_final: 0.8672 (mmt) REVERT: F 398 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.6861 (mp0) REVERT: F 430 HIS cc_start: 0.7987 (m-70) cc_final: 0.7769 (m90) REVERT: D 103 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8105 (mm-30) REVERT: D 284 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.7459 (m-10) REVERT: D 297 GLU cc_start: 0.8461 (tp30) cc_final: 0.8125 (tp30) REVERT: D 433 LYS cc_start: 0.6587 (mmtt) cc_final: 0.6025 (mptt) REVERT: D 460 PHE cc_start: 0.6748 (m-10) cc_final: 0.6498 (m-10) REVERT: D 467 GLU cc_start: 0.7074 (tt0) cc_final: 0.6552 (mp0) REVERT: G 37 GLU cc_start: 0.7529 (mp0) cc_final: 0.7238 (mp0) REVERT: G 66 HIS cc_start: 0.7642 (t70) cc_final: 0.7247 (t-90) REVERT: G 113 ARG cc_start: 0.8599 (ttp80) cc_final: 0.7873 (ttp80) REVERT: O 113 ARG cc_start: 0.6227 (ptp-170) cc_final: 0.5919 (ptp-110) REVERT: O 163 ILE cc_start: 0.8469 (mm) cc_final: 0.8149 (tp) REVERT: O 180 GLN cc_start: 0.9213 (mm-40) cc_final: 0.8856 (mm-40) outliers start: 104 outliers final: 79 residues processed: 755 average time/residue: 0.2231 time to fit residues: 272.9190 Evaluate side-chains 746 residues out of total 4012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 661 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 18 VAL Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 5 residue 15 THR Chi-restraints excluded: chain 5 residue 16 VAL Chi-restraints excluded: chain 5 residue 21 SER Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 54 PHE Chi-restraints excluded: chain 5 residue 71 ILE Chi-restraints excluded: chain 6 residue 62 LEU Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 65 LEU Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain 8 residue 69 PHE Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 32 LEU Chi-restraints excluded: chain 1 residue 33 ILE Chi-restraints excluded: chain 1 residue 62 LEU Chi-restraints excluded: chain 1 residue 69 PHE Chi-restraints excluded: chain 1 residue 72 LEU Chi-restraints excluded: chain 2 residue 16 VAL Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 2 residue 72 LEU Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 3 residue 65 LEU Chi-restraints excluded: chain H residue 59 ARG Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 68 ASP Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 91 LYS Chi-restraints excluded: chain S residue 50 GLN Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain T residue 38 GLU Chi-restraints excluded: chain T residue 41 ARG Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain E residue 225 MET Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 398 GLU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 284 TYR Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 155 ASP Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 429 optimal weight: 6.9990 chunk 228 optimal weight: 5.9990 chunk 445 optimal weight: 5.9990 chunk 411 optimal weight: 3.9990 chunk 274 optimal weight: 3.9990 chunk 190 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 99 optimal weight: 0.3980 chunk 94 optimal weight: 10.0000 chunk 409 optimal weight: 3.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 31 ASN A 208 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.133792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.103885 restraints weight = 73524.389| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.58 r_work: 0.3289 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 38546 Z= 0.172 Angle : 0.641 13.638 52151 Z= 0.314 Chirality : 0.044 0.247 6078 Planarity : 0.004 0.059 6644 Dihedral : 5.600 88.701 5436 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.50 % Favored : 97.48 % Rotamer: Outliers : 2.45 % Allowed : 21.11 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.11 % 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 aren not related in a simple way. whole: 0.65 (0.12), residues: 4885 helix: 1.54 (0.10), residues: 2612 sheet: -1.03 (0.21), residues: 563 loop : -0.72 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG T 42 TYR 0.029 0.001 TYR C 397 PHE 0.031 0.001 PHE 4 54 TRP 0.012 0.001 TRP P 10 HIS 0.016 0.001 HIS C 476 Details of bonding type rmsd covalent geometry : bond 0.00402 (38546) covalent geometry : angle 0.64055 (52151) hydrogen bonds : bond 0.04539 ( 2221) hydrogen bonds : angle 4.38713 ( 6459) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 4012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 657 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 63 PHE cc_start: 0.7250 (m-80) cc_final: 0.6937 (m-80) REVERT: 6 66 MET cc_start: 0.6741 (ttp) cc_final: 0.5701 (tpt) REVERT: 7 58 GLU cc_start: 0.8100 (tp30) cc_final: 0.7874 (mm-30) REVERT: 8 45 GLN cc_start: 0.6937 (tp40) cc_final: 0.6412 (tp-100) REVERT: 8 66 MET cc_start: 0.8035 (ttp) cc_final: 0.7268 (mmt) REVERT: 1 69 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.8234 (t80) REVERT: 1 75 MET cc_start: 0.5496 (mmt) cc_final: 0.5213 (mmm) REVERT: 2 39 ASN cc_start: 0.8369 (t0) cc_final: 0.8084 (t0) REVERT: 2 44 GLN cc_start: 0.8183 (pm20) cc_final: 0.7888 (tm-30) REVERT: 2 47 PHE cc_start: 0.8526 (t80) cc_final: 0.8174 (t80) REVERT: 2 66 MET cc_start: 0.8764 (tmm) cc_final: 0.8465 (tmm) REVERT: 3 21 SER cc_start: 0.8490 (t) cc_final: 0.8170 (m) REVERT: H 25 GLN cc_start: 0.7903 (tm-30) cc_final: 0.7425 (tm-30) REVERT: H 59 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7364 (ptt90) REVERT: H 136 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8536 (mt-10) REVERT: H 139 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8653 (mt-10) REVERT: K 134 MET cc_start: 0.8801 (ttm) cc_final: 0.8400 (ttt) REVERT: N 56 GLN cc_start: 0.8610 (tt0) cc_final: 0.8133 (tt0) REVERT: N 145 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8211 (mm-30) REVERT: N 152 GLN cc_start: 0.8705 (mt0) cc_final: 0.8417 (mp10) REVERT: S 47 ARG cc_start: 0.8889 (tpm170) cc_final: 0.7366 (tpm170) REVERT: S 50 GLN cc_start: 0.9315 (OUTLIER) cc_final: 0.9087 (pp30) REVERT: S 70 LYS cc_start: 0.7159 (tptt) cc_final: 0.6802 (tptt) REVERT: T 42 ARG cc_start: 0.8138 (mmp80) cc_final: 0.7880 (mmp80) REVERT: L 41 LYS cc_start: 0.8404 (tptt) cc_final: 0.7966 (tptp) REVERT: L 87 MET cc_start: 0.6786 (tpt) cc_final: 0.6381 (mmm) REVERT: A 52 MET cc_start: 0.8584 (ttp) cc_final: 0.8331 (ttp) REVERT: A 399 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7574 (pp20) REVERT: A 416 GLN cc_start: 0.8209 (tm-30) cc_final: 0.7876 (tm-30) REVERT: A 463 LYS cc_start: 0.8829 (mtpt) cc_final: 0.8568 (mtpp) REVERT: B 224 ASP cc_start: 0.8774 (t0) cc_final: 0.8516 (t0) REVERT: B 397 TYR cc_start: 0.8536 (t80) cc_final: 0.8329 (t80) REVERT: B 415 GLN cc_start: 0.7549 (mt0) cc_final: 0.6972 (mm-40) REVERT: B 475 GLN cc_start: 0.7392 (mp10) cc_final: 0.6908 (mp10) REVERT: B 477 GLN cc_start: 0.7643 (mm-40) cc_final: 0.7001 (tm-30) REVERT: C 45 ARG cc_start: 0.8253 (mmm160) cc_final: 0.7856 (mmm-85) REVERT: C 353 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8416 (mt-10) REVERT: E 263 ARG cc_start: 0.7239 (mtt180) cc_final: 0.6979 (mtm-85) REVERT: E 266 GLN cc_start: 0.7870 (mm110) cc_final: 0.7582 (mt0) REVERT: E 347 ILE cc_start: 0.9226 (mm) cc_final: 0.8832 (mm) REVERT: E 384 TYR cc_start: 0.8444 (t80) cc_final: 0.8175 (t80) REVERT: E 458 GLN cc_start: 0.7911 (mm110) cc_final: 0.7268 (tp40) REVERT: E 462 MET cc_start: 0.8476 (mmt) cc_final: 0.8242 (mmm) REVERT: F 70 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8315 (pt0) REVERT: F 398 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.6853 (mp0) REVERT: F 430 HIS cc_start: 0.7998 (m-70) cc_final: 0.7776 (m90) REVERT: D 103 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8143 (mm-30) REVERT: D 284 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.7918 (m-10) REVERT: D 297 GLU cc_start: 0.8508 (tp30) cc_final: 0.8172 (tp30) REVERT: D 433 LYS cc_start: 0.6595 (mmtt) cc_final: 0.6031 (mptt) REVERT: D 460 PHE cc_start: 0.6785 (m-10) cc_final: 0.6513 (m-10) REVERT: D 467 GLU cc_start: 0.7098 (tt0) cc_final: 0.6553 (mp0) REVERT: G 37 GLU cc_start: 0.7563 (mp0) cc_final: 0.7268 (mp0) REVERT: G 113 ARG cc_start: 0.8613 (ttp80) cc_final: 0.7888 (ttp80) REVERT: O 113 ARG cc_start: 0.6193 (ptp-170) cc_final: 0.5880 (ptp-110) REVERT: O 163 ILE cc_start: 0.8480 (mm) cc_final: 0.8162 (tp) REVERT: O 180 GLN cc_start: 0.9199 (mm-40) cc_final: 0.8825 (mm-40) outliers start: 98 outliers final: 83 residues processed: 719 average time/residue: 0.2395 time to fit residues: 278.7133 Evaluate side-chains 728 residues out of total 4012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 639 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 18 VAL Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 5 residue 15 THR Chi-restraints excluded: chain 5 residue 16 VAL Chi-restraints excluded: chain 5 residue 21 SER Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 54 PHE Chi-restraints excluded: chain 5 residue 71 ILE Chi-restraints excluded: chain 6 residue 62 LEU Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 8 residue 33 ILE Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 65 LEU Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain 8 residue 69 PHE Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 32 LEU Chi-restraints excluded: chain 1 residue 33 ILE Chi-restraints excluded: chain 1 residue 69 PHE Chi-restraints excluded: chain 1 residue 72 LEU Chi-restraints excluded: chain 2 residue 16 VAL Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 2 residue 72 LEU Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 3 residue 65 LEU Chi-restraints excluded: chain H residue 59 ARG Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 68 ASP Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain N residue 174 ILE Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain S residue 50 GLN Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain E residue 225 MET Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 398 GLU Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 284 TYR Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 134 LEU Chi-restraints excluded: chain O residue 155 ASP Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 231 optimal weight: 0.6980 chunk 333 optimal weight: 0.7980 chunk 203 optimal weight: 0.7980 chunk 380 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 396 optimal weight: 2.9990 chunk 189 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 285 optimal weight: 2.9990 chunk 430 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 66 HIS K 23 GLN ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 GLN B 379 GLN B 432 GLN C 476 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.136106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.106388 restraints weight = 72551.261| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.56 r_work: 0.3329 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 38546 Z= 0.126 Angle : 0.625 13.592 52151 Z= 0.305 Chirality : 0.043 0.259 6078 Planarity : 0.004 0.063 6644 Dihedral : 5.435 88.249 5436 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.09 % Favored : 97.89 % Rotamer: Outliers : 2.08 % Allowed : 21.61 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.11 % 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 aren not related in a simple way. whole: 0.80 (0.12), residues: 4885 helix: 1.65 (0.10), residues: 2608 sheet: -0.91 (0.22), residues: 551 loop : -0.66 (0.15), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 133 TYR 0.026 0.001 TYR C 397 PHE 0.040 0.001 PHE L 82 TRP 0.021 0.001 TRP P 10 HIS 0.021 0.001 HIS C 476 Details of bonding type rmsd covalent geometry : bond 0.00274 (38546) covalent geometry : angle 0.62504 (52151) hydrogen bonds : bond 0.04242 ( 2221) hydrogen bonds : angle 4.31014 ( 6459) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 4012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 688 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 63 PHE cc_start: 0.7238 (m-80) cc_final: 0.6915 (m-80) REVERT: 6 60 MET cc_start: 0.7216 (mmt) cc_final: 0.6986 (mmt) REVERT: 6 66 MET cc_start: 0.6508 (ttp) cc_final: 0.5491 (tpt) REVERT: 8 45 GLN cc_start: 0.6829 (tp40) cc_final: 0.6340 (tp-100) REVERT: 8 66 MET cc_start: 0.8062 (ttp) cc_final: 0.7279 (mmt) REVERT: 1 69 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.8187 (t80) REVERT: 1 75 MET cc_start: 0.5449 (mmt) cc_final: 0.5173 (mmm) REVERT: 2 39 ASN cc_start: 0.8258 (t0) cc_final: 0.7986 (t0) REVERT: 2 44 GLN cc_start: 0.8131 (pm20) cc_final: 0.7856 (tm-30) REVERT: 2 47 PHE cc_start: 0.8482 (t80) cc_final: 0.8143 (t80) REVERT: 2 66 MET cc_start: 0.8728 (tmm) cc_final: 0.8436 (tmm) REVERT: 3 21 SER cc_start: 0.8442 (t) cc_final: 0.8122 (m) REVERT: H 25 GLN cc_start: 0.7879 (tm-30) cc_final: 0.7419 (tm-30) REVERT: H 59 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7314 (ptt90) REVERT: H 136 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8494 (mt-10) REVERT: H 139 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8647 (mt-10) REVERT: K 134 MET cc_start: 0.8794 (ttm) cc_final: 0.8398 (ttt) REVERT: N 56 GLN cc_start: 0.8556 (tt0) cc_final: 0.8088 (tt0) REVERT: N 145 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8211 (mm-30) REVERT: N 221 TYR cc_start: 0.8539 (m-80) cc_final: 0.8259 (m-80) REVERT: P 7 LYS cc_start: 0.8647 (tmtt) cc_final: 0.8410 (mttt) REVERT: Q 12 MET cc_start: 0.9111 (mmt) cc_final: 0.8579 (mmt) REVERT: S 70 LYS cc_start: 0.7165 (tptt) cc_final: 0.6844 (tptt) REVERT: L 41 LYS cc_start: 0.8388 (tptt) cc_final: 0.7995 (tptp) REVERT: L 87 MET cc_start: 0.6501 (tpt) cc_final: 0.6285 (mmm) REVERT: A 52 MET cc_start: 0.8518 (ttp) cc_final: 0.8266 (ttp) REVERT: A 416 GLN cc_start: 0.8224 (tm-30) cc_final: 0.7908 (tm-30) REVERT: A 463 LYS cc_start: 0.8900 (mtpt) cc_final: 0.8653 (mtpp) REVERT: B 80 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8895 (pttt) REVERT: B 224 ASP cc_start: 0.8771 (t0) cc_final: 0.8509 (t0) REVERT: B 397 TYR cc_start: 0.8522 (t80) cc_final: 0.8312 (t80) REVERT: B 415 GLN cc_start: 0.7558 (mt0) cc_final: 0.6968 (mm-40) REVERT: B 475 GLN cc_start: 0.7398 (mp10) cc_final: 0.6922 (mp10) REVERT: B 477 GLN cc_start: 0.7633 (mm-40) cc_final: 0.6984 (tm-30) REVERT: C 45 ARG cc_start: 0.8227 (mmm160) cc_final: 0.7837 (mmm-85) REVERT: C 143 ARG cc_start: 0.7490 (mtm110) cc_final: 0.7226 (mtm180) REVERT: C 353 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8444 (mt-10) REVERT: C 393 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7262 (mt-10) REVERT: E 266 GLN cc_start: 0.7856 (mm110) cc_final: 0.7585 (mt0) REVERT: E 291 ASP cc_start: 0.7690 (m-30) cc_final: 0.7262 (m-30) REVERT: E 347 ILE cc_start: 0.9212 (mm) cc_final: 0.8801 (mm) REVERT: E 458 GLN cc_start: 0.7929 (mm110) cc_final: 0.7270 (tp40) REVERT: E 462 MET cc_start: 0.8430 (mmt) cc_final: 0.8225 (mmm) REVERT: F 70 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8281 (pt0) REVERT: F 398 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.6809 (mp0) REVERT: F 430 HIS cc_start: 0.7957 (m-70) cc_final: 0.7745 (m90) REVERT: D 79 LEU cc_start: 0.8592 (tp) cc_final: 0.8231 (mm) REVERT: D 101 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8183 (pt) REVERT: D 284 TYR cc_start: 0.8541 (OUTLIER) cc_final: 0.8054 (m-10) REVERT: D 297 GLU cc_start: 0.8424 (tp30) cc_final: 0.8100 (tp30) REVERT: D 433 LYS cc_start: 0.6610 (mmtt) cc_final: 0.5997 (mptt) REVERT: D 460 PHE cc_start: 0.6730 (m-10) cc_final: 0.6494 (m-10) REVERT: D 467 GLU cc_start: 0.7052 (tt0) cc_final: 0.6538 (mp0) REVERT: G 66 HIS cc_start: 0.7661 (t70) cc_final: 0.7277 (t-90) REVERT: G 113 ARG cc_start: 0.8574 (ttp80) cc_final: 0.7853 (ttp80) REVERT: G 201 LEU cc_start: 0.8697 (mt) cc_final: 0.8166 (mt) REVERT: O 113 ARG cc_start: 0.6123 (ptp-170) cc_final: 0.5848 (ptp-110) REVERT: O 163 ILE cc_start: 0.8491 (mm) cc_final: 0.8172 (tp) REVERT: O 180 GLN cc_start: 0.9208 (mm-40) cc_final: 0.8850 (mm-40) outliers start: 83 outliers final: 65 residues processed: 742 average time/residue: 0.2365 time to fit residues: 283.7440 Evaluate side-chains 727 residues out of total 4012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 655 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 18 VAL Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 5 residue 15 THR Chi-restraints excluded: chain 5 residue 16 VAL Chi-restraints excluded: chain 5 residue 21 SER Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 54 PHE Chi-restraints excluded: chain 5 residue 71 ILE Chi-restraints excluded: chain 6 residue 62 LEU Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 8 residue 65 LEU Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 32 LEU Chi-restraints excluded: chain 1 residue 33 ILE Chi-restraints excluded: chain 1 residue 69 PHE Chi-restraints excluded: chain 1 residue 72 LEU Chi-restraints excluded: chain 2 residue 16 VAL Chi-restraints excluded: chain 2 residue 72 LEU Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain H residue 59 ARG Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 68 ASP Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain S residue 50 GLN Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 379 GLN Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 225 MET Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 398 GLU Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 284 TYR Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 155 ASP Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 115 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 403 optimal weight: 4.9990 chunk 211 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 321 optimal weight: 7.9990 chunk 362 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 212 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 GLN B 65 ASN B 379 GLN F 458 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.134316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.105109 restraints weight = 72254.159| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.57 r_work: 0.3292 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 38546 Z= 0.182 Angle : 0.665 15.063 52151 Z= 0.327 Chirality : 0.045 0.372 6078 Planarity : 0.004 0.066 6644 Dihedral : 5.527 89.138 5436 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.46 % Favored : 97.52 % Rotamer: Outliers : 2.18 % Allowed : 21.94 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.11 % 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 aren not related in a simple way. whole: 0.71 (0.12), residues: 4885 helix: 1.55 (0.10), residues: 2614 sheet: -0.96 (0.21), residues: 594 loop : -0.63 (0.16), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 133 TYR 0.038 0.001 TYR E 384 PHE 0.029 0.002 PHE L 82 TRP 0.026 0.001 TRP P 10 HIS 0.008 0.001 HIS A 476 Details of bonding type rmsd covalent geometry : bond 0.00428 (38546) covalent geometry : angle 0.66467 (52151) hydrogen bonds : bond 0.04543 ( 2221) hydrogen bonds : angle 4.42256 ( 6459) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11723.68 seconds wall clock time: 200 minutes 53.23 seconds (12053.23 seconds total)