Starting phenix.real_space_refine on Sun Feb 25 12:02:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spe_10283/02_2024/6spe_10283.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spe_10283/02_2024/6spe_10283.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spe_10283/02_2024/6spe_10283.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spe_10283/02_2024/6spe_10283.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spe_10283/02_2024/6spe_10283.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spe_10283/02_2024/6spe_10283.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1525 5.49 5 S 67 5.16 5 C 26260 2.51 5 N 9608 2.21 5 O 13969 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "c ARG 59": "NH1" <-> "NH2" Residue "c ARG 88": "NH1" <-> "NH2" Residue "c ARG 156": "NH1" <-> "NH2" Residue "c TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 38": "NH1" <-> "NH2" Residue "f ARG 86": "NH1" <-> "NH2" Residue "g ARG 5": "NH1" <-> "NH2" Residue "k ARG 127": "NH1" <-> "NH2" Residue "n ARG 81": "NH1" <-> "NH2" Residue "p ARG 5": "NH1" <-> "NH2" Residue "p ARG 31": "NH1" <-> "NH2" Residue "p PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 49": "NH1" <-> "NH2" Residue "r ARG 8": "NH1" <-> "NH2" Residue "u ARG 35": "NH1" <-> "NH2" Residue "u ARG 66": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 51429 Number of models: 1 Model: "" Number of chains: 21 Chain: "a" Number of atoms: 32744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1526, 32744 Classifications: {'RNA': 1526} Modifications used: {'5*END': 1, 'rna2p_pur': 125, 'rna2p_pyr': 83, 'rna3p_pur': 747, 'rna3p_pyr': 571} Link IDs: {'rna2p': 208, 'rna3p': 1317} Chain: "b" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1822 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "c" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1627 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 198} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "d" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1603 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 200} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "e" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1145 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 150} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "f" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 853 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 103} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "g" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1190 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 148} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "h" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 982 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "i" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 994 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "j" Number of atoms: 765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 765 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "k" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 838 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 107} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "l" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 949 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain: "m" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 859 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "n" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 778 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "o" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 686 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "p" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 74} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "q" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 619 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "r" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 556 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 68} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "s" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 635 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 75} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "t" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 655 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 82} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 4 Chain: "u" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 519 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain breaks: 1 Time building chain proxies: 27.15, per 1000 atoms: 0.53 Number of scatterers: 51429 At special positions: 0 Unit cell: (239.8, 194.7, 190.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 67 16.00 P 1525 15.00 O 13969 8.00 N 9608 7.00 C 26260 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS d 9 " - pdb=" SG CYS d 32 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 24.49 Conformation dependent library (CDL) restraints added in 3.6 seconds 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4414 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 21 sheets defined 39.3% alpha, 13.5% beta 398 base pairs and 838 stacking pairs defined. Time for finding SS restraints: 22.47 Creating SS restraints... Processing helix chain 'b' and resid 5 through 13 removed outlier: 3.823A pdb=" N MET b 9 " --> pdb=" O ASN b 5 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY b 13 " --> pdb=" O MET b 9 " (cutoff:3.500A) Processing helix chain 'b' and resid 27 through 29 No H-bonds generated for 'chain 'b' and resid 27 through 29' Processing helix chain 'b' and resid 34 through 38 removed outlier: 3.659A pdb=" N LYS b 37 " --> pdb=" O ALA b 34 " (cutoff:3.500A) Processing helix chain 'b' and resid 45 through 62 removed outlier: 3.881A pdb=" N MET b 49 " --> pdb=" O LYS b 45 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU b 54 " --> pdb=" O PHE b 50 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE b 56 " --> pdb=" O GLU b 52 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA b 62 " --> pdb=" O GLU b 58 " (cutoff:3.500A) Processing helix chain 'b' and resid 77 through 83 Processing helix chain 'b' and resid 103 through 111 removed outlier: 3.561A pdb=" N ILE b 107 " --> pdb=" O ASN b 103 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN b 109 " --> pdb=" O LYS b 105 " (cutoff:3.500A) Processing helix chain 'b' and resid 113 through 121 removed outlier: 4.280A pdb=" N GLU b 118 " --> pdb=" O LEU b 114 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N THR b 119 " --> pdb=" O ARG b 115 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER b 121 " --> pdb=" O LEU b 117 " (cutoff:3.500A) Processing helix chain 'b' and resid 131 through 139 removed outlier: 3.827A pdb=" N LEU b 135 " --> pdb=" O LYS b 131 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG b 137 " --> pdb=" O GLU b 133 " (cutoff:3.500A) Processing helix chain 'b' and resid 139 through 148 removed outlier: 3.974A pdb=" N LYS b 143 " --> pdb=" O ARG b 139 " (cutoff:3.500A) Processing helix chain 'b' and resid 170 through 178 Processing helix chain 'b' and resid 206 through 213 Processing helix chain 'b' and resid 214 through 232 removed outlier: 3.510A pdb=" N GLU b 219 " --> pdb=" O ASN b 215 " (cutoff:3.500A) Processing helix chain 'c' and resid 28 through 47 removed outlier: 3.566A pdb=" N LEU c 33 " --> pdb=" O TYR c 29 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N PHE c 34 " --> pdb=" O ALA c 30 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA c 35 " --> pdb=" O ASP c 31 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS c 38 " --> pdb=" O PHE c 34 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG c 40 " --> pdb=" O ASP c 36 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU c 41 " --> pdb=" O LEU c 37 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR c 42 " --> pdb=" O LYS c 38 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN c 44 " --> pdb=" O ARG c 40 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP c 45 " --> pdb=" O GLU c 41 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 77 removed outlier: 4.188A pdb=" N VAL c 76 " --> pdb=" O ARG c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 83 through 92 removed outlier: 3.718A pdb=" N ASP c 90 " --> pdb=" O LYS c 86 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR c 92 " --> pdb=" O ARG c 88 " (cutoff:3.500A) Processing helix chain 'c' and resid 108 through 111 Processing helix chain 'c' and resid 112 through 124 removed outlier: 3.795A pdb=" N SER c 119 " --> pdb=" O LEU c 115 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA c 121 " --> pdb=" O ALA c 117 " (cutoff:3.500A) Processing helix chain 'c' and resid 131 through 144 removed outlier: 4.031A pdb=" N ARG c 136 " --> pdb=" O ARG c 132 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN c 139 " --> pdb=" O LYS c 135 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA c 141 " --> pdb=" O ALA c 137 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE c 144 " --> pdb=" O ASN c 140 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 16 removed outlier: 3.803A pdb=" N SER d 12 " --> pdb=" O LYS d 8 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU d 15 " --> pdb=" O LEU d 11 " (cutoff:3.500A) Processing helix chain 'd' and resid 49 through 66 removed outlier: 3.772A pdb=" N GLN d 54 " --> pdb=" O ASP d 50 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR d 65 " --> pdb=" O VAL d 61 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY d 66 " --> pdb=" O ARG d 62 " (cutoff:3.500A) Processing helix chain 'd' and resid 68 through 82 removed outlier: 3.615A pdb=" N GLY d 74 " --> pdb=" O ARG d 70 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG d 82 " --> pdb=" O GLU d 78 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 96 removed outlier: 3.591A pdb=" N LEU d 94 " --> pdb=" O LEU d 90 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS d 96 " --> pdb=" O GLN d 92 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 106 removed outlier: 3.671A pdb=" N TYR d 103 " --> pdb=" O ASP d 99 " (cutoff:3.500A) Processing helix chain 'd' and resid 110 through 120 removed outlier: 3.791A pdb=" N SER d 114 " --> pdb=" O THR d 110 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN d 116 " --> pdb=" O SER d 112 " (cutoff:3.500A) Processing helix chain 'd' and resid 147 through 150 removed outlier: 3.847A pdb=" N LYS d 150 " --> pdb=" O GLU d 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 147 through 150' Processing helix chain 'd' and resid 152 through 159 removed outlier: 3.740A pdb=" N ALA d 158 " --> pdb=" O ARG d 154 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU d 159 " --> pdb=" O ILE d 155 " (cutoff:3.500A) Processing helix chain 'd' and resid 199 through 204 removed outlier: 3.541A pdb=" N TYR d 204 " --> pdb=" O ILE d 200 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 69 removed outlier: 4.143A pdb=" N GLN e 62 " --> pdb=" O PRO e 58 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG e 69 " --> pdb=" O MET e 65 " (cutoff:3.500A) Processing helix chain 'e' and resid 111 through 119 removed outlier: 3.846A pdb=" N VAL e 115 " --> pdb=" O ALA e 111 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL e 118 " --> pdb=" O ALA e 114 " (cutoff:3.500A) Processing helix chain 'e' and resid 136 through 146 removed outlier: 3.589A pdb=" N ALA e 140 " --> pdb=" O ASN e 136 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY e 144 " --> pdb=" O ALA e 140 " (cutoff:3.500A) Processing helix chain 'f' and resid 12 through 16 removed outlier: 3.703A pdb=" N SER f 15 " --> pdb=" O PRO f 12 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLU f 16 " --> pdb=" O ASP f 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 12 through 16' Processing helix chain 'f' and resid 17 through 33 removed outlier: 3.536A pdb=" N MET f 21 " --> pdb=" O GLN f 17 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU f 23 " --> pdb=" O GLY f 19 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR f 25 " --> pdb=" O MET f 21 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ALA f 28 " --> pdb=" O ARG f 24 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE f 29 " --> pdb=" O TYR f 25 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 78 removed outlier: 3.544A pdb=" N LEU f 71 " --> pdb=" O SER f 67 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA f 72 " --> pdb=" O ALA f 68 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP f 76 " --> pdb=" O ALA f 72 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE f 78 " --> pdb=" O LEU f 74 " (cutoff:3.500A) Processing helix chain 'f' and resid 101 through 106 Processing helix chain 'g' and resid 21 through 29 removed outlier: 3.669A pdb=" N LYS g 25 " --> pdb=" O GLN g 21 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS g 29 " --> pdb=" O LYS g 25 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 44 removed outlier: 3.675A pdb=" N ARG g 41 " --> pdb=" O ALA g 37 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE g 42 " --> pdb=" O VAL g 38 " (cutoff:3.500A) Processing helix chain 'g' and resid 47 through 54 Processing helix chain 'g' and resid 57 through 67 removed outlier: 3.726A pdb=" N THR g 61 " --> pdb=" O ASP g 57 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP g 67 " --> pdb=" O GLU g 63 " (cutoff:3.500A) Processing helix chain 'g' and resid 95 through 109 removed outlier: 3.566A pdb=" N LEU g 99 " --> pdb=" O ARG g 95 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA g 100 " --> pdb=" O ARG g 96 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL g 105 " --> pdb=" O MET g 101 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP g 106 " --> pdb=" O ARG g 102 " (cutoff:3.500A) Processing helix chain 'g' and resid 116 through 127 removed outlier: 3.633A pdb=" N LEU g 120 " --> pdb=" O MET g 116 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 148 removed outlier: 3.744A pdb=" N VAL g 141 " --> pdb=" O LYS g 137 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA g 145 " --> pdb=" O VAL g 141 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU g 146 " --> pdb=" O HIS g 142 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA g 147 " --> pdb=" O ARG g 143 " (cutoff:3.500A) Processing helix chain 'g' and resid 149 through 152 Processing helix chain 'h' and resid 6 through 18 removed outlier: 3.536A pdb=" N LEU h 11 " --> pdb=" O LEU h 7 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR h 12 " --> pdb=" O ALA h 8 " (cutoff:3.500A) Processing helix chain 'h' and resid 32 through 44 removed outlier: 4.120A pdb=" N LYS h 38 " --> pdb=" O ALA h 34 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL h 39 " --> pdb=" O ALA h 35 " (cutoff:3.500A) Processing helix chain 'h' and resid 113 through 120 removed outlier: 3.693A pdb=" N ALA h 118 " --> pdb=" O ARG h 114 " (cutoff:3.500A) Processing helix chain 'i' and resid 35 through 39 removed outlier: 3.571A pdb=" N PHE i 39 " --> pdb=" O LEU i 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 35 through 39' Processing helix chain 'i' and resid 43 through 48 removed outlier: 3.706A pdb=" N VAL i 47 " --> pdb=" O THR i 43 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 55 Processing helix chain 'i' and resid 71 through 88 removed outlier: 3.798A pdb=" N ALA i 76 " --> pdb=" O VAL i 72 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY i 77 " --> pdb=" O SER i 73 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR i 84 " --> pdb=" O ARG i 80 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG i 85 " --> pdb=" O HIS i 81 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE i 88 " --> pdb=" O THR i 84 " (cutoff:3.500A) Processing helix chain 'i' and resid 95 through 100 Processing helix chain 'j' and resid 17 through 21 removed outlier: 3.614A pdb=" N SER j 21 " --> pdb=" O ILE j 18 " (cutoff:3.500A) Processing helix chain 'j' and resid 22 through 31 removed outlier: 4.327A pdb=" N THR j 28 " --> pdb=" O GLU j 24 " (cutoff:3.500A) Processing helix chain 'j' and resid 82 through 87 removed outlier: 3.506A pdb=" N ALA j 86 " --> pdb=" O LYS j 82 " (cutoff:3.500A) Processing helix chain 'j' and resid 87 through 92 removed outlier: 3.650A pdb=" N ASP j 91 " --> pdb=" O LEU j 87 " (cutoff:3.500A) Processing helix chain 'k' and resid 55 through 59 removed outlier: 3.678A pdb=" N SER k 58 " --> pdb=" O SER k 55 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR k 59 " --> pdb=" O ARG k 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 55 through 59' Processing helix chain 'k' and resid 61 through 71 removed outlier: 3.923A pdb=" N ALA k 67 " --> pdb=" O ALA k 63 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 8 removed outlier: 3.517A pdb=" N LEU l 7 " --> pdb=" O THR l 3 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 19 Processing helix chain 'm' and resid 20 through 23 removed outlier: 3.726A pdb=" N TYR m 23 " --> pdb=" O THR m 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 20 through 23' Processing helix chain 'm' and resid 28 through 38 removed outlier: 3.613A pdb=" N SER m 32 " --> pdb=" O THR m 28 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N CYS m 34 " --> pdb=" O ALA m 30 " (cutoff:3.500A) Processing helix chain 'm' and resid 52 through 61 removed outlier: 3.502A pdb=" N GLU m 59 " --> pdb=" O GLN m 55 " (cutoff:3.500A) Processing helix chain 'm' and resid 65 through 83 removed outlier: 4.435A pdb=" N ARG m 71 " --> pdb=" O GLY m 67 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU m 80 " --> pdb=" O ASN m 76 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU m 83 " --> pdb=" O ARG m 79 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 94 removed outlier: 3.738A pdb=" N HIS m 91 " --> pdb=" O ARG m 87 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG m 93 " --> pdb=" O LEU m 89 " (cutoff:3.500A) Processing helix chain 'n' and resid 4 through 10 removed outlier: 3.683A pdb=" N ARG n 9 " --> pdb=" O SER n 5 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU n 10 " --> pdb=" O MET n 6 " (cutoff:3.500A) Processing helix chain 'n' and resid 11 through 21 removed outlier: 3.506A pdb=" N LEU n 15 " --> pdb=" O LEU n 11 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR n 20 " --> pdb=" O THR n 16 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA n 21 " --> pdb=" O VAL n 17 " (cutoff:3.500A) Processing helix chain 'n' and resid 22 through 32 removed outlier: 3.625A pdb=" N ILE n 31 " --> pdb=" O LEU n 27 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA n 32 " --> pdb=" O LYS n 28 " (cutoff:3.500A) Processing helix chain 'n' and resid 37 through 50 removed outlier: 3.651A pdb=" N ASN n 43 " --> pdb=" O GLU n 39 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA n 44 " --> pdb=" O GLU n 40 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL n 46 " --> pdb=" O TRP n 42 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA n 47 " --> pdb=" O ASN n 43 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU n 48 " --> pdb=" O ALA n 44 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN n 49 " --> pdb=" O GLN n 45 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 60 Processing helix chain 'n' and resid 83 through 89 Processing helix chain 'o' and resid 4 through 15 removed outlier: 3.544A pdb=" N LYS o 8 " --> pdb=" O SER o 4 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE o 11 " --> pdb=" O GLU o 7 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 40 removed outlier: 3.925A pdb=" N ALA o 30 " --> pdb=" O GLU o 26 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN o 35 " --> pdb=" O LEU o 31 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN o 37 " --> pdb=" O SER o 33 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS o 38 " --> pdb=" O ALA o 34 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU o 39 " --> pdb=" O ASN o 35 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN o 40 " --> pdb=" O ILE o 36 " (cutoff:3.500A) Processing helix chain 'o' and resid 41 through 46 removed outlier: 3.610A pdb=" N ALA o 45 " --> pdb=" O ASP o 41 " (cutoff:3.500A) Processing helix chain 'o' and resid 52 through 72 removed outlier: 3.794A pdb=" N LEU o 56 " --> pdb=" O SER o 52 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE o 57 " --> pdb=" O ARG o 53 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG o 58 " --> pdb=" O ARG o 54 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET o 59 " --> pdb=" O GLY o 55 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP o 68 " --> pdb=" O ARG o 64 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 removed outlier: 3.563A pdb=" N LEU o 81 " --> pdb=" O ARG o 77 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG o 84 " --> pdb=" O ALA o 80 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 62 removed outlier: 3.801A pdb=" N ALA p 57 " --> pdb=" O ASP p 53 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU p 61 " --> pdb=" O ALA p 57 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY p 62 " --> pdb=" O THR p 58 " (cutoff:3.500A) Processing helix chain 'p' and resid 70 through 75 Processing helix chain 'r' and resid 5 through 9 removed outlier: 3.568A pdb=" N ARG r 9 " --> pdb=" O PHE r 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 5 through 9' Processing helix chain 'r' and resid 10 through 15 Processing helix chain 'r' and resid 25 through 30 Processing helix chain 'r' and resid 31 through 33 No H-bonds generated for 'chain 'r' and resid 31 through 33' Processing helix chain 'r' and resid 48 through 65 removed outlier: 3.723A pdb=" N ARG r 53 " --> pdb=" O ALA r 49 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR r 57 " --> pdb=" O ARG r 53 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA r 58 " --> pdb=" O GLN r 54 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR r 64 " --> pdb=" O LYS r 60 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 25 removed outlier: 3.650A pdb=" N VAL s 21 " --> pdb=" O LYS s 17 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ALA s 22 " --> pdb=" O LYS s 18 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU s 24 " --> pdb=" O GLU s 20 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS s 25 " --> pdb=" O VAL s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 74 removed outlier: 3.627A pdb=" N GLU s 73 " --> pdb=" O LYS s 70 " (cutoff:3.500A) Processing helix chain 't' and resid 6 through 40 removed outlier: 3.629A pdb=" N LYS t 12 " --> pdb=" O LYS t 8 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA t 14 " --> pdb=" O ARG t 10 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU t 15 " --> pdb=" O ALA t 11 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS t 16 " --> pdb=" O LYS t 12 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG t 17 " --> pdb=" O GLN t 13 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N HIS t 20 " --> pdb=" O LYS t 16 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER t 23 " --> pdb=" O SER t 19 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU t 24 " --> pdb=" O HIS t 20 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL t 28 " --> pdb=" O LEU t 24 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG t 29 " --> pdb=" O ARG t 25 " (cutoff:3.500A) WARNING: missing atoms! removed outlier: 4.430A pdb=" N VAL t 35 " --> pdb=" O TYR t 31 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP t 40 " --> pdb=" O VAL t 36 " (cutoff:3.500A) Processing helix chain 't' and resid 43 through 53 removed outlier: 3.866A pdb=" N ALA t 47 " --> pdb=" O ASP t 43 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA t 53 " --> pdb=" O ALA t 49 " (cutoff:3.500A) Processing helix chain 't' and resid 54 through 64 removed outlier: 3.606A pdb=" N ASP t 63 " --> pdb=" O ASP t 59 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS t 64 " --> pdb=" O ARG t 60 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 84 removed outlier: 3.673A pdb=" N ARG t 74 " --> pdb=" O ASN t 70 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS t 75 " --> pdb=" O LYS t 71 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS t 76 " --> pdb=" O ALA t 72 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER t 77 " --> pdb=" O ALA t 73 " (cutoff:3.500A) Processing helix chain 'u' and resid 11 through 27 removed outlier: 4.034A pdb=" N ALA u 15 " --> pdb=" O PRO u 11 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG u 21 " --> pdb=" O ARG u 17 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER u 22 " --> pdb=" O ARG u 18 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU u 24 " --> pdb=" O LYS u 20 " (cutoff:3.500A) Processing helix chain 'u' and resid 29 through 34 removed outlier: 3.685A pdb=" N ARG u 33 " --> pdb=" O LEU u 29 " (cutoff:3.500A) Processing helix chain 'u' and resid 40 through 57 removed outlier: 3.692A pdb=" N ARG u 47 " --> pdb=" O ALA u 43 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS u 48 " --> pdb=" O GLU u 44 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA u 52 " --> pdb=" O LYS u 48 " (cutoff:3.500A) Processing helix chain 'u' and resid 57 through 66 removed outlier: 4.278A pdb=" N GLU u 63 " --> pdb=" O LYS u 59 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN u 64 " --> pdb=" O VAL u 60 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG u 65 " --> pdb=" O GLN u 61 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'b' and resid 31 through 33 removed outlier: 6.538A pdb=" N ILE b 40 " --> pdb=" O PHE b 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'b' and resid 68 through 69 removed outlier: 6.442A pdb=" N LEU b 68 " --> pdb=" O PHE b 162 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU b 161 " --> pdb=" O ILE b 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'c' and resid 20 through 21 removed outlier: 4.434A pdb=" N ARG c 54 " --> pdb=" O HIS c 69 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE c 66 " --> pdb=" O ASN c 102 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLU c 104 " --> pdb=" O ILE c 66 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ILE c 68 " --> pdb=" O GLU c 104 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'c' and resid 165 through 166 Processing sheet with id=AA5, first strand: chain 'c' and resid 165 through 166 removed outlier: 3.531A pdb=" N TYR c 187 " --> pdb=" O VAL c 198 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA c 185 " --> pdb=" O VAL c 200 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'd' and resid 123 through 124 Processing sheet with id=AA7, first strand: chain 'e' and resid 13 through 19 removed outlier: 6.735A pdb=" N LEU e 37 " --> pdb=" O VAL e 17 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL e 19 " --> pdb=" O THR e 35 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR e 35 " --> pdb=" O VAL e 19 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'e' and resid 13 through 19 removed outlier: 6.735A pdb=" N LEU e 37 " --> pdb=" O VAL e 17 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL e 19 " --> pdb=" O THR e 35 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR e 35 " --> pdb=" O VAL e 19 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'e' and resid 86 through 89 Processing sheet with id=AB1, first strand: chain 'f' and resid 36 through 43 removed outlier: 3.824A pdb=" N ARG f 38 " --> pdb=" O ASN f 63 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS f 58 " --> pdb=" O VAL f 10 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG f 86 " --> pdb=" O LEU f 9 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'g' and resid 73 through 74 Processing sheet with id=AB3, first strand: chain 'h' and resid 24 through 28 removed outlier: 6.335A pdb=" N SER h 60 " --> pdb=" O PHE h 49 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE h 49 " --> pdb=" O SER h 60 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLU h 62 " --> pdb=" O ALA h 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'h' and resid 86 through 87 removed outlier: 6.108A pdb=" N VAL h 125 " --> pdb=" O SER h 105 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N SER h 105 " --> pdb=" O VAL h 125 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N CYS h 127 " --> pdb=" O ILE h 103 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY h 109 " --> pdb=" O THR h 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'i' and resid 6 through 10 removed outlier: 3.657A pdb=" N GLY i 10 " --> pdb=" O ALA i 17 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N SER i 29 " --> pdb=" O VAL i 65 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N VAL i 67 " --> pdb=" O SER i 29 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'j' and resid 40 through 41 Processing sheet with id=AB7, first strand: chain 'j' and resid 45 through 52 Processing sheet with id=AB8, first strand: chain 'k' and resid 41 through 46 removed outlier: 8.114A pdb=" N LEU k 82 " --> pdb=" O ALA k 108 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE k 110 " --> pdb=" O LEU k 82 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL k 84 " --> pdb=" O ILE k 110 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASP k 112 " --> pdb=" O VAL k 84 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL k 86 " --> pdb=" O ASP k 112 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'l' and resid 62 through 66 removed outlier: 3.526A pdb=" N CYS l 53 " --> pdb=" O SER l 65 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ARG l 50 " --> pdb=" O THR l 39 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR l 39 " --> pdb=" O ARG l 50 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL l 52 " --> pdb=" O VAL l 37 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL l 37 " --> pdb=" O VAL l 52 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ARG l 54 " --> pdb=" O THR l 35 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG l 83 " --> pdb=" O HIS l 96 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'p' and resid 34 through 35 removed outlier: 3.693A pdb=" N GLU p 34 " --> pdb=" O VAL p 21 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL p 2 " --> pdb=" O GLN p 66 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'q' and resid 46 through 47 removed outlier: 3.619A pdb=" N LEU q 47 " --> pdb=" O VAL q 26 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL q 26 " --> pdb=" O LEU q 47 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR q 25 " --> pdb=" O VAL q 16 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LEU q 61 " --> pdb=" O ILE q 81 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE q 81 " --> pdb=" O LEU q 61 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N THR q 63 " --> pdb=" O VAL q 79 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG q 65 " --> pdb=" O THR q 77 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ALA q 75 " --> pdb=" O THR q 67 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU q 78 " --> pdb=" O HIS q 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 's' and resid 31 through 33 removed outlier: 6.523A pdb=" N ILE s 31 " --> pdb=" O ALA s 50 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N HIS s 52 " --> pdb=" O ILE s 31 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N THR s 33 " --> pdb=" O HIS s 52 " (cutoff:3.500A) 567 hydrogen bonds defined for protein. 1623 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 961 hydrogen bonds 1592 hydrogen bond angles 0 basepair planarities 398 basepair parallelities 838 stacking parallelities Total time for adding SS restraints: 43.09 Time building geometry restraints manager: 26.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6499 1.32 - 1.45: 23029 1.45 - 1.57: 22923 1.57 - 1.69: 3050 1.69 - 1.81: 115 Bond restraints: 55616 Sorted by residual: bond pdb=" CG LEU l 24 " pdb=" CD2 LEU l 24 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.09e+00 bond pdb=" C5 A a 383 " pdb=" C6 A a 383 " ideal model delta sigma weight residual 1.406 1.366 0.040 2.00e-02 2.50e+03 4.07e+00 bond pdb=" CA ARG q 31 " pdb=" CB ARG q 31 " ideal model delta sigma weight residual 1.526 1.497 0.029 1.53e-02 4.27e+03 3.64e+00 bond pdb=" C5 A a 810 " pdb=" C6 A a 810 " ideal model delta sigma weight residual 1.406 1.370 0.036 2.00e-02 2.50e+03 3.20e+00 bond pdb=" N1 C a 873 " pdb=" C2 C a 873 " ideal model delta sigma weight residual 1.397 1.365 0.032 2.00e-02 2.50e+03 2.60e+00 ... (remaining 55611 not shown) Histogram of bond angle deviations from ideal: 97.95 - 105.66: 8062 105.66 - 113.38: 33871 113.38 - 121.10: 25708 121.10 - 128.81: 13551 128.81 - 136.53: 1458 Bond angle restraints: 82650 Sorted by residual: angle pdb=" C3' A a 963 " pdb=" O3' A a 963 " pdb=" P C a 964 " ideal model delta sigma weight residual 120.20 127.96 -7.76 1.50e+00 4.44e-01 2.68e+01 angle pdb=" C3' A a1195 " pdb=" O3' A a1195 " pdb=" P U a1196 " ideal model delta sigma weight residual 120.20 127.57 -7.37 1.50e+00 4.44e-01 2.42e+01 angle pdb=" C4' A a 963 " pdb=" C3' A a 963 " pdb=" O3' A a 963 " ideal model delta sigma weight residual 109.40 116.63 -7.23 1.50e+00 4.44e-01 2.32e+01 angle pdb=" C3' G a1341 " pdb=" O3' G a1341 " pdb=" P U a1342 " ideal model delta sigma weight residual 120.20 127.34 -7.14 1.50e+00 4.44e-01 2.26e+01 angle pdb=" C3' C a 893 " pdb=" O3' C a 893 " pdb=" P A a 894 " ideal model delta sigma weight residual 120.20 126.84 -6.64 1.50e+00 4.44e-01 1.96e+01 ... (remaining 82645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 31696 35.88 - 71.76: 3423 71.76 - 107.63: 419 107.63 - 143.51: 12 143.51 - 179.39: 18 Dihedral angle restraints: 35568 sinusoidal: 28715 harmonic: 6853 Sorted by residual: dihedral pdb=" O4' U a 975 " pdb=" C1' U a 975 " pdb=" N1 U a 975 " pdb=" C2 U a 975 " ideal model delta sinusoidal sigma weight residual -160.00 12.62 -172.62 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' C a 104 " pdb=" C1' C a 104 " pdb=" N1 C a 104 " pdb=" C2 C a 104 " ideal model delta sinusoidal sigma weight residual -160.00 7.96 -167.96 1 1.50e+01 4.44e-03 8.44e+01 dihedral pdb=" O4' U a1024 " pdb=" C1' U a1024 " pdb=" N1 U a1024 " pdb=" C2 U a1024 " ideal model delta sinusoidal sigma weight residual 200.00 37.95 162.05 1 1.50e+01 4.44e-03 8.33e+01 ... (remaining 35565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 9342 0.069 - 0.139: 1020 0.139 - 0.208: 84 0.208 - 0.277: 12 0.277 - 0.346: 8 Chirality restraints: 10466 Sorted by residual: chirality pdb=" C3' G a1341 " pdb=" C4' G a1341 " pdb=" O3' G a1341 " pdb=" C2' G a1341 " both_signs ideal model delta sigma weight residual False -2.74 -2.40 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" C3' A a 709 " pdb=" C4' A a 709 " pdb=" O3' A a 709 " pdb=" C2' A a 709 " both_signs ideal model delta sigma weight residual False -2.48 -2.13 -0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" C3' C a 87 " pdb=" C4' C a 87 " pdb=" O3' C a 87 " pdb=" C2' C a 87 " both_signs ideal model delta sigma weight residual False -2.48 -2.15 -0.33 2.00e-01 2.50e+01 2.72e+00 ... (remaining 10463 not shown) Planarity restraints: 4829 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE c 106 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C ILE c 106 " 0.059 2.00e-02 2.50e+03 pdb=" O ILE c 106 " -0.022 2.00e-02 2.50e+03 pdb=" N ARG c 107 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G a 829 " 0.036 2.00e-02 2.50e+03 1.69e-02 8.61e+00 pdb=" N9 G a 829 " -0.043 2.00e-02 2.50e+03 pdb=" C8 G a 829 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G a 829 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G a 829 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G a 829 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G a 829 " 0.015 2.00e-02 2.50e+03 pdb=" N1 G a 829 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G a 829 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G a 829 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G a 829 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G a 829 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR c 63 " 0.014 2.00e-02 2.50e+03 2.83e-02 8.02e+00 pdb=" C THR c 63 " -0.049 2.00e-02 2.50e+03 pdb=" O THR c 63 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA c 64 " 0.017 2.00e-02 2.50e+03 ... (remaining 4826 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 13057 2.80 - 3.33: 41658 3.33 - 3.85: 100069 3.85 - 4.38: 119722 4.38 - 4.90: 164809 Nonbonded interactions: 439315 Sorted by model distance: nonbonded pdb=" OP2 U a 20 " pdb=" OG SER e 131 " model vdw 2.277 2.440 nonbonded pdb=" O2' U a1046 " pdb=" OP2 A a1049 " model vdw 2.288 2.440 nonbonded pdb=" O2' C a 853 " pdb=" O4' A a 854 " model vdw 2.289 2.440 nonbonded pdb=" O2' G a1047 " pdb=" OP2 U a1193 " model vdw 2.296 2.440 nonbonded pdb=" N6 A a 445 " pdb=" O2' U a 474 " model vdw 2.297 2.520 ... (remaining 439310 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.700 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: 0.040 Extract box with map and model: 15.800 Check model and map are aligned: 0.690 Set scattering table: 0.410 Process input model: 163.550 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 188.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 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 : 0.007 0.067 55616 Z= 0.432 Angle : 0.851 15.004 82650 Z= 0.434 Chirality : 0.045 0.346 10466 Planarity : 0.005 0.061 4829 Dihedral : 22.600 179.390 31151 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 0.10 % Allowed : 2.84 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.99 (0.13), residues: 2348 helix: -4.24 (0.09), residues: 802 sheet: -2.71 (0.24), residues: 391 loop : -2.74 (0.15), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP n 42 HIS 0.017 0.002 HIS f 37 PHE 0.022 0.003 PHE p 38 TYR 0.026 0.003 TYR e 12 ARG 0.016 0.001 ARG d 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 830 time to evaluate : 3.124 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 TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 9 MET cc_start: 0.7682 (mmm) cc_final: 0.7336 (ttt) REVERT: b 42 ASN cc_start: 0.7709 (t0) cc_final: 0.6723 (t0) REVERT: b 65 ASN cc_start: 0.7336 (p0) cc_final: 0.7104 (p0) REVERT: b 136 MET cc_start: 0.8062 (mtp) cc_final: 0.7753 (mtm) REVERT: b 216 SER cc_start: 0.8437 (m) cc_final: 0.8114 (m) REVERT: d 20 PHE cc_start: 0.8307 (m-80) cc_final: 0.8080 (m-80) REVERT: e 15 LYS cc_start: 0.8794 (tptt) cc_final: 0.8495 (ttmt) REVERT: e 55 ARG cc_start: 0.8475 (mmm-85) cc_final: 0.8251 (tpp-160) REVERT: e 66 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7596 (tm-30) REVERT: e 88 SER cc_start: 0.9050 (m) cc_final: 0.8842 (p) REVERT: e 164 GLU cc_start: 0.6823 (pp20) cc_final: 0.6232 (pp20) REVERT: f 4 TYR cc_start: 0.8845 (m-80) cc_final: 0.8579 (m-80) REVERT: f 13 ASP cc_start: 0.9197 (m-30) cc_final: 0.8893 (p0) REVERT: f 18 VAL cc_start: 0.9137 (p) cc_final: 0.8627 (p) REVERT: f 21 MET cc_start: 0.8534 (mtp) cc_final: 0.8218 (mtt) REVERT: f 22 VAL cc_start: 0.9469 (t) cc_final: 0.9267 (p) REVERT: f 42 TRP cc_start: 0.8900 (m-10) cc_final: 0.7995 (m-10) REVERT: f 47 LEU cc_start: 0.8862 (mt) cc_final: 0.8394 (mt) REVERT: f 77 ASN cc_start: 0.9169 (m-40) cc_final: 0.8958 (p0) REVERT: f 85 ILE cc_start: 0.9017 (tt) cc_final: 0.8797 (tp) REVERT: g 97 ASN cc_start: 0.8531 (m110) cc_final: 0.8214 (m-40) REVERT: h 23 THR cc_start: 0.9230 (m) cc_final: 0.8898 (t) REVERT: h 113 ASP cc_start: 0.7914 (p0) cc_final: 0.7709 (p0) REVERT: i 54 LEU cc_start: 0.9141 (tp) cc_final: 0.8932 (tt) REVERT: j 54 SER cc_start: 0.9370 (t) cc_final: 0.9168 (t) REVERT: j 77 VAL cc_start: 0.9126 (t) cc_final: 0.7980 (t) REVERT: j 88 MET cc_start: 0.7478 (ttt) cc_final: 0.6813 (tmm) REVERT: k 30 THR cc_start: 0.9582 (m) cc_final: 0.9100 (p) REVERT: k 47 SER cc_start: 0.9494 (m) cc_final: 0.8949 (m) REVERT: k 65 VAL cc_start: 0.9442 (t) cc_final: 0.9039 (p) REVERT: k 93 ARG cc_start: 0.7993 (ttt90) cc_final: 0.7662 (ttt90) REVERT: k 100 LEU cc_start: 0.9044 (mt) cc_final: 0.8631 (mt) REVERT: k 122 ARG cc_start: 0.8975 (ptm160) cc_final: 0.8547 (ptm160) REVERT: l 15 MET cc_start: 0.6532 (pmt) cc_final: 0.6056 (ptt) REVERT: l 38 TYR cc_start: 0.6751 (m-80) cc_final: 0.5753 (m-80) REVERT: l 78 SER cc_start: 0.9143 (m) cc_final: 0.8776 (p) REVERT: l 88 LYS cc_start: 0.8658 (tttm) cc_final: 0.8437 (ttmt) REVERT: m 47 ASP cc_start: 0.8355 (m-30) cc_final: 0.8086 (m-30) REVERT: m 97 VAL cc_start: 0.9404 (t) cc_final: 0.9112 (p) REVERT: m 110 LYS cc_start: 0.8382 (mtmt) cc_final: 0.7992 (mtpp) REVERT: n 23 LYS cc_start: 0.8755 (mtmm) cc_final: 0.8282 (mtmm) REVERT: o 10 GLN cc_start: 0.9153 (tp40) cc_final: 0.8844 (tm-30) REVERT: o 11 ILE cc_start: 0.9603 (mt) cc_final: 0.9137 (mt) REVERT: o 16 LYS cc_start: 0.9161 (ttmt) cc_final: 0.8948 (ttmt) REVERT: p 53 ASP cc_start: 0.8323 (m-30) cc_final: 0.7944 (p0) REVERT: p 77 ASP cc_start: 0.7992 (m-30) cc_final: 0.7654 (m-30) REVERT: q 57 ARG cc_start: 0.8044 (mmp80) cc_final: 0.7062 (ptt180) REVERT: q 58 ILE cc_start: 0.9277 (mt) cc_final: 0.8623 (mt) REVERT: q 60 ASP cc_start: 0.7431 (m-30) cc_final: 0.6742 (m-30) REVERT: r 7 ARG cc_start: 0.7773 (mtt90) cc_final: 0.7501 (mtt-85) REVERT: r 73 SER cc_start: 0.8227 (t) cc_final: 0.7934 (m) REVERT: s 60 VAL cc_start: 0.8931 (t) cc_final: 0.8633 (p) REVERT: t 25 ARG cc_start: 0.8839 (ttm170) cc_final: 0.8635 (ttm-80) REVERT: u 10 GLU cc_start: 0.6706 (mm-30) cc_final: 0.5989 (mp0) REVERT: u 21 ARG cc_start: 0.8024 (tpp-160) cc_final: 0.7583 (mmm-85) REVERT: u 45 ARG cc_start: 0.8350 (mpp80) cc_final: 0.8024 (mtm180) REVERT: u 58 LYS cc_start: 0.8178 (tptm) cc_final: 0.7936 (tttt) outliers start: 2 outliers final: 1 residues processed: 831 average time/residue: 0.7391 time to fit residues: 951.8573 Evaluate side-chains 573 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 572 time to evaluate : 3.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain t residue 27 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 322 optimal weight: 10.0000 chunk 289 optimal weight: 0.9980 chunk 160 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 195 optimal weight: 0.9990 chunk 154 optimal weight: 8.9990 chunk 299 optimal weight: 0.9990 chunk 115 optimal weight: 10.0000 chunk 182 optimal weight: 10.0000 chunk 222 optimal weight: 2.9990 chunk 346 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 24 ASN ** c 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 6 HIS c 69 HIS c 190 HIS d 100 ASN e 20 ASN e 98 GLN f 81 ASN ** g 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 58 GLN i 6 ASN i 50 GLN k 81 ASN k 85 ASN ** k 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 72 HIS m 40 ASN m 91 HIS m 105 ASN p 54 GLN p 73 GLN q 34 HIS s 52 HIS ** s 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 68 HIS u 56 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 55616 Z= 0.216 Angle : 0.661 8.813 82650 Z= 0.336 Chirality : 0.038 0.266 10466 Planarity : 0.005 0.053 4829 Dihedral : 23.716 179.990 26508 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.20 % Allowed : 14.29 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.15), residues: 2348 helix: -2.63 (0.14), residues: 875 sheet: -2.24 (0.25), residues: 400 loop : -2.35 (0.18), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP d 170 HIS 0.006 0.001 HIS q 34 PHE 0.016 0.001 PHE p 38 TYR 0.019 0.002 TYR l 117 ARG 0.006 0.001 ARG q 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 615 time to evaluate : 3.003 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 TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: b 154 MET cc_start: 0.5060 (ttt) cc_final: 0.4748 (tmm) REVERT: c 140 ASN cc_start: 0.8557 (p0) cc_final: 0.8251 (p0) REVERT: e 15 LYS cc_start: 0.8702 (tptt) cc_final: 0.8280 (ttmt) REVERT: e 66 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7774 (tm-30) REVERT: e 88 SER cc_start: 0.9264 (m) cc_final: 0.8845 (p) REVERT: f 14 GLN cc_start: 0.8984 (mm110) cc_final: 0.8665 (mm110) REVERT: f 18 VAL cc_start: 0.9158 (p) cc_final: 0.8937 (p) REVERT: f 42 TRP cc_start: 0.8641 (m-10) cc_final: 0.8291 (m-10) REVERT: f 56 LYS cc_start: 0.9227 (mmtm) cc_final: 0.8905 (mmmt) REVERT: f 71 LEU cc_start: 0.9005 (tp) cc_final: 0.8801 (tt) REVERT: f 77 ASN cc_start: 0.8994 (m-40) cc_final: 0.8556 (p0) REVERT: g 27 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7476 (tpp) REVERT: g 97 ASN cc_start: 0.8668 (m110) cc_final: 0.8372 (m-40) REVERT: g 107 PHE cc_start: 0.8077 (m-10) cc_final: 0.7818 (m-80) REVERT: g 143 ARG cc_start: 0.8840 (ttp80) cc_final: 0.8576 (ttp80) REVERT: h 23 THR cc_start: 0.9188 (m) cc_final: 0.8821 (t) REVERT: j 58 ASN cc_start: 0.8194 (t0) cc_final: 0.7993 (t0) REVERT: j 88 MET cc_start: 0.7526 (ttt) cc_final: 0.6796 (tmm) REVERT: k 38 GLN cc_start: 0.9094 (mm-40) cc_final: 0.8821 (mp10) REVERT: k 68 GLU cc_start: 0.8400 (pp20) cc_final: 0.7653 (pp20) REVERT: k 93 ARG cc_start: 0.7955 (ttt90) cc_final: 0.7668 (ttt180) REVERT: k 100 LEU cc_start: 0.9007 (mt) cc_final: 0.8557 (mt) REVERT: k 109 SER cc_start: 0.8811 (m) cc_final: 0.7900 (m) REVERT: l 15 MET cc_start: 0.6616 (pmt) cc_final: 0.5832 (ptt) REVERT: l 73 ASN cc_start: 0.9060 (p0) cc_final: 0.8852 (p0) REVERT: l 78 SER cc_start: 0.9232 (m) cc_final: 0.8773 (p) REVERT: l 88 LYS cc_start: 0.8772 (tttm) cc_final: 0.8520 (ttpt) REVERT: n 4 GLU cc_start: 0.8447 (tp30) cc_final: 0.8109 (tp30) REVERT: n 7 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8846 (ptmt) REVERT: o 54 ARG cc_start: 0.8480 (mmm-85) cc_final: 0.8014 (mmm160) REVERT: p 53 ASP cc_start: 0.8173 (m-30) cc_final: 0.7840 (p0) REVERT: q 22 LYS cc_start: 0.8957 (mtmt) cc_final: 0.8494 (mtpp) REVERT: q 37 TYR cc_start: 0.8628 (m-80) cc_final: 0.8404 (m-80) REVERT: q 57 ARG cc_start: 0.7830 (mmp80) cc_final: 0.7200 (ptt-90) REVERT: q 60 ASP cc_start: 0.7745 (m-30) cc_final: 0.7341 (m-30) REVERT: r 7 ARG cc_start: 0.7736 (mtt90) cc_final: 0.7491 (mtt180) REVERT: t 20 HIS cc_start: 0.8965 (t70) cc_final: 0.8735 (t-170) REVERT: t 25 ARG cc_start: 0.8933 (ttm170) cc_final: 0.8559 (ttm-80) REVERT: u 10 GLU cc_start: 0.6647 (mm-30) cc_final: 0.5767 (mp0) REVERT: u 58 LYS cc_start: 0.8020 (tptm) cc_final: 0.7747 (tttt) outliers start: 62 outliers final: 43 residues processed: 642 average time/residue: 0.6672 time to fit residues: 696.9624 Evaluate side-chains 594 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 549 time to evaluate : 3.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 44 GLU Chi-restraints excluded: chain b residue 80 VAL Chi-restraints excluded: chain b residue 81 ARG Chi-restraints excluded: chain c residue 94 GLN Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain d residue 9 CYS Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 174 ASP Chi-restraints excluded: chain d residue 190 ASP Chi-restraints excluded: chain f residue 46 GLN Chi-restraints excluded: chain f residue 74 LEU Chi-restraints excluded: chain g residue 27 MET Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain h residue 7 LEU Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain i residue 32 ASN Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 83 THR Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain m residue 33 ILE Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain n residue 7 LYS Chi-restraints excluded: chain n residue 26 GLU Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain p residue 58 THR Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 5 LEU Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain t residue 4 THR Chi-restraints excluded: chain t residue 19 SER Chi-restraints excluded: chain t residue 36 VAL Chi-restraints excluded: chain u residue 16 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 192 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 288 optimal weight: 6.9990 chunk 236 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 347 optimal weight: 7.9990 chunk 375 optimal weight: 3.9990 chunk 309 optimal weight: 3.9990 chunk 344 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 278 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 168 HIS ** c 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 190 HIS ** f 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 50 GLN j 56 HIS j 64 GLN k 85 ASN ** l 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 77 HIS p 54 GLN q 48 HIS ** s 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 3 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 55616 Z= 0.397 Angle : 0.726 9.336 82650 Z= 0.366 Chirality : 0.041 0.271 10466 Planarity : 0.006 0.061 4829 Dihedral : 23.692 179.637 26505 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 5.78 % Allowed : 16.61 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.16), residues: 2348 helix: -1.76 (0.16), residues: 862 sheet: -1.91 (0.27), residues: 373 loop : -2.17 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP b 23 HIS 0.009 0.002 HIS s 57 PHE 0.017 0.002 PHE p 38 TYR 0.017 0.002 TYR d 103 ARG 0.009 0.001 ARG m 109 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 556 time to evaluate : 3.279 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 TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: c 32 TYR cc_start: 0.8582 (m-10) cc_final: 0.8381 (m-10) REVERT: c 114 MET cc_start: 0.8311 (tpp) cc_final: 0.7931 (tpp) REVERT: d 196 ASN cc_start: 0.8922 (m110) cc_final: 0.8675 (m-40) REVERT: e 15 LYS cc_start: 0.8835 (tptt) cc_final: 0.8413 (ttmt) REVERT: e 66 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7939 (tm-30) REVERT: e 88 SER cc_start: 0.9296 (m) cc_final: 0.8871 (p) REVERT: e 133 ASN cc_start: 0.9016 (t0) cc_final: 0.8629 (t0) REVERT: f 5 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7762 (tm-30) REVERT: f 27 LYS cc_start: 0.9141 (mmtp) cc_final: 0.8840 (mmtp) REVERT: f 42 TRP cc_start: 0.8713 (m-10) cc_final: 0.8378 (m-10) REVERT: f 56 LYS cc_start: 0.9317 (mmtm) cc_final: 0.9011 (mmmt) REVERT: h 80 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8145 (ptm-80) REVERT: j 9 ARG cc_start: 0.8839 (ptp-170) cc_final: 0.8575 (ptp-110) REVERT: j 16 ARG cc_start: 0.8640 (mmt180) cc_final: 0.8386 (mmt180) REVERT: j 88 MET cc_start: 0.7227 (ttt) cc_final: 0.6754 (tmm) REVERT: k 68 GLU cc_start: 0.8479 (pp20) cc_final: 0.7726 (pp20) REVERT: l 15 MET cc_start: 0.6609 (pmt) cc_final: 0.5783 (ptt) REVERT: l 78 SER cc_start: 0.9380 (m) cc_final: 0.8703 (p) REVERT: l 88 LYS cc_start: 0.8838 (tttm) cc_final: 0.8509 (ttmt) REVERT: o 54 ARG cc_start: 0.8378 (mmm-85) cc_final: 0.8051 (mmm160) REVERT: p 53 ASP cc_start: 0.8199 (m-30) cc_final: 0.7789 (p0) REVERT: q 22 LYS cc_start: 0.9044 (mtmt) cc_final: 0.8585 (mtpp) REVERT: q 57 ARG cc_start: 0.8088 (mmp80) cc_final: 0.7424 (ptt180) REVERT: q 60 ASP cc_start: 0.7920 (m-30) cc_final: 0.7463 (m-30) REVERT: r 4 PHE cc_start: 0.5965 (m-80) cc_final: 0.5060 (m-80) REVERT: r 7 ARG cc_start: 0.7799 (mtt90) cc_final: 0.7368 (mtp85) REVERT: t 25 ARG cc_start: 0.8982 (ttm170) cc_final: 0.8720 (ttm-80) REVERT: t 48 GLN cc_start: 0.8923 (mm-40) cc_final: 0.8663 (mm-40) REVERT: u 58 LYS cc_start: 0.8004 (tptm) cc_final: 0.7681 (tttt) outliers start: 112 outliers final: 86 residues processed: 609 average time/residue: 0.6417 time to fit residues: 641.0886 Evaluate side-chains 606 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 519 time to evaluate : 3.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 39 HIS Chi-restraints excluded: chain b residue 44 GLU Chi-restraints excluded: chain b residue 67 ILE Chi-restraints excluded: chain b residue 80 VAL Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 216 SER Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 94 GLN Chi-restraints excluded: chain c residue 111 LEU Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain c residue 202 ILE Chi-restraints excluded: chain d residue 9 CYS Chi-restraints excluded: chain d residue 32 CYS Chi-restraints excluded: chain d residue 50 ASP Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 141 ASP Chi-restraints excluded: chain d residue 174 ASP Chi-restraints excluded: chain d residue 190 ASP Chi-restraints excluded: chain e residue 81 THR Chi-restraints excluded: chain f residue 46 GLN Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 62 MET Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain g residue 101 MET Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 7 LEU Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 80 ARG Chi-restraints excluded: chain h residue 83 LEU Chi-restraints excluded: chain h residue 128 THR Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 32 ASN Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 20 GLN Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 74 LEU Chi-restraints excluded: chain j residue 83 THR Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 47 SER Chi-restraints excluded: chain k residue 58 SER Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain o residue 4 SER Chi-restraints excluded: chain o residue 16 LYS Chi-restraints excluded: chain o residue 33 SER Chi-restraints excluded: chain o residue 48 LYS Chi-restraints excluded: chain p residue 11 SER Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain p residue 58 THR Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 32 VAL Chi-restraints excluded: chain q residue 41 VAL Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain q residue 58 ILE Chi-restraints excluded: chain r residue 65 LEU Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 5 LEU Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain t residue 4 THR Chi-restraints excluded: chain t residue 19 SER Chi-restraints excluded: chain t residue 36 VAL Chi-restraints excluded: chain t residue 59 ASP Chi-restraints excluded: chain u residue 16 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 343 optimal weight: 10.0000 chunk 261 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 233 optimal weight: 0.6980 chunk 348 optimal weight: 3.9990 chunk 369 optimal weight: 0.0050 chunk 182 optimal weight: 10.0000 chunk 330 optimal weight: 0.9980 chunk 99 optimal weight: 10.0000 overall best weight: 1.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 190 HIS f 17 GLN g 148 ASN ** h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 50 GLN ** j 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 77 HIS p 54 GLN ** s 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 55616 Z= 0.187 Angle : 0.592 12.158 82650 Z= 0.304 Chirality : 0.035 0.253 10466 Planarity : 0.004 0.045 4829 Dihedral : 23.555 179.176 26505 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 4.80 % Allowed : 19.19 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.17), residues: 2348 helix: -1.26 (0.16), residues: 866 sheet: -1.72 (0.27), residues: 389 loop : -2.01 (0.19), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP b 23 HIS 0.005 0.001 HIS s 57 PHE 0.017 0.001 PHE h 66 TYR 0.020 0.001 TYR l 117 ARG 0.007 0.000 ARG g 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 566 time to evaluate : 3.542 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 TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: c 3 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7687 (pm20) REVERT: e 15 LYS cc_start: 0.8795 (tptt) cc_final: 0.8372 (ttmt) REVERT: e 66 GLU cc_start: 0.8359 (tm-30) cc_final: 0.8137 (tm-30) REVERT: e 88 SER cc_start: 0.9272 (m) cc_final: 0.8870 (p) REVERT: e 133 ASN cc_start: 0.9033 (t0) cc_final: 0.8642 (t0) REVERT: f 5 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7412 (tm-30) REVERT: f 42 TRP cc_start: 0.8656 (m-10) cc_final: 0.8318 (m-10) REVERT: f 56 LYS cc_start: 0.9260 (mmtm) cc_final: 0.8994 (mmmt) REVERT: h 21 GLU cc_start: 0.7563 (mp0) cc_final: 0.7324 (mp0) REVERT: h 23 THR cc_start: 0.9086 (m) cc_final: 0.8776 (t) REVERT: i 91 ASP cc_start: 0.6424 (p0) cc_final: 0.6046 (p0) REVERT: j 9 ARG cc_start: 0.8868 (ptp-170) cc_final: 0.8558 (ptp-110) REVERT: j 88 MET cc_start: 0.7142 (ttt) cc_final: 0.6704 (tmm) REVERT: k 30 THR cc_start: 0.9617 (m) cc_final: 0.9224 (p) REVERT: k 38 GLN cc_start: 0.9045 (mm-40) cc_final: 0.8682 (mp10) REVERT: k 68 GLU cc_start: 0.8438 (pp20) cc_final: 0.7673 (pp20) REVERT: l 15 MET cc_start: 0.6572 (pmt) cc_final: 0.5792 (ptt) REVERT: l 78 SER cc_start: 0.9359 (m) cc_final: 0.8703 (p) REVERT: m 72 GLU cc_start: 0.8452 (pp20) cc_final: 0.8227 (pp20) REVERT: n 4 GLU cc_start: 0.8521 (tp30) cc_final: 0.8270 (tp30) REVERT: n 10 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8426 (tm-30) REVERT: o 7 GLU cc_start: 0.9321 (tp30) cc_final: 0.9051 (tp30) REVERT: o 54 ARG cc_start: 0.8249 (mmm-85) cc_final: 0.7997 (mmm160) REVERT: p 53 ASP cc_start: 0.8096 (m-30) cc_final: 0.7713 (p0) REVERT: q 22 LYS cc_start: 0.8863 (mtmt) cc_final: 0.8486 (mtpp) REVERT: q 37 TYR cc_start: 0.8676 (m-80) cc_final: 0.8432 (m-80) REVERT: r 4 PHE cc_start: 0.5878 (m-80) cc_final: 0.5099 (m-80) REVERT: r 7 ARG cc_start: 0.7800 (mtt90) cc_final: 0.7336 (mtp85) REVERT: r 25 ASP cc_start: 0.8406 (t0) cc_final: 0.7759 (t70) REVERT: r 27 ASN cc_start: 0.9086 (m-40) cc_final: 0.8606 (p0) REVERT: s 24 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7685 (mp0) REVERT: s 44 MET cc_start: 0.8151 (mtm) cc_final: 0.7936 (ptp) REVERT: t 25 ARG cc_start: 0.8990 (ttm170) cc_final: 0.8762 (ttm-80) REVERT: t 48 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8527 (mm-40) REVERT: u 58 LYS cc_start: 0.7950 (tptm) cc_final: 0.7645 (tttt) outliers start: 93 outliers final: 66 residues processed: 607 average time/residue: 0.6403 time to fit residues: 643.1753 Evaluate side-chains 597 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 530 time to evaluate : 3.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 44 GLU Chi-restraints excluded: chain b residue 67 ILE Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 80 VAL Chi-restraints excluded: chain b residue 147 SER Chi-restraints excluded: chain b residue 216 SER Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 94 GLN Chi-restraints excluded: chain c residue 111 LEU Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain d residue 9 CYS Chi-restraints excluded: chain d residue 32 CYS Chi-restraints excluded: chain d residue 50 ASP Chi-restraints excluded: chain d residue 174 ASP Chi-restraints excluded: chain d residue 190 ASP Chi-restraints excluded: chain e residue 19 VAL Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain f residue 62 MET Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain g residue 101 MET Chi-restraints excluded: chain g residue 153 HIS Chi-restraints excluded: chain h residue 7 LEU Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 32 ASN Chi-restraints excluded: chain i residue 62 ASP Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 30 LYS Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 47 SER Chi-restraints excluded: chain k residue 58 SER Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 110 ILE Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain n residue 26 GLU Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain o residue 33 SER Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 32 VAL Chi-restraints excluded: chain q residue 41 VAL Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain q residue 58 ILE Chi-restraints excluded: chain r residue 65 LEU Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain t residue 19 SER Chi-restraints excluded: chain t residue 27 MET Chi-restraints excluded: chain t residue 36 VAL Chi-restraints excluded: chain u residue 16 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 307 optimal weight: 0.9980 chunk 209 optimal weight: 0.2980 chunk 5 optimal weight: 7.9990 chunk 274 optimal weight: 9.9990 chunk 152 optimal weight: 6.9990 chunk 315 optimal weight: 2.9990 chunk 255 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 188 optimal weight: 0.9980 chunk 331 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 190 HIS f 77 ASN ** h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 29 GLN l 77 HIS n 45 GLN p 54 GLN ** q 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 55616 Z= 0.213 Angle : 0.593 11.268 82650 Z= 0.302 Chirality : 0.035 0.327 10466 Planarity : 0.004 0.044 4829 Dihedral : 23.489 179.983 26505 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 5.52 % Allowed : 19.70 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.17), residues: 2348 helix: -0.96 (0.17), residues: 871 sheet: -1.47 (0.27), residues: 391 loop : -1.97 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP d 170 HIS 0.004 0.001 HIS s 57 PHE 0.017 0.001 PHE h 66 TYR 0.020 0.001 TYR l 117 ARG 0.006 0.000 ARG k 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 541 time to evaluate : 3.099 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 TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: c 3 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8069 (pm20) REVERT: c 114 MET cc_start: 0.8388 (tpp) cc_final: 0.8033 (tpp) REVERT: e 15 LYS cc_start: 0.8800 (tptt) cc_final: 0.8378 (ttmt) REVERT: e 66 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8075 (tm-30) REVERT: e 88 SER cc_start: 0.9275 (m) cc_final: 0.8904 (p) REVERT: e 133 ASN cc_start: 0.9060 (t0) cc_final: 0.8663 (t0) REVERT: f 27 LYS cc_start: 0.9374 (mmmm) cc_final: 0.9098 (mmtp) REVERT: f 56 LYS cc_start: 0.9169 (mmtm) cc_final: 0.8859 (mmmt) REVERT: g 27 MET cc_start: 0.7422 (tpp) cc_final: 0.7216 (tpp) REVERT: h 21 GLU cc_start: 0.7580 (mp0) cc_final: 0.7349 (mp0) REVERT: h 23 THR cc_start: 0.9066 (m) cc_final: 0.8781 (t) REVERT: h 80 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8139 (ptm-80) REVERT: i 91 ASP cc_start: 0.6316 (p0) cc_final: 0.6085 (p0) REVERT: j 9 ARG cc_start: 0.8874 (ptp-170) cc_final: 0.8557 (ptp-110) REVERT: j 88 MET cc_start: 0.7145 (ttt) cc_final: 0.6685 (tmm) REVERT: k 30 THR cc_start: 0.9630 (m) cc_final: 0.9233 (p) REVERT: l 15 MET cc_start: 0.6569 (pmt) cc_final: 0.5806 (ptt) REVERT: l 78 SER cc_start: 0.9378 (m) cc_final: 0.8699 (p) REVERT: l 114 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8440 (mpp80) REVERT: m 95 LEU cc_start: 0.7647 (mt) cc_final: 0.7344 (mm) REVERT: n 4 GLU cc_start: 0.8565 (tp30) cc_final: 0.8322 (tp30) REVERT: n 10 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8297 (tm-30) REVERT: o 54 ARG cc_start: 0.8219 (mmm-85) cc_final: 0.8002 (mmm160) REVERT: p 53 ASP cc_start: 0.8105 (m-30) cc_final: 0.7702 (p0) REVERT: q 22 LYS cc_start: 0.8858 (mtmt) cc_final: 0.8531 (mtpp) REVERT: q 52 GLU cc_start: 0.7719 (tp30) cc_final: 0.7455 (mm-30) REVERT: r 4 PHE cc_start: 0.5930 (m-80) cc_final: 0.5141 (m-80) REVERT: r 7 ARG cc_start: 0.7783 (mtt90) cc_final: 0.7326 (mtp85) REVERT: s 44 MET cc_start: 0.8144 (mtm) cc_final: 0.7786 (ptp) REVERT: t 25 ARG cc_start: 0.8989 (ttm170) cc_final: 0.8613 (ttm-80) REVERT: t 48 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8549 (mm-40) REVERT: u 58 LYS cc_start: 0.7954 (tptm) cc_final: 0.7643 (tttt) outliers start: 107 outliers final: 91 residues processed: 583 average time/residue: 0.6218 time to fit residues: 602.3059 Evaluate side-chains 611 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 517 time to evaluate : 2.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 39 HIS Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 67 ILE Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 80 VAL Chi-restraints excluded: chain b residue 147 SER Chi-restraints excluded: chain b residue 216 SER Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 19 THR Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 94 GLN Chi-restraints excluded: chain c residue 111 LEU Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain d residue 9 CYS Chi-restraints excluded: chain d residue 32 CYS Chi-restraints excluded: chain d residue 50 ASP Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 174 ASP Chi-restraints excluded: chain d residue 190 ASP Chi-restraints excluded: chain e residue 19 VAL Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 82 LEU Chi-restraints excluded: chain f residue 62 MET Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain g residue 67 ASP Chi-restraints excluded: chain g residue 86 GLN Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain g residue 97 ASN Chi-restraints excluded: chain g residue 153 HIS Chi-restraints excluded: chain h residue 7 LEU Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 80 ARG Chi-restraints excluded: chain h residue 128 THR Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 32 ASN Chi-restraints excluded: chain i residue 62 ASP Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 30 LYS Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 74 LEU Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 47 SER Chi-restraints excluded: chain k residue 58 SER Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 110 ILE Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 101 SER Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain l residue 114 ARG Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 51 GLU Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain n residue 26 GLU Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain o residue 33 SER Chi-restraints excluded: chain o residue 48 LYS Chi-restraints excluded: chain p residue 11 SER Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 32 VAL Chi-restraints excluded: chain q residue 41 VAL Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain q residue 60 ASP Chi-restraints excluded: chain r residue 26 LEU Chi-restraints excluded: chain r residue 65 LEU Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 5 LEU Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain t residue 4 THR Chi-restraints excluded: chain t residue 19 SER Chi-restraints excluded: chain t residue 27 MET Chi-restraints excluded: chain t residue 36 VAL Chi-restraints excluded: chain t residue 59 ASP Chi-restraints excluded: chain u residue 16 LEU Chi-restraints excluded: chain u residue 34 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 124 optimal weight: 10.0000 chunk 332 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 216 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 369 optimal weight: 0.0030 chunk 306 optimal weight: 4.9990 chunk 171 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 overall best weight: 3.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 190 HIS ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 77 HIS ** n 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 45 GLN p 54 GLN q 34 HIS ** s 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 55616 Z= 0.327 Angle : 0.656 11.681 82650 Z= 0.332 Chirality : 0.038 0.327 10466 Planarity : 0.005 0.050 4829 Dihedral : 23.494 179.035 26505 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 6.76 % Allowed : 19.80 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.17), residues: 2348 helix: -0.88 (0.17), residues: 871 sheet: -1.55 (0.26), residues: 413 loop : -1.92 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP d 170 HIS 0.005 0.001 HIS c 6 PHE 0.014 0.001 PHE p 38 TYR 0.021 0.002 TYR l 117 ARG 0.005 0.001 ARG d 97 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 534 time to evaluate : 3.157 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 TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: c 3 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8016 (pm20) REVERT: c 114 MET cc_start: 0.8465 (tpp) cc_final: 0.8176 (tpp) REVERT: e 15 LYS cc_start: 0.8833 (tptt) cc_final: 0.8415 (ttmt) REVERT: e 88 SER cc_start: 0.9281 (m) cc_final: 0.8898 (p) REVERT: e 133 ASN cc_start: 0.9024 (t0) cc_final: 0.8636 (t0) REVERT: f 5 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7394 (tm-30) REVERT: f 56 LYS cc_start: 0.9209 (mmtm) cc_final: 0.8960 (mmmt) REVERT: h 23 THR cc_start: 0.9087 (m) cc_final: 0.8781 (t) REVERT: h 80 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8256 (ptm-80) REVERT: i 91 ASP cc_start: 0.6569 (p0) cc_final: 0.6224 (p0) REVERT: j 9 ARG cc_start: 0.8870 (ptp-170) cc_final: 0.8648 (ptp-110) REVERT: j 16 ARG cc_start: 0.8467 (mmt180) cc_final: 0.8257 (mmt180) REVERT: j 20 GLN cc_start: 0.9214 (tm-30) cc_final: 0.9002 (tm-30) REVERT: j 24 GLU cc_start: 0.8381 (pm20) cc_final: 0.7885 (pm20) REVERT: j 78 GLN cc_start: 0.7333 (pp30) cc_final: 0.7026 (tm-30) REVERT: j 88 MET cc_start: 0.7160 (ttt) cc_final: 0.6649 (tmm) REVERT: k 30 THR cc_start: 0.9635 (m) cc_final: 0.9230 (p) REVERT: l 15 MET cc_start: 0.6443 (pmt) cc_final: 0.5652 (ptt) REVERT: l 78 SER cc_start: 0.9396 (m) cc_final: 0.8694 (p) REVERT: l 114 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8687 (mpp80) REVERT: m 37 THR cc_start: 0.7595 (m) cc_final: 0.7267 (p) REVERT: m 86 TYR cc_start: 0.8390 (t80) cc_final: 0.8119 (t80) REVERT: n 4 GLU cc_start: 0.8705 (tp30) cc_final: 0.8447 (tp30) REVERT: n 62 ASN cc_start: 0.7802 (OUTLIER) cc_final: 0.7521 (p0) REVERT: o 54 ARG cc_start: 0.8302 (mmm-85) cc_final: 0.8091 (mmm160) REVERT: p 53 ASP cc_start: 0.8052 (m-30) cc_final: 0.7756 (p0) REVERT: r 4 PHE cc_start: 0.6084 (m-80) cc_final: 0.5665 (m-80) REVERT: s 44 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7859 (ptp) REVERT: t 25 ARG cc_start: 0.9026 (ttm170) cc_final: 0.8686 (ttm-80) REVERT: t 48 GLN cc_start: 0.8904 (mm-40) cc_final: 0.8562 (mm-40) REVERT: u 58 LYS cc_start: 0.7926 (tptm) cc_final: 0.7618 (tttt) outliers start: 131 outliers final: 110 residues processed: 592 average time/residue: 0.6341 time to fit residues: 624.0395 Evaluate side-chains 633 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 518 time to evaluate : 3.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 27 MET Chi-restraints excluded: chain b residue 39 HIS Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 44 GLU Chi-restraints excluded: chain b residue 67 ILE Chi-restraints excluded: chain b residue 80 VAL Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 147 SER Chi-restraints excluded: chain b residue 216 SER Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 19 THR Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 94 GLN Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 202 ILE Chi-restraints excluded: chain d residue 9 CYS Chi-restraints excluded: chain d residue 32 CYS Chi-restraints excluded: chain d residue 50 ASP Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 141 ASP Chi-restraints excluded: chain d residue 174 ASP Chi-restraints excluded: chain d residue 190 ASP Chi-restraints excluded: chain e residue 19 VAL Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 82 LEU Chi-restraints excluded: chain e residue 142 PHE Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 62 MET Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain g residue 67 ASP Chi-restraints excluded: chain g residue 86 GLN Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain g residue 97 ASN Chi-restraints excluded: chain g residue 101 MET Chi-restraints excluded: chain g residue 153 HIS Chi-restraints excluded: chain h residue 7 LEU Chi-restraints excluded: chain h residue 46 ILE Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 80 ARG Chi-restraints excluded: chain h residue 83 LEU Chi-restraints excluded: chain h residue 107 ASN Chi-restraints excluded: chain h residue 112 THR Chi-restraints excluded: chain h residue 128 THR Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 32 ASN Chi-restraints excluded: chain i residue 62 ASP Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 30 LYS Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 74 LEU Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 47 SER Chi-restraints excluded: chain k residue 58 SER Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 110 ILE Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain l residue 27 CYS Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 101 SER Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain l residue 114 ARG Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 51 GLU Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain n residue 26 GLU Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain n residue 62 ASN Chi-restraints excluded: chain o residue 4 SER Chi-restraints excluded: chain o residue 16 LYS Chi-restraints excluded: chain o residue 33 SER Chi-restraints excluded: chain o residue 41 ASP Chi-restraints excluded: chain o residue 48 LYS Chi-restraints excluded: chain o residue 68 ASP Chi-restraints excluded: chain p residue 11 SER Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain p residue 55 GLU Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 32 VAL Chi-restraints excluded: chain q residue 41 VAL Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain q residue 60 ASP Chi-restraints excluded: chain r residue 26 LEU Chi-restraints excluded: chain r residue 65 LEU Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 5 LEU Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 44 MET Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain t residue 4 THR Chi-restraints excluded: chain t residue 19 SER Chi-restraints excluded: chain t residue 27 MET Chi-restraints excluded: chain t residue 36 VAL Chi-restraints excluded: chain t residue 59 ASP Chi-restraints excluded: chain t residue 79 LEU Chi-restraints excluded: chain u residue 16 LEU Chi-restraints excluded: chain u residue 34 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 356 optimal weight: 0.6980 chunk 41 optimal weight: 10.0000 chunk 210 optimal weight: 5.9990 chunk 269 optimal weight: 9.9990 chunk 209 optimal weight: 0.3980 chunk 311 optimal weight: 7.9990 chunk 206 optimal weight: 6.9990 chunk 368 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 chunk 224 optimal weight: 8.9990 chunk 169 optimal weight: 7.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 190 HIS ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 50 GLN ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 77 HIS ** n 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 45 GLN p 54 GLN ** s 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 55616 Z= 0.255 Angle : 0.617 11.147 82650 Z= 0.314 Chirality : 0.036 0.258 10466 Planarity : 0.004 0.048 4829 Dihedral : 23.450 179.411 26505 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 6.34 % Allowed : 21.30 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.17), residues: 2348 helix: -0.72 (0.17), residues: 868 sheet: -1.51 (0.26), residues: 415 loop : -1.86 (0.20), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP d 170 HIS 0.004 0.001 HIS c 6 PHE 0.013 0.001 PHE p 38 TYR 0.022 0.002 TYR l 117 ARG 0.007 0.000 ARG k 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 532 time to evaluate : 2.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: c 3 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8136 (pm20) REVERT: c 114 MET cc_start: 0.8433 (tpp) cc_final: 0.8142 (tpp) REVERT: e 15 LYS cc_start: 0.8813 (tptt) cc_final: 0.8369 (ttmt) REVERT: e 88 SER cc_start: 0.9281 (m) cc_final: 0.8900 (p) REVERT: e 133 ASN cc_start: 0.9020 (t0) cc_final: 0.8612 (t0) REVERT: f 5 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7276 (tm-30) REVERT: f 27 LYS cc_start: 0.9356 (mmmm) cc_final: 0.9116 (mmtp) REVERT: f 56 LYS cc_start: 0.9140 (mmtm) cc_final: 0.8856 (mmmt) REVERT: h 23 THR cc_start: 0.9135 (m) cc_final: 0.8815 (t) REVERT: h 80 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.8149 (ptm-80) REVERT: i 91 ASP cc_start: 0.6454 (p0) cc_final: 0.6160 (p0) REVERT: j 9 ARG cc_start: 0.8867 (ptp-170) cc_final: 0.8647 (ptp-110) REVERT: j 16 ARG cc_start: 0.8452 (mmt180) cc_final: 0.8229 (mmt180) REVERT: j 24 GLU cc_start: 0.8439 (pm20) cc_final: 0.8044 (pm20) REVERT: j 78 GLN cc_start: 0.7466 (pp30) cc_final: 0.7242 (tm-30) REVERT: j 88 MET cc_start: 0.7174 (ttt) cc_final: 0.6663 (tmm) REVERT: k 30 THR cc_start: 0.9634 (OUTLIER) cc_final: 0.9247 (p) REVERT: l 15 MET cc_start: 0.6409 (pmt) cc_final: 0.5607 (ptm) REVERT: l 62 GLU cc_start: 0.7609 (tp30) cc_final: 0.7219 (tp30) REVERT: l 78 SER cc_start: 0.9377 (m) cc_final: 0.8698 (p) REVERT: l 114 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8542 (mpp80) REVERT: m 37 THR cc_start: 0.7592 (m) cc_final: 0.7255 (p) REVERT: m 78 LYS cc_start: 0.9120 (mmmm) cc_final: 0.8892 (mmmt) REVERT: n 4 GLU cc_start: 0.8708 (tp30) cc_final: 0.8490 (tp30) REVERT: n 62 ASN cc_start: 0.7748 (OUTLIER) cc_final: 0.7491 (p0) REVERT: n 89 MET cc_start: 0.8890 (mmt) cc_final: 0.8656 (mmt) REVERT: o 7 GLU cc_start: 0.9367 (tp30) cc_final: 0.9009 (tp30) REVERT: p 53 ASP cc_start: 0.8034 (m-30) cc_final: 0.7752 (p0) REVERT: r 4 PHE cc_start: 0.6024 (m-80) cc_final: 0.5660 (m-80) REVERT: r 32 TYR cc_start: 0.9019 (m-10) cc_final: 0.8773 (m-10) REVERT: s 44 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7815 (ptp) REVERT: t 24 LEU cc_start: 0.9554 (tp) cc_final: 0.9320 (tp) REVERT: t 25 ARG cc_start: 0.8988 (ttm170) cc_final: 0.8769 (ttm-80) REVERT: t 48 GLN cc_start: 0.8896 (mm-40) cc_final: 0.8563 (mm-40) REVERT: u 58 LYS cc_start: 0.7968 (tptm) cc_final: 0.7654 (tttt) outliers start: 123 outliers final: 102 residues processed: 582 average time/residue: 0.6389 time to fit residues: 616.6270 Evaluate side-chains 628 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 520 time to evaluate : 3.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 27 MET Chi-restraints excluded: chain b residue 39 HIS Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 67 ILE Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 80 VAL Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 216 SER Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 19 THR Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain d residue 9 CYS Chi-restraints excluded: chain d residue 32 CYS Chi-restraints excluded: chain d residue 50 ASP Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 174 ASP Chi-restraints excluded: chain d residue 190 ASP Chi-restraints excluded: chain e residue 19 VAL Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 82 LEU Chi-restraints excluded: chain e residue 142 PHE Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 62 MET Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain g residue 67 ASP Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain g residue 97 ASN Chi-restraints excluded: chain g residue 101 MET Chi-restraints excluded: chain g residue 153 HIS Chi-restraints excluded: chain h residue 7 LEU Chi-restraints excluded: chain h residue 46 ILE Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 80 ARG Chi-restraints excluded: chain h residue 107 ASN Chi-restraints excluded: chain h residue 112 THR Chi-restraints excluded: chain h residue 128 THR Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 32 ASN Chi-restraints excluded: chain i residue 62 ASP Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 30 LYS Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 74 LEU Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 47 SER Chi-restraints excluded: chain k residue 58 SER Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 110 ILE Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain l residue 27 CYS Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 101 SER Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain l residue 114 ARG Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 51 GLU Chi-restraints excluded: chain m residue 91 HIS Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain n residue 26 GLU Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain n residue 62 ASN Chi-restraints excluded: chain o residue 4 SER Chi-restraints excluded: chain o residue 16 LYS Chi-restraints excluded: chain o residue 33 SER Chi-restraints excluded: chain o residue 41 ASP Chi-restraints excluded: chain o residue 48 LYS Chi-restraints excluded: chain p residue 11 SER Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 32 VAL Chi-restraints excluded: chain q residue 41 VAL Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain q residue 60 ASP Chi-restraints excluded: chain r residue 26 LEU Chi-restraints excluded: chain r residue 65 LEU Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 5 LEU Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 44 MET Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain t residue 4 THR Chi-restraints excluded: chain t residue 19 SER Chi-restraints excluded: chain t residue 27 MET Chi-restraints excluded: chain t residue 36 VAL Chi-restraints excluded: chain t residue 59 ASP Chi-restraints excluded: chain t residue 79 LEU Chi-restraints excluded: chain u residue 34 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 227 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 219 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 234 optimal weight: 9.9990 chunk 250 optimal weight: 1.9990 chunk 182 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 289 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 190 HIS ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 50 GLN ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 77 HIS ** n 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 45 GLN ** s 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 55616 Z= 0.393 Angle : 0.707 11.556 82650 Z= 0.356 Chirality : 0.040 0.267 10466 Planarity : 0.005 0.052 4829 Dihedral : 23.503 178.108 26505 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 6.60 % Allowed : 21.76 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.17), residues: 2348 helix: -0.79 (0.17), residues: 866 sheet: -1.45 (0.27), residues: 395 loop : -1.95 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP d 170 HIS 0.006 0.001 HIS c 6 PHE 0.036 0.002 PHE h 66 TYR 0.022 0.002 TYR l 117 ARG 0.008 0.001 ARG j 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 522 time to evaluate : 3.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: c 3 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8103 (pm20) REVERT: c 44 GLN cc_start: 0.9267 (mm-40) cc_final: 0.8862 (mm-40) REVERT: c 114 MET cc_start: 0.8499 (tpp) cc_final: 0.8246 (tpp) REVERT: e 15 LYS cc_start: 0.8863 (tptt) cc_final: 0.8427 (ttmt) REVERT: e 88 SER cc_start: 0.9305 (m) cc_final: 0.8909 (p) REVERT: e 133 ASN cc_start: 0.9042 (t0) cc_final: 0.8640 (t0) REVERT: f 5 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7384 (tm-30) REVERT: f 27 LYS cc_start: 0.9338 (mmmm) cc_final: 0.9084 (mmtp) REVERT: f 56 LYS cc_start: 0.9265 (mmtm) cc_final: 0.8988 (mmmt) REVERT: h 23 THR cc_start: 0.9161 (m) cc_final: 0.8838 (t) REVERT: h 80 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8325 (ptm-80) REVERT: i 91 ASP cc_start: 0.6722 (p0) cc_final: 0.6369 (p0) REVERT: j 9 ARG cc_start: 0.8894 (ptp-170) cc_final: 0.8556 (ptp-110) REVERT: j 24 GLU cc_start: 0.8446 (pm20) cc_final: 0.8116 (pm20) REVERT: j 88 MET cc_start: 0.7242 (ttt) cc_final: 0.6722 (tmm) REVERT: k 30 THR cc_start: 0.9644 (m) cc_final: 0.9244 (p) REVERT: l 15 MET cc_start: 0.6328 (pmt) cc_final: 0.5557 (ptm) REVERT: l 62 GLU cc_start: 0.7709 (tp30) cc_final: 0.7369 (tp30) REVERT: l 78 SER cc_start: 0.9381 (m) cc_final: 0.8688 (p) REVERT: m 37 THR cc_start: 0.7619 (m) cc_final: 0.7270 (p) REVERT: m 78 LYS cc_start: 0.9131 (mmmm) cc_final: 0.8869 (mmmt) REVERT: m 86 TYR cc_start: 0.8460 (t80) cc_final: 0.8224 (t80) REVERT: n 4 GLU cc_start: 0.8807 (tp30) cc_final: 0.8570 (tp30) REVERT: n 62 ASN cc_start: 0.7877 (OUTLIER) cc_final: 0.7568 (p0) REVERT: n 89 MET cc_start: 0.8898 (mmt) cc_final: 0.8674 (mmt) REVERT: o 7 GLU cc_start: 0.9396 (tp30) cc_final: 0.9085 (tp30) REVERT: p 53 ASP cc_start: 0.8292 (m-30) cc_final: 0.7773 (p0) REVERT: q 57 ARG cc_start: 0.8151 (mmm160) cc_final: 0.7661 (ptm-80) REVERT: r 4 PHE cc_start: 0.6218 (m-80) cc_final: 0.5704 (m-80) REVERT: r 7 ARG cc_start: 0.7924 (mtp85) cc_final: 0.7699 (mtp85) REVERT: r 32 TYR cc_start: 0.9065 (m-10) cc_final: 0.8825 (m-10) REVERT: s 44 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7794 (ptp) REVERT: t 25 ARG cc_start: 0.9012 (ttm170) cc_final: 0.8646 (ttm-80) REVERT: t 48 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8568 (mm-40) REVERT: u 58 LYS cc_start: 0.7975 (tptm) cc_final: 0.7656 (tttt) outliers start: 128 outliers final: 107 residues processed: 578 average time/residue: 0.6361 time to fit residues: 607.8009 Evaluate side-chains 621 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 510 time to evaluate : 3.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 27 MET Chi-restraints excluded: chain b residue 39 HIS Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 67 ILE Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 80 VAL Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 147 SER Chi-restraints excluded: chain b residue 216 SER Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 94 GLN Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 202 ILE Chi-restraints excluded: chain d residue 9 CYS Chi-restraints excluded: chain d residue 32 CYS Chi-restraints excluded: chain d residue 50 ASP Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 110 THR Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain d residue 141 ASP Chi-restraints excluded: chain d residue 174 ASP Chi-restraints excluded: chain d residue 190 ASP Chi-restraints excluded: chain e residue 19 VAL Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 82 LEU Chi-restraints excluded: chain e residue 142 PHE Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 62 MET Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain g residue 67 ASP Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain g residue 97 ASN Chi-restraints excluded: chain g residue 101 MET Chi-restraints excluded: chain g residue 153 HIS Chi-restraints excluded: chain h residue 7 LEU Chi-restraints excluded: chain h residue 46 ILE Chi-restraints excluded: chain h residue 72 ILE Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 80 ARG Chi-restraints excluded: chain h residue 83 LEU Chi-restraints excluded: chain h residue 107 ASN Chi-restraints excluded: chain h residue 112 THR Chi-restraints excluded: chain h residue 128 THR Chi-restraints excluded: chain i residue 32 ASN Chi-restraints excluded: chain i residue 62 ASP Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 30 LYS Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 74 LEU Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 47 SER Chi-restraints excluded: chain k residue 58 SER Chi-restraints excluded: chain k residue 79 LEU Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 110 ILE Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain l residue 27 CYS Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 101 SER Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 51 GLU Chi-restraints excluded: chain m residue 91 HIS Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain n residue 26 GLU Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain n residue 62 ASN Chi-restraints excluded: chain n residue 86 GLU Chi-restraints excluded: chain o residue 16 LYS Chi-restraints excluded: chain o residue 33 SER Chi-restraints excluded: chain o residue 48 LYS Chi-restraints excluded: chain p residue 11 SER Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 32 VAL Chi-restraints excluded: chain q residue 41 VAL Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain q residue 60 ASP Chi-restraints excluded: chain r residue 65 LEU Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 5 LEU Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 44 MET Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain t residue 4 THR Chi-restraints excluded: chain t residue 19 SER Chi-restraints excluded: chain t residue 27 MET Chi-restraints excluded: chain t residue 36 VAL Chi-restraints excluded: chain t residue 59 ASP Chi-restraints excluded: chain t residue 79 LEU Chi-restraints excluded: chain u residue 34 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 334 optimal weight: 0.0170 chunk 352 optimal weight: 0.8980 chunk 321 optimal weight: 10.0000 chunk 343 optimal weight: 1.9990 chunk 206 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 269 optimal weight: 8.9990 chunk 105 optimal weight: 7.9990 chunk 310 optimal weight: 8.9990 chunk 324 optimal weight: 9.9990 chunk 341 optimal weight: 0.9990 overall best weight: 1.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 190 HIS f 37 HIS ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 77 HIS ** n 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 73 GLN r 54 GLN ** s 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 55616 Z= 0.175 Angle : 0.586 12.161 82650 Z= 0.299 Chirality : 0.034 0.258 10466 Planarity : 0.004 0.046 4829 Dihedral : 23.397 179.931 26505 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 4.64 % Allowed : 24.19 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.18), residues: 2348 helix: -0.53 (0.17), residues: 869 sheet: -1.35 (0.27), residues: 406 loop : -1.87 (0.19), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP d 170 HIS 0.003 0.001 HIS s 57 PHE 0.030 0.001 PHE h 66 TYR 0.021 0.001 TYR l 117 ARG 0.007 0.000 ARG k 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 531 time to evaluate : 3.096 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 TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: c 3 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8158 (pm20) REVERT: c 114 MET cc_start: 0.8357 (tpp) cc_final: 0.8068 (tpp) REVERT: c 123 GLN cc_start: 0.8340 (mt0) cc_final: 0.7944 (mt0) REVERT: e 15 LYS cc_start: 0.8798 (tptt) cc_final: 0.8387 (ttmt) REVERT: e 88 SER cc_start: 0.9299 (m) cc_final: 0.8930 (p) REVERT: e 133 ASN cc_start: 0.9036 (t0) cc_final: 0.8664 (t0) REVERT: f 27 LYS cc_start: 0.9318 (mmmm) cc_final: 0.9043 (mmtp) REVERT: f 56 LYS cc_start: 0.9186 (mmtm) cc_final: 0.8926 (mmmt) REVERT: g 67 ASP cc_start: 0.7901 (m-30) cc_final: 0.7491 (p0) REVERT: h 23 THR cc_start: 0.9137 (m) cc_final: 0.8825 (t) REVERT: h 80 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8180 (ptm-80) REVERT: i 91 ASP cc_start: 0.6661 (p0) cc_final: 0.6402 (p0) REVERT: j 9 ARG cc_start: 0.8885 (ptp-170) cc_final: 0.8541 (ptp-110) REVERT: j 24 GLU cc_start: 0.8473 (pm20) cc_final: 0.8150 (pm20) REVERT: j 88 MET cc_start: 0.7174 (ttt) cc_final: 0.6677 (tmm) REVERT: k 30 THR cc_start: 0.9634 (OUTLIER) cc_final: 0.9268 (p) REVERT: k 65 VAL cc_start: 0.9172 (p) cc_final: 0.8698 (p) REVERT: l 15 MET cc_start: 0.6354 (pmt) cc_final: 0.5731 (ptt) REVERT: l 62 GLU cc_start: 0.7711 (tp30) cc_final: 0.7415 (tp30) REVERT: l 78 SER cc_start: 0.9327 (m) cc_final: 0.8663 (p) REVERT: m 37 THR cc_start: 0.7562 (m) cc_final: 0.7172 (p) REVERT: m 78 LYS cc_start: 0.9148 (mmmm) cc_final: 0.8915 (mmmt) REVERT: n 4 GLU cc_start: 0.8671 (tp30) cc_final: 0.8469 (tp30) REVERT: n 62 ASN cc_start: 0.7773 (OUTLIER) cc_final: 0.7494 (p0) REVERT: o 7 GLU cc_start: 0.9316 (tp30) cc_final: 0.8971 (tp30) REVERT: p 53 ASP cc_start: 0.8197 (m-30) cc_final: 0.7709 (p0) REVERT: q 57 ARG cc_start: 0.8078 (mmm160) cc_final: 0.7623 (ptm-80) REVERT: r 7 ARG cc_start: 0.7792 (mtp85) cc_final: 0.7400 (mtp85) REVERT: r 52 GLN cc_start: 0.9214 (tp40) cc_final: 0.8792 (tt0) REVERT: t 25 ARG cc_start: 0.8924 (ttm170) cc_final: 0.8650 (ttm-80) REVERT: u 58 LYS cc_start: 0.8000 (tptm) cc_final: 0.7655 (tttt) outliers start: 90 outliers final: 74 residues processed: 569 average time/residue: 0.6219 time to fit residues: 585.0901 Evaluate side-chains 598 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 520 time to evaluate : 3.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 39 HIS Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 67 ILE Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 147 SER Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain d residue 9 CYS Chi-restraints excluded: chain d residue 32 CYS Chi-restraints excluded: chain d residue 50 ASP Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 174 ASP Chi-restraints excluded: chain d residue 190 ASP Chi-restraints excluded: chain e residue 19 VAL Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 142 PHE Chi-restraints excluded: chain f residue 62 MET Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain g residue 97 ASN Chi-restraints excluded: chain g residue 101 MET Chi-restraints excluded: chain g residue 153 HIS Chi-restraints excluded: chain h residue 7 LEU Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 80 ARG Chi-restraints excluded: chain h residue 107 ASN Chi-restraints excluded: chain i residue 31 ASN Chi-restraints excluded: chain i residue 32 ASN Chi-restraints excluded: chain i residue 62 ASP Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 30 LYS Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 47 SER Chi-restraints excluded: chain k residue 58 SER Chi-restraints excluded: chain k residue 79 LEU Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 110 ILE Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain l residue 27 CYS Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain n residue 26 GLU Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain n residue 62 ASN Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 33 SER Chi-restraints excluded: chain o residue 48 LYS Chi-restraints excluded: chain p residue 11 SER Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 41 VAL Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain q residue 60 ASP Chi-restraints excluded: chain r residue 65 LEU Chi-restraints excluded: chain s residue 5 LEU Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain t residue 4 THR Chi-restraints excluded: chain t residue 19 SER Chi-restraints excluded: chain u residue 34 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 225 optimal weight: 1.9990 chunk 362 optimal weight: 7.9990 chunk 221 optimal weight: 9.9990 chunk 172 optimal weight: 3.9990 chunk 252 optimal weight: 0.5980 chunk 380 optimal weight: 5.9990 chunk 350 optimal weight: 8.9990 chunk 303 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 234 optimal weight: 8.9990 chunk 185 optimal weight: 0.5980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 190 HIS ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 50 GLN ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 77 HIS ** n 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 45 GLN p 73 GLN r 54 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 55616 Z= 0.229 Angle : 0.606 13.286 82650 Z= 0.307 Chirality : 0.035 0.272 10466 Planarity : 0.004 0.057 4829 Dihedral : 23.367 178.944 26505 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 4.38 % Allowed : 24.76 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.18), residues: 2348 helix: -0.44 (0.18), residues: 872 sheet: -1.33 (0.27), residues: 404 loop : -1.82 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP d 170 HIS 0.007 0.001 HIS g 153 PHE 0.030 0.001 PHE h 66 TYR 0.026 0.002 TYR o 78 ARG 0.015 0.000 ARG q 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 528 time to evaluate : 3.050 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 TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: c 3 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8196 (pm20) REVERT: c 114 MET cc_start: 0.8394 (tpp) cc_final: 0.8118 (tpp) REVERT: c 122 GLN cc_start: 0.8684 (tt0) cc_final: 0.8343 (tm-30) REVERT: c 123 GLN cc_start: 0.8353 (mt0) cc_final: 0.7865 (mt0) REVERT: e 15 LYS cc_start: 0.8844 (tptt) cc_final: 0.8393 (ttmt) REVERT: e 88 SER cc_start: 0.9310 (m) cc_final: 0.8936 (p) REVERT: e 133 ASN cc_start: 0.9034 (t0) cc_final: 0.8643 (t0) REVERT: f 27 LYS cc_start: 0.9303 (mmmm) cc_final: 0.9064 (mmtp) REVERT: f 56 LYS cc_start: 0.9176 (mmtm) cc_final: 0.8910 (mmmt) REVERT: g 67 ASP cc_start: 0.7949 (m-30) cc_final: 0.7552 (p0) REVERT: h 23 THR cc_start: 0.9137 (m) cc_final: 0.8827 (t) REVERT: h 80 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8146 (ptm-80) REVERT: i 91 ASP cc_start: 0.6599 (p0) cc_final: 0.6253 (p0) REVERT: j 9 ARG cc_start: 0.8891 (ptp-170) cc_final: 0.8538 (ptp-110) REVERT: j 23 GLN cc_start: 0.9153 (mp10) cc_final: 0.8563 (mp10) REVERT: j 24 GLU cc_start: 0.8484 (pm20) cc_final: 0.8180 (pm20) REVERT: j 88 MET cc_start: 0.7188 (ttt) cc_final: 0.6658 (tmm) REVERT: k 30 THR cc_start: 0.9649 (OUTLIER) cc_final: 0.9257 (p) REVERT: l 15 MET cc_start: 0.6354 (pmt) cc_final: 0.5705 (ptt) REVERT: l 62 GLU cc_start: 0.7677 (tp30) cc_final: 0.7399 (tp30) REVERT: l 78 SER cc_start: 0.9334 (m) cc_final: 0.8659 (p) REVERT: m 37 THR cc_start: 0.7605 (m) cc_final: 0.7213 (p) REVERT: m 78 LYS cc_start: 0.9181 (mmmm) cc_final: 0.8967 (mmmt) REVERT: n 4 GLU cc_start: 0.8715 (tp30) cc_final: 0.8487 (tp30) REVERT: n 62 ASN cc_start: 0.7850 (OUTLIER) cc_final: 0.7564 (p0) REVERT: o 7 GLU cc_start: 0.9346 (tp30) cc_final: 0.8965 (tp30) REVERT: p 53 ASP cc_start: 0.8223 (m-30) cc_final: 0.7739 (p0) REVERT: q 57 ARG cc_start: 0.8112 (mmm160) cc_final: 0.7634 (ptm-80) REVERT: r 7 ARG cc_start: 0.7811 (mtp85) cc_final: 0.7461 (mtp85) REVERT: r 52 GLN cc_start: 0.9213 (tp40) cc_final: 0.8832 (tt0) REVERT: t 25 ARG cc_start: 0.8865 (ttm170) cc_final: 0.8620 (ttm-80) REVERT: u 58 LYS cc_start: 0.7979 (tptm) cc_final: 0.7657 (tttt) outliers start: 85 outliers final: 77 residues processed: 568 average time/residue: 0.6418 time to fit residues: 607.9227 Evaluate side-chains 597 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 516 time to evaluate : 3.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 39 HIS Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 67 ILE Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 147 SER Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain d residue 9 CYS Chi-restraints excluded: chain d residue 32 CYS Chi-restraints excluded: chain d residue 50 ASP Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 174 ASP Chi-restraints excluded: chain d residue 190 ASP Chi-restraints excluded: chain e residue 19 VAL Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 142 PHE Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 62 MET Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain g residue 97 ASN Chi-restraints excluded: chain g residue 101 MET Chi-restraints excluded: chain h residue 7 LEU Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 80 ARG Chi-restraints excluded: chain h residue 107 ASN Chi-restraints excluded: chain i residue 31 ASN Chi-restraints excluded: chain i residue 32 ASN Chi-restraints excluded: chain i residue 62 ASP Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 30 LYS Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 47 SER Chi-restraints excluded: chain k residue 58 SER Chi-restraints excluded: chain k residue 79 LEU Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 110 ILE Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain l residue 27 CYS Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain n residue 26 GLU Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain n residue 62 ASN Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 33 SER Chi-restraints excluded: chain o residue 48 LYS Chi-restraints excluded: chain p residue 11 SER Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 32 VAL Chi-restraints excluded: chain q residue 41 VAL Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain q residue 60 ASP Chi-restraints excluded: chain r residue 65 LEU Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 5 LEU Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain t residue 4 THR Chi-restraints excluded: chain t residue 19 SER Chi-restraints excluded: chain u residue 34 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 240 optimal weight: 7.9990 chunk 322 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 279 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 84 optimal weight: 8.9990 chunk 303 optimal weight: 0.0010 chunk 127 optimal weight: 10.0000 chunk 311 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 overall best weight: 4.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 190 HIS ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 70 HIS ** j 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 77 HIS ** m 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 54 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.067724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.054704 restraints weight = 230607.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.055948 restraints weight = 90414.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.056679 restraints weight = 55388.705| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 55616 Z= 0.365 Angle : 0.695 13.395 82650 Z= 0.350 Chirality : 0.039 0.285 10466 Planarity : 0.005 0.060 4829 Dihedral : 23.442 178.155 26505 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 5.21 % Allowed : 24.19 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.17), residues: 2348 helix: -0.57 (0.17), residues: 872 sheet: -1.27 (0.27), residues: 392 loop : -1.93 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP d 170 HIS 0.006 0.001 HIS c 6 PHE 0.029 0.002 PHE h 66 TYR 0.026 0.002 TYR o 78 ARG 0.015 0.001 ARG q 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11320.55 seconds wall clock time: 205 minutes 39.72 seconds (12339.72 seconds total)