Starting phenix.real_space_refine on Sun Feb 25 00:45:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w77_21569/02_2024/6w77_21569.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w77_21569/02_2024/6w77_21569.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/6w77_21569/02_2024/6w77_21569.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w77_21569/02_2024/6w77_21569.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w77_21569/02_2024/6w77_21569.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w77_21569/02_2024/6w77_21569.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= 0.000 sd= 1.000 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 1519 5.49 5 S 54 5.16 5 C 24131 2.51 5 N 8951 2.21 5 O 13285 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 35": "OD1" <-> "OD2" Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C GLU 151": "OE1" <-> "OE2" Residue "C GLU 160": "OE1" <-> "OE2" Residue "C ASP 182": "OD1" <-> "OD2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "D TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 73": "NH1" <-> "NH2" Residue "D GLU 78": "OE1" <-> "OE2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D GLU 95": "OE1" <-> "OE2" Residue "D ASP 99": "OD1" <-> "OD2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "D TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 141": "OD1" <-> "OD2" Residue "D PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 194": "OD1" <-> "OD2" Residue "D TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E ARG 54": "NH1" <-> "NH2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "E ARG 68": "NH1" <-> "NH2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "E ARG 93": "NH1" <-> "NH2" Residue "E ARG 157": "NH1" <-> "NH2" Residue "F GLU 16": "OE1" <-> "OE2" Residue "F GLU 33": "OE1" <-> "OE2" Residue "F ASP 41": "OD1" <-> "OD2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 73": "OE1" <-> "OE2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "H ASP 9": "OD1" <-> "OD2" Residue "H PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 113": "OD1" <-> "OD2" Residue "I TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 88": "OE1" <-> "OE2" Residue "I PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 19": "OD1" <-> "OD2" Residue "J PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 60": "OD1" <-> "OD2" Residue "J ASP 63": "OD1" <-> "OD2" Residue "J TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 75": "OD1" <-> "OD2" Residue "J ASP 91": "OD1" <-> "OD2" Residue "J ASP 97": "OD1" <-> "OD2" Residue "K ASP 18": "OD1" <-> "OD2" Residue "K PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 72": "OD1" <-> "OD2" Residue "K TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 94": "OE1" <-> "OE2" Residue "K ASP 112": "OD1" <-> "OD2" Residue "L ARG 9": "NH1" <-> "NH2" Residue "L ARG 14": "NH1" <-> "NH2" Residue "L GLU 25": "OE1" <-> "OE2" Residue "L ARG 50": "NH1" <-> "NH2" Residue "L PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "L ARG 83": "NH1" <-> "NH2" Residue "M ASP 10": "OD1" <-> "OD2" Residue "M TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 49": "OE1" <-> "OE2" Residue "M ASP 57": "OD1" <-> "OD2" Residue "M GLU 58": "OE1" <-> "OE2" Residue "N ASP 17": "OD1" <-> "OD2" Residue "N GLU 25": "OE1" <-> "OE2" Residue "N ASP 32": "OD1" <-> "OD2" Residue "N PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 72": "NH1" <-> "NH2" Residue "O ARG 89": "NH1" <-> "NH2" Residue "P ASP 23": "OD1" <-> "OD2" Residue "P ARG 28": "NH1" <-> "NH2" Residue "P PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 51": "NH1" <-> "NH2" Residue "P GLU 77": "OE1" <-> "OE2" Residue "Q ARG 11": "NH1" <-> "NH2" Residue "Q ASP 15": "OD1" <-> "OD2" Residue "Q GLU 26": "OE1" <-> "OE2" Residue "Q ARG 27": "NH1" <-> "NH2" Residue "Q ARG 65": "NH1" <-> "NH2" Residue "Q ARG 77": "NH1" <-> "NH2" Residue "Q GLU 80": "OE1" <-> "OE2" Residue "R GLU 16": "OE1" <-> "OE2" Residue "R GLU 20": "OE1" <-> "OE2" Residue "R ARG 61": "NH1" <-> "NH2" Residue "S PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 26": "OD1" <-> "OD2" Residue "S GLU 72": "OE1" <-> "OE2" Residue "S TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 15": "OE1" <-> "OE2" Residue "T ASP 59": "OD1" <-> "OD2" Residue "T ARG 60": "NH1" <-> "NH2" Residue "T ARG 74": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 47940 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 32594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1519, 32594 Classifications: {'RNA': 1519} Modifications used: {'rna2p_pur': 111, 'rna2p_pyr': 84, 'rna3p_pur': 755, 'rna3p_pyr': 569} Link IDs: {'rna2p': 194, 'rna3p': 1324} Chain breaks: 3 Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "F" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 848 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "I" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1016 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "K" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 858 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 7, 'TRANS': 107} Chain: "L" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 949 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 114} Chain: "M" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 867 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain: "N" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "O" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 708 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'TRANS': 86} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 544 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "S" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "T" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 664 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Time building chain proxies: 26.04, per 1000 atoms: 0.54 Number of scatterers: 47940 At special positions: 0 Unit cell: (204.943, 221.038, 168.461, 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 54 16.00 P 1519 15.00 O 13285 8.00 N 8951 7.00 C 24131 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 28.27 Conformation dependent library (CDL) restraints added in 3.3 seconds 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3604 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 18 sheets defined 40.6% alpha, 18.3% beta 487 base pairs and 770 stacking pairs defined. Time for finding SS restraints: 21.93 Creating SS restraints... Processing helix chain 'C' and resid 5 through 10 removed outlier: 3.627A pdb=" N ARG C 10 " --> pdb=" O PRO C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 46 Processing helix chain 'C' and resid 71 through 77 removed outlier: 3.879A pdb=" N VAL C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 95 removed outlier: 3.857A pdb=" N ASP C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE C 93 " --> pdb=" O VAL C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 110 Processing helix chain 'C' and resid 111 through 125 Processing helix chain 'C' and resid 128 through 139 removed outlier: 4.068A pdb=" N VAL C 137 " --> pdb=" O MET C 133 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN C 139 " --> pdb=" O ARG C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 144 removed outlier: 3.660A pdb=" N GLY C 144 " --> pdb=" O MET C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 179 Processing helix chain 'D' and resid 8 through 16 removed outlier: 4.018A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 68 through 82 removed outlier: 3.505A pdb=" N LEU D 82 " --> pdb=" O GLU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 96 Processing helix chain 'D' and resid 97 through 105 Processing helix chain 'D' and resid 110 through 119 Processing helix chain 'D' and resid 147 through 150 Processing helix chain 'D' and resid 152 through 165 removed outlier: 3.962A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 205 removed outlier: 4.435A pdb=" N ILE D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR D 204 " --> pdb=" O ILE D 200 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER D 205 " --> pdb=" O VAL D 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 Processing helix chain 'E' and resid 110 through 119 removed outlier: 3.591A pdb=" N VAL E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 146 Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 160 through 164 removed outlier: 3.731A pdb=" N ILE E 164 " --> pdb=" O VAL E 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 15 Processing helix chain 'F' and resid 17 through 31 removed outlier: 3.878A pdb=" N ALA F 28 " --> pdb=" O ARG F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 81 removed outlier: 3.986A pdb=" N ILE F 71 " --> pdb=" O PRO F 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 20 removed outlier: 3.666A pdb=" N ASP H 9 " --> pdb=" O ASP H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 44 Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.922A pdb=" N LEU H 92 " --> pdb=" O LYS H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 99 Processing helix chain 'H' and resid 113 through 120 Processing helix chain 'I' and resid 33 through 38 Processing helix chain 'I' and resid 43 through 47 removed outlier: 3.517A pdb=" N VAL I 46 " --> pdb=" O ALA I 43 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL I 47 " --> pdb=" O ARG I 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 43 through 47' Processing helix chain 'I' and resid 48 through 54 removed outlier: 3.671A pdb=" N GLU I 52 " --> pdb=" O ARG I 48 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU I 53 " --> pdb=" O GLN I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 90 removed outlier: 3.682A pdb=" N MET I 87 " --> pdb=" O THR I 83 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU I 88 " --> pdb=" O ARG I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 101 removed outlier: 3.884A pdb=" N LEU I 97 " --> pdb=" O LEU I 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 29 removed outlier: 4.926A pdb=" N GLN J 20 " --> pdb=" O ARG J 16 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE J 25 " --> pdb=" O ALA J 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 58 Processing helix chain 'K' and resid 59 through 72 Processing helix chain 'K' and resid 73 through 75 No H-bonds generated for 'chain 'K' and resid 73 through 75' Processing helix chain 'K' and resid 94 through 103 Processing helix chain 'L' and resid 3 through 9 Processing helix chain 'L' and resid 114 through 118 Processing helix chain 'M' and resid 13 through 19 Processing helix chain 'M' and resid 25 through 37 Processing helix chain 'M' and resid 43 through 47 Processing helix chain 'M' and resid 48 through 59 removed outlier: 4.587A pdb=" N THR M 54 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU M 55 " --> pdb=" O GLN M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 78 Processing helix chain 'M' and resid 84 through 91 Processing helix chain 'M' and resid 105 through 110 removed outlier: 3.665A pdb=" N LYS M 109 " --> pdb=" O ALA M 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 20 removed outlier: 3.759A pdb=" N ALA N 7 " --> pdb=" O GLN N 3 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG N 8 " --> pdb=" O SER N 4 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU N 9 " --> pdb=" O MET N 5 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL N 10 " --> pdb=" O LYS N 6 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 31 removed outlier: 4.421A pdb=" N LEU N 26 " --> pdb=" O LYS N 22 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS N 27 " --> pdb=" O ARG N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 48 removed outlier: 3.537A pdb=" N LEU N 45 " --> pdb=" O TRP N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 89 Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 39 Processing helix chain 'O' and resid 41 through 45 removed outlier: 4.100A pdb=" N GLU O 45 " --> pdb=" O HIS O 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 4.659A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 85 removed outlier: 3.521A pdb=" N TYR O 78 " --> pdb=" O ASP O 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 64 Processing helix chain 'P' and resid 68 through 81 Processing helix chain 'R' and resid 11 through 17 removed outlier: 3.635A pdb=" N ALA R 15 " --> pdb=" O CYS R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 31 Processing helix chain 'R' and resid 41 through 46 removed outlier: 4.077A pdb=" N THR R 45 " --> pdb=" O PRO R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 65 Processing helix chain 'S' and resid 11 through 24 Processing helix chain 'S' and resid 40 through 44 Processing helix chain 'S' and resid 69 through 74 Processing helix chain 'T' and resid 4 through 41 removed outlier: 3.789A pdb=" N VAL T 35 " --> pdb=" O PHE T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 64 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 68 through 84 removed outlier: 3.713A pdb=" N ALA T 72 " --> pdb=" O HIS T 68 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 51 through 55 removed outlier: 3.802A pdb=" N ARG C 53 " --> pdb=" O HIS C 68 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL C 65 " --> pdb=" O GLN C 99 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 168 through 169 Processing sheet with id=AA3, first strand: chain 'D' and resid 128 through 130 removed outlier: 4.554A pdb=" N ILE D 123 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE D 182 " --> pdb=" O ASP D 141 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU D 179 " --> pdb=" O ASP D 174 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 12 through 17 removed outlier: 4.912A pdb=" N GLU E 13 " --> pdb=" O GLY E 40 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLY E 40 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LEU E 15 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL E 38 " --> pdb=" O LEU E 15 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 22 through 24 Processing sheet with id=AA6, first strand: chain 'E' and resid 85 through 88 removed outlier: 6.768A pdb=" N ILE E 106 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ALA E 127 " --> pdb=" O ILE E 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 35 through 46 removed outlier: 7.803A pdb=" N HIS F 37 " --> pdb=" O GLU F 65 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N GLU F 65 " --> pdb=" O HIS F 37 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU F 39 " --> pdb=" O ASN F 63 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ASN F 63 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ASP F 41 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N LEU F 61 " --> pdb=" O ASP F 41 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY F 43 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 24 through 28 removed outlier: 6.181A pdb=" N GLU H 58 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL H 51 " --> pdb=" O GLU H 58 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLU H 60 " --> pdb=" O PHE H 49 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE H 49 " --> pdb=" O GLU H 60 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR H 62 " --> pdb=" O GLU H 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 74 through 77 Processing sheet with id=AB1, first strand: chain 'H' and resid 74 through 77 removed outlier: 6.951A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N TYR H 128 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE H 101 " --> pdb=" O TYR H 128 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 5 through 7 removed outlier: 4.044A pdb=" N GLY I 7 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL I 18 " --> pdb=" O GLY I 7 " (cutoff:3.500A) removed outlier: 18.981A pdb=" N LYS I 26 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 14.205A pdb=" N VAL I 66 " --> pdb=" O LYS I 26 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL I 28 " --> pdb=" O ILE I 64 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 45 through 51 Processing sheet with id=AB4, first strand: chain 'J' and resid 45 through 51 removed outlier: 3.653A pdb=" N LYS N 96 " --> pdb=" O GLU J 66 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 41 through 44 removed outlier: 7.024A pdb=" N ILE K 34 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TRP K 44 " --> pdb=" O VAL K 32 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL K 32 " --> pdb=" O TRP K 44 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE K 23 " --> pdb=" O MET K 85 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU K 82 " --> pdb=" O ILE K 107 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ASN K 109 " --> pdb=" O LEU K 82 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL K 84 " --> pdb=" O ASN K 109 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR K 111 " --> pdb=" O VAL K 84 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 79 through 82 removed outlier: 6.800A pdb=" N ARG L 54 " --> pdb=" O THR L 35 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N VAL L 37 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL L 52 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N THR L 39 " --> pdb=" O ARG L 50 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ARG L 50 " --> pdb=" O THR L 39 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TYR L 95 " --> pdb=" O THR L 64 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 50 through 51 removed outlier: 6.196A pdb=" N ARG P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL P 21 " --> pdb=" O ARG P 35 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY P 37 " --> pdb=" O VAL P 19 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL P 2 " --> pdb=" O THR P 66 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Q' and resid 8 through 14 removed outlier: 8.484A pdb=" N GLN Q 9 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N GLU Q 26 " --> pdb=" O GLN Q 9 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG Q 11 " --> pdb=" O ALA Q 24 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL Q 22 " --> pdb=" O VAL Q 13 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N LYS Q 71 " --> pdb=" O LYS Q 43 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N HIS Q 45 " --> pdb=" O LYS Q 71 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TRP Q 73 " --> pdb=" O HIS Q 45 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU Q 75 " --> pdb=" O HIS Q 47 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N SER Q 72 " --> pdb=" O CYS Q 64 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR Q 74 " --> pdb=" O ARG Q 62 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL Q 78 " --> pdb=" O VAL Q 58 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL Q 58 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'S' and resid 30 through 32 removed outlier: 5.802A pdb=" N LEU S 30 " --> pdb=" O ALA S 49 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N HIS S 51 " --> pdb=" O LEU S 30 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N THR S 32 " --> pdb=" O HIS S 51 " (cutoff:3.500A) 657 hydrogen bonds defined for protein. 1842 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1224 hydrogen bonds 1964 hydrogen bond angles 0 basepair planarities 487 basepair parallelities 770 stacking parallelities Total time for adding SS restraints: 49.01 Time building geometry restraints manager: 29.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7077 1.33 - 1.45: 21313 1.45 - 1.57: 20542 1.57 - 1.69: 3031 1.69 - 1.81: 95 Bond restraints: 52058 Sorted by residual: bond pdb=" O3' U A1078 " pdb=" P G A1079 " ideal model delta sigma weight residual 1.607 1.550 0.057 1.50e-02 4.44e+03 1.43e+01 bond pdb=" O3' U A1075 " pdb=" P U A1076 " ideal model delta sigma weight residual 1.607 1.564 0.043 1.50e-02 4.44e+03 8.11e+00 bond pdb=" O3' G A1079 " pdb=" P A A1080 " ideal model delta sigma weight residual 1.607 1.570 0.037 1.50e-02 4.44e+03 6.17e+00 bond pdb=" C3' U A1083 " pdb=" O3' U A1083 " ideal model delta sigma weight residual 1.417 1.454 -0.037 1.50e-02 4.44e+03 5.95e+00 bond pdb=" O3' A A1082 " pdb=" P U A1083 " ideal model delta sigma weight residual 1.607 1.572 0.035 1.50e-02 4.44e+03 5.54e+00 ... (remaining 52053 not shown) Histogram of bond angle deviations from ideal: 90.92 - 99.53: 5 99.53 - 108.15: 15425 108.15 - 116.76: 31168 116.76 - 125.38: 25420 125.38 - 133.99: 5794 Bond angle restraints: 77812 Sorted by residual: angle pdb=" O2' C A 924 " pdb=" C2' C A 924 " pdb=" C1' C A 924 " ideal model delta sigma weight residual 108.40 90.92 17.48 1.50e+00 4.44e-01 1.36e+02 angle pdb=" O3' C A 924 " pdb=" C3' C A 924 " pdb=" C2' C A 924 " ideal model delta sigma weight residual 113.70 96.51 17.19 1.50e+00 4.44e-01 1.31e+02 angle pdb=" C3' C A 924 " pdb=" C2' C A 924 " pdb=" O2' C A 924 " ideal model delta sigma weight residual 110.70 122.59 -11.89 1.50e+00 4.44e-01 6.29e+01 angle pdb=" O2' A A1082 " pdb=" C2' A A1082 " pdb=" C1' A A1082 " ideal model delta sigma weight residual 108.40 97.95 10.45 1.50e+00 4.44e-01 4.86e+01 angle pdb=" C3' U A1076 " pdb=" C2' U A1076 " pdb=" O2' U A1076 " ideal model delta sigma weight residual 110.70 101.75 8.95 1.50e+00 4.44e-01 3.56e+01 ... (remaining 77807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 29445 35.82 - 71.64: 3496 71.64 - 107.45: 429 107.45 - 143.27: 9 143.27 - 179.09: 12 Dihedral angle restraints: 33391 sinusoidal: 27810 harmonic: 5581 Sorted by residual: dihedral pdb=" C4' A A1431 " pdb=" C3' A A1431 " pdb=" C2' A A1431 " pdb=" C1' A A1431 " ideal model delta sinusoidal sigma weight residual -35.00 30.96 -65.96 1 8.00e+00 1.56e-02 8.89e+01 dihedral pdb=" O4' U A 439 " pdb=" C1' U A 439 " pdb=" N1 U A 439 " pdb=" C2 U A 439 " ideal model delta sinusoidal sigma weight residual 200.00 35.96 164.04 1 1.50e+01 4.44e-03 8.37e+01 dihedral pdb=" C5' A A1431 " pdb=" C4' A A1431 " pdb=" C3' A A1431 " pdb=" O3' A A1431 " ideal model delta sinusoidal sigma weight residual 147.00 84.17 62.83 1 8.00e+00 1.56e-02 8.15e+01 ... (remaining 33388 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 9824 0.117 - 0.235: 100 0.235 - 0.352: 6 0.352 - 0.469: 2 0.469 - 0.587: 1 Chirality restraints: 9933 Sorted by residual: chirality pdb=" C3' U A1065 " pdb=" C4' U A1065 " pdb=" O3' U A1065 " pdb=" C2' U A1065 " both_signs ideal model delta sigma weight residual False -2.74 -2.16 -0.59 2.00e-01 2.50e+01 8.60e+00 chirality pdb=" C3' C A 924 " pdb=" C4' C A 924 " pdb=" O3' C A 924 " pdb=" C2' C A 924 " both_signs ideal model delta sigma weight residual False -2.48 -2.85 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" C2' U A1073 " pdb=" C3' U A1073 " pdb=" O2' U A1073 " pdb=" C1' U A1073 " both_signs ideal model delta sigma weight residual False -2.75 -2.39 -0.36 2.00e-01 2.50e+01 3.23e+00 ... (remaining 9930 not shown) Planarity restraints: 4217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A1077 " -0.062 2.00e-02 2.50e+03 2.60e-02 2.03e+01 pdb=" N9 G A1077 " 0.058 2.00e-02 2.50e+03 pdb=" C8 G A1077 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G A1077 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G A1077 " 0.007 2.00e-02 2.50e+03 pdb=" C6 G A1077 " -0.015 2.00e-02 2.50e+03 pdb=" O6 G A1077 " -0.016 2.00e-02 2.50e+03 pdb=" N1 G A1077 " -0.009 2.00e-02 2.50e+03 pdb=" C2 G A1077 " 0.006 2.00e-02 2.50e+03 pdb=" N2 G A1077 " 0.006 2.00e-02 2.50e+03 pdb=" N3 G A1077 " 0.007 2.00e-02 2.50e+03 pdb=" C4 G A1077 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A1083 " 0.031 2.00e-02 2.50e+03 1.49e-02 5.03e+00 pdb=" N1 U A1083 " -0.027 2.00e-02 2.50e+03 pdb=" C2 U A1083 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U A1083 " -0.007 2.00e-02 2.50e+03 pdb=" N3 U A1083 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U A1083 " 0.003 2.00e-02 2.50e+03 pdb=" O4 U A1083 " 0.010 2.00e-02 2.50e+03 pdb=" C5 U A1083 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U A1083 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A1082 " -0.027 2.00e-02 2.50e+03 1.32e-02 4.80e+00 pdb=" N9 A A1082 " 0.032 2.00e-02 2.50e+03 pdb=" C8 A A1082 " 0.005 2.00e-02 2.50e+03 pdb=" N7 A A1082 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A A1082 " -0.008 2.00e-02 2.50e+03 pdb=" C6 A A1082 " -0.005 2.00e-02 2.50e+03 pdb=" N6 A A1082 " -0.002 2.00e-02 2.50e+03 pdb=" N1 A A1082 " -0.000 2.00e-02 2.50e+03 pdb=" C2 A A1082 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A A1082 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A A1082 " 0.002 2.00e-02 2.50e+03 ... (remaining 4214 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 1568 2.65 - 3.21: 39875 3.21 - 3.77: 92755 3.77 - 4.34: 120307 4.34 - 4.90: 162775 Nonbonded interactions: 417280 Sorted by model distance: nonbonded pdb=" OP1 C A 738 " pdb=" OH TYR F 4 " model vdw 2.084 2.440 nonbonded pdb=" O2' G A 925 " pdb=" O4' G A 926 " model vdw 2.147 2.440 nonbonded pdb=" O6 G A1419 " pdb=" O4 U A1481 " model vdw 2.158 2.432 nonbonded pdb=" O6 G A1064 " pdb=" N4 C A1192 " model vdw 2.171 2.520 nonbonded pdb=" OG SER D 192 " pdb=" OD1 ASP D 194 " model vdw 2.181 2.440 ... (remaining 417275 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: 1.400 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: 0.050 Extract box with map and model: 8.870 Check model and map are aligned: 0.790 Set scattering table: 0.460 Process input model: 171.950 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.170 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 187.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 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 : 0.002 0.057 52058 Z= 0.133 Angle : 0.530 17.481 77812 Z= 0.301 Chirality : 0.033 0.587 9933 Planarity : 0.003 0.040 4217 Dihedral : 23.069 179.089 29787 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.06 % Favored : 93.73 % Rotamer: Outliers : 0.12 % Allowed : 4.53 % Favored : 95.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: -3.22 (0.17), residues: 1913 helix: -1.41 (0.17), residues: 666 sheet: -1.79 (0.24), residues: 346 loop : -2.85 (0.18), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 200 HIS 0.006 0.001 HIS T 75 PHE 0.018 0.001 PHE N 20 TYR 0.008 0.001 TYR O 78 ARG 0.007 0.000 ARG D 73 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 575 time to evaluate : 3.159 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: C 40 GLN cc_start: 0.7369 (tt0) cc_final: 0.7165 (tm-30) REVERT: C 41 TYR cc_start: 0.6724 (t80) cc_final: 0.5591 (t80) REVERT: C 167 TYR cc_start: 0.5368 (m-80) cc_final: 0.5143 (m-80) REVERT: D 116 GLN cc_start: 0.8181 (tm-30) cc_final: 0.7373 (tm-30) REVERT: E 26 LYS cc_start: 0.8503 (ptmm) cc_final: 0.8073 (pttm) REVERT: E 116 GLU cc_start: 0.7209 (pp20) cc_final: 0.6434 (tp30) REVERT: H 94 LYS cc_start: 0.7841 (ttmm) cc_final: 0.6904 (tppt) REVERT: J 24 GLU cc_start: 0.4683 (pt0) cc_final: 0.4428 (pt0) REVERT: K 93 ARG cc_start: 0.5066 (mpt180) cc_final: 0.4748 (ttp80) REVERT: K 125 LYS cc_start: 0.6547 (mtpt) cc_final: 0.6110 (mmtt) REVERT: L 11 PRO cc_start: 0.8319 (Cg_endo) cc_final: 0.8004 (Cg_exo) REVERT: O 36 ILE cc_start: 0.7763 (mt) cc_final: 0.7535 (mt) REVERT: O 63 ARG cc_start: 0.6320 (ttp-170) cc_final: 0.6001 (ttp80) REVERT: Q 70 THR cc_start: 0.7808 (m) cc_final: 0.7545 (p) REVERT: S 80 ARG cc_start: 0.4736 (mmp80) cc_final: 0.4029 (mmm160) REVERT: T 23 SER cc_start: 0.9003 (t) cc_final: 0.8632 (m) REVERT: T 57 ILE cc_start: 0.8368 (tt) cc_final: 0.7450 (mp) REVERT: T 78 ASN cc_start: 0.7857 (m-40) cc_final: 0.7543 (m110) outliers start: 2 outliers final: 0 residues processed: 575 average time/residue: 0.7704 time to fit residues: 682.9971 Evaluate side-chains 394 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 394 time to evaluate : 3.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 284 optimal weight: 5.9990 chunk 255 optimal weight: 6.9990 chunk 141 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 172 optimal weight: 8.9990 chunk 136 optimal weight: 9.9990 chunk 264 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 chunk 160 optimal weight: 0.0980 chunk 196 optimal weight: 5.9990 chunk 306 optimal weight: 6.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 GLN C 101 ASN C 175 HIS D 74 ASN D 120 HIS D 131 ASN D 136 GLN D 164 GLN E 70 ASN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 ASN H 16 ASN H 21 ASN I 49 GLN J 58 ASN J 70 HIS ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN K 119 ASN L 5 ASN M 7 ASN M 13 HIS N 70 HIS O 40 GLN P 59 HIS R 31 ASN R 52 GLN T 21 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 52058 Z= 0.319 Angle : 0.811 12.329 77812 Z= 0.407 Chirality : 0.042 0.263 9933 Planarity : 0.007 0.077 4217 Dihedral : 23.705 174.321 25905 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.41 % Favored : 90.43 % Rotamer: Outliers : 5.65 % Allowed : 18.49 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.89 (0.17), residues: 1913 helix: -1.11 (0.17), residues: 710 sheet: -1.31 (0.26), residues: 341 loop : -2.87 (0.18), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP F 42 HIS 0.006 0.002 HIS O 46 PHE 0.017 0.003 PHE H 49 TYR 0.038 0.003 TYR C 192 ARG 0.017 0.001 ARG N 23 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 437 time to evaluate : 2.599 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: C 22 PHE cc_start: 0.7272 (t80) cc_final: 0.6746 (t80) REVERT: C 28 PHE cc_start: 0.6480 (OUTLIER) cc_final: 0.6207 (m-80) REVERT: C 41 TYR cc_start: 0.6646 (t80) cc_final: 0.6020 (t80) REVERT: C 42 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6596 (mp) REVERT: D 4 TYR cc_start: 0.7067 (t80) cc_final: 0.6820 (t80) REVERT: E 26 LYS cc_start: 0.8713 (ptmm) cc_final: 0.8176 (pttm) REVERT: J 80 THR cc_start: 0.3520 (OUTLIER) cc_final: 0.3261 (m) REVERT: K 69 ARG cc_start: 0.4700 (ptp90) cc_final: 0.4312 (ptm-80) REVERT: M 52 ILE cc_start: 0.6357 (OUTLIER) cc_final: 0.5855 (tt) REVERT: N 9 GLU cc_start: 0.4554 (OUTLIER) cc_final: 0.3252 (tp30) REVERT: N 15 LEU cc_start: 0.5511 (OUTLIER) cc_final: 0.5290 (pp) REVERT: O 29 VAL cc_start: 0.7225 (t) cc_final: 0.7018 (t) REVERT: O 78 TYR cc_start: 0.6827 (t80) cc_final: 0.6497 (t80) REVERT: P 1 MET cc_start: 0.7158 (pmm) cc_final: 0.6329 (pmm) REVERT: Q 30 LYS cc_start: 0.8251 (tttp) cc_final: 0.8027 (tttm) REVERT: Q 37 PHE cc_start: 0.7624 (m-10) cc_final: 0.7279 (m-80) REVERT: Q 68 SER cc_start: 0.8672 (p) cc_final: 0.8399 (t) REVERT: S 80 ARG cc_start: 0.5613 (mmp80) cc_final: 0.4739 (mmm160) REVERT: T 23 SER cc_start: 0.8962 (t) cc_final: 0.8550 (m) REVERT: T 61 GLN cc_start: 0.8304 (mm-40) cc_final: 0.7770 (mm-40) REVERT: T 78 ASN cc_start: 0.7730 (m-40) cc_final: 0.7353 (m110) outliers start: 91 outliers final: 56 residues processed: 486 average time/residue: 0.7002 time to fit residues: 532.2539 Evaluate side-chains 451 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 389 time to evaluate : 2.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 121 HIS Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain F residue 3 HIS Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 127 CYS Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain N residue 9 GLU Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 34 ASN Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 39 LYS Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 65 MET Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 80 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 170 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 254 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 306 optimal weight: 5.9990 chunk 331 optimal weight: 3.9990 chunk 273 optimal weight: 9.9990 chunk 304 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 245 optimal weight: 0.1980 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 5 HIS C 122 GLN C 138 GLN D 74 ASN D 131 ASN D 164 GLN F 52 ASN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 ASN I 36 GLN I 80 HIS ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 ASN N 3 GLN T 61 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 52058 Z= 0.244 Angle : 0.661 10.000 77812 Z= 0.335 Chirality : 0.038 0.312 9933 Planarity : 0.005 0.046 4217 Dihedral : 23.615 176.058 25905 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.73 % Favored : 91.11 % Rotamer: Outliers : 5.40 % Allowed : 22.64 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.46 (0.18), residues: 1913 helix: -0.69 (0.18), residues: 699 sheet: -1.02 (0.28), residues: 332 loop : -2.70 (0.18), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 200 HIS 0.005 0.001 HIS O 46 PHE 0.013 0.002 PHE R 13 TYR 0.023 0.002 TYR C 192 ARG 0.008 0.001 ARG H 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 399 time to evaluate : 2.802 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: C 22 PHE cc_start: 0.7242 (t80) cc_final: 0.6945 (t80) REVERT: C 28 PHE cc_start: 0.6697 (OUTLIER) cc_final: 0.6187 (m-80) REVERT: C 41 TYR cc_start: 0.6590 (t80) cc_final: 0.5899 (t80) REVERT: C 125 ARG cc_start: 0.6470 (OUTLIER) cc_final: 0.5526 (mpp80) REVERT: C 134 LYS cc_start: 0.7093 (tppt) cc_final: 0.6597 (mtpp) REVERT: C 168 ARG cc_start: 0.6936 (tmt170) cc_final: 0.6342 (tmm-80) REVERT: E 26 LYS cc_start: 0.8654 (ptmm) cc_final: 0.8182 (pttm) REVERT: I 108 ARG cc_start: 0.6578 (ptt180) cc_final: 0.6364 (ptt180) REVERT: I 112 ARG cc_start: 0.7382 (ptm-80) cc_final: 0.7051 (ptm160) REVERT: J 45 ARG cc_start: 0.6677 (ttt180) cc_final: 0.5706 (ttt180) REVERT: K 64 GLN cc_start: 0.4384 (mm110) cc_final: 0.4047 (mm-40) REVERT: M 52 ILE cc_start: 0.6452 (OUTLIER) cc_final: 0.6215 (tp) REVERT: N 6 LYS cc_start: 0.6306 (OUTLIER) cc_final: 0.5932 (pttt) REVERT: O 81 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.7935 (mp) REVERT: P 1 MET cc_start: 0.7186 (pmm) cc_final: 0.6320 (pmm) REVERT: Q 30 LYS cc_start: 0.8296 (tttp) cc_final: 0.8090 (tttm) REVERT: Q 37 PHE cc_start: 0.7612 (m-10) cc_final: 0.7317 (m-10) REVERT: Q 75 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7721 (tt) REVERT: S 80 ARG cc_start: 0.5408 (mmp80) cc_final: 0.4438 (mmm160) REVERT: T 23 SER cc_start: 0.8947 (t) cc_final: 0.8543 (m) REVERT: T 78 ASN cc_start: 0.7735 (m-40) cc_final: 0.7385 (m110) outliers start: 87 outliers final: 56 residues processed: 450 average time/residue: 0.7154 time to fit residues: 502.3160 Evaluate side-chains 431 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 369 time to evaluate : 2.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 122 GLN Chi-restraints excluded: chain C residue 125 ARG Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 121 HIS Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 74 GLN Chi-restraints excluded: chain J residue 70 HIS Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain Q residue 18 GLU Chi-restraints excluded: chain Q residue 67 LEU Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 57 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 302 optimal weight: 9.9990 chunk 230 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 205 optimal weight: 0.4980 chunk 307 optimal weight: 3.9990 chunk 325 optimal weight: 8.9990 chunk 160 optimal weight: 20.0000 chunk 291 optimal weight: 0.7980 chunk 87 optimal weight: 9.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 GLN D 74 ASN D 164 GLN F 52 ASN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 ASN I 3 ASN I 36 GLN ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 ASN T 61 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 52058 Z= 0.170 Angle : 0.587 9.707 77812 Z= 0.299 Chirality : 0.035 0.286 9933 Planarity : 0.004 0.041 4217 Dihedral : 23.489 177.189 25905 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.31 % Favored : 91.53 % Rotamer: Outliers : 5.77 % Allowed : 23.76 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.10 (0.18), residues: 1913 helix: -0.24 (0.19), residues: 706 sheet: -0.92 (0.28), residues: 325 loop : -2.58 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 42 HIS 0.004 0.001 HIS F 37 PHE 0.011 0.001 PHE R 13 TYR 0.018 0.002 TYR I 89 ARG 0.006 0.000 ARG H 84 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 402 time to evaluate : 2.791 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: C 28 PHE cc_start: 0.6732 (OUTLIER) cc_final: 0.6194 (m-80) REVERT: C 40 GLN cc_start: 0.8316 (tt0) cc_final: 0.7490 (tm-30) REVERT: C 41 TYR cc_start: 0.6590 (t80) cc_final: 0.5637 (t80) REVERT: C 168 ARG cc_start: 0.6990 (tmt170) cc_final: 0.6606 (ttp-170) REVERT: D 116 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7376 (tm-30) REVERT: E 26 LYS cc_start: 0.8572 (ptmm) cc_final: 0.8124 (pttm) REVERT: H 76 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.7938 (pt0) REVERT: I 21 LYS cc_start: 0.7592 (ttpt) cc_final: 0.7385 (ttpp) REVERT: I 112 ARG cc_start: 0.7370 (ptm-80) cc_final: 0.7036 (ptm160) REVERT: J 45 ARG cc_start: 0.6773 (ttt180) cc_final: 0.6410 (ttt180) REVERT: J 80 THR cc_start: 0.3764 (OUTLIER) cc_final: 0.3526 (m) REVERT: K 69 ARG cc_start: 0.4926 (ptp90) cc_final: 0.4592 (ptm-80) REVERT: L 15 LYS cc_start: 0.8114 (tppt) cc_final: 0.7812 (tppt) REVERT: M 52 ILE cc_start: 0.6387 (OUTLIER) cc_final: 0.5973 (tp) REVERT: O 81 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7958 (mp) REVERT: P 1 MET cc_start: 0.7042 (pmm) cc_final: 0.6289 (pmm) REVERT: Q 30 LYS cc_start: 0.8287 (tttp) cc_final: 0.8079 (tttm) REVERT: Q 37 PHE cc_start: 0.7540 (m-10) cc_final: 0.7249 (m-10) REVERT: Q 75 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7583 (tt) REVERT: S 35 ARG cc_start: 0.5933 (ptm-80) cc_final: 0.5590 (ptm-80) REVERT: S 80 ARG cc_start: 0.5408 (mmp80) cc_final: 0.4454 (mmm160) REVERT: T 23 SER cc_start: 0.8948 (t) cc_final: 0.8511 (m) REVERT: T 61 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8115 (mm110) REVERT: T 78 ASN cc_start: 0.7681 (m-40) cc_final: 0.7188 (m110) outliers start: 93 outliers final: 59 residues processed: 462 average time/residue: 0.7585 time to fit residues: 552.8306 Evaluate side-chains 441 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 375 time to evaluate : 3.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 116 GLN Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 3 ASN Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 99 SER Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain Q residue 18 GLU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 76 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 271 optimal weight: 4.9990 chunk 184 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 242 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 chunk 277 optimal weight: 1.9990 chunk 225 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 166 optimal weight: 3.9990 chunk 292 optimal weight: 0.6980 chunk 82 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 7 ASN D 40 GLN D 74 ASN D 131 ASN D 164 GLN F 52 ASN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 ASN I 4 GLN J 70 HIS ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 ASN S 42 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 52058 Z= 0.196 Angle : 0.614 10.405 77812 Z= 0.312 Chirality : 0.035 0.266 9933 Planarity : 0.005 0.044 4217 Dihedral : 23.486 176.415 25905 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.25 % Favored : 90.59 % Rotamer: Outliers : 7.13 % Allowed : 23.64 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.97 (0.18), residues: 1913 helix: -0.08 (0.19), residues: 706 sheet: -0.87 (0.28), residues: 331 loop : -2.57 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 42 HIS 0.005 0.001 HIS O 46 PHE 0.031 0.002 PHE C 22 TYR 0.019 0.002 TYR C 192 ARG 0.014 0.001 ARG K 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 377 time to evaluate : 2.719 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: C 28 PHE cc_start: 0.6749 (OUTLIER) cc_final: 0.6190 (m-80) REVERT: C 40 GLN cc_start: 0.8388 (tt0) cc_final: 0.7508 (tm-30) REVERT: C 125 ARG cc_start: 0.6417 (OUTLIER) cc_final: 0.5532 (mpp80) REVERT: D 116 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7283 (tm-30) REVERT: E 26 LYS cc_start: 0.8569 (ptmm) cc_final: 0.8165 (pttm) REVERT: E 121 HIS cc_start: 0.6795 (OUTLIER) cc_final: 0.6333 (m90) REVERT: H 76 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.7934 (pt0) REVERT: I 112 ARG cc_start: 0.7238 (ptm-80) cc_final: 0.6440 (ptm160) REVERT: J 31 ARG cc_start: 0.3832 (OUTLIER) cc_final: 0.1843 (ptp-170) REVERT: J 80 THR cc_start: 0.3629 (OUTLIER) cc_final: 0.3398 (m) REVERT: K 33 THR cc_start: 0.5514 (p) cc_final: 0.5151 (p) REVERT: K 69 ARG cc_start: 0.5044 (ptp90) cc_final: 0.4641 (ptm-80) REVERT: M 68 LEU cc_start: 0.4773 (pt) cc_final: 0.4139 (tp) REVERT: O 81 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7904 (mp) REVERT: P 1 MET cc_start: 0.7037 (pmm) cc_final: 0.6279 (pmm) REVERT: Q 30 LYS cc_start: 0.8302 (tttp) cc_final: 0.8101 (tttm) REVERT: Q 37 PHE cc_start: 0.7541 (m-10) cc_final: 0.7295 (m-10) REVERT: Q 75 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7579 (tt) REVERT: R 73 ARG cc_start: 0.5352 (OUTLIER) cc_final: 0.4641 (mtm110) REVERT: S 35 ARG cc_start: 0.6228 (ptm-80) cc_final: 0.5891 (ptm-80) REVERT: S 80 ARG cc_start: 0.5342 (mmp80) cc_final: 0.4387 (mmm160) REVERT: T 23 SER cc_start: 0.8957 (OUTLIER) cc_final: 0.8496 (m) REVERT: T 54 MET cc_start: 0.6470 (OUTLIER) cc_final: 0.6095 (tmm) REVERT: T 78 ASN cc_start: 0.7667 (m-40) cc_final: 0.7307 (m110) outliers start: 115 outliers final: 80 residues processed: 455 average time/residue: 0.6967 time to fit residues: 496.9783 Evaluate side-chains 449 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 357 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 HIS Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 125 ARG Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 116 GLN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 121 HIS Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 31 ARG Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain O residue 3 LEU Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain Q residue 18 GLU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 39 LYS Chi-restraints excluded: chain Q residue 67 LEU Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 73 ARG Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 54 MET Chi-restraints excluded: chain T residue 80 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 109 optimal weight: 9.9990 chunk 293 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 191 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 326 optimal weight: 0.8980 chunk 270 optimal weight: 8.9990 chunk 150 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 171 optimal weight: 7.9990 overall best weight: 6.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 HIS D 74 ASN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 GLN J 58 ASN J 70 HIS ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 ASN T 61 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.112 52058 Z= 0.467 Angle : 0.990 12.080 77812 Z= 0.487 Chirality : 0.051 0.814 9933 Planarity : 0.008 0.087 4217 Dihedral : 24.061 172.322 25905 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.34 % Favored : 87.51 % Rotamer: Outliers : 9.12 % Allowed : 24.13 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.77 (0.17), residues: 1913 helix: -0.84 (0.18), residues: 684 sheet: -1.29 (0.28), residues: 332 loop : -2.91 (0.18), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.005 TRP F 42 HIS 0.008 0.002 HIS D 41 PHE 0.046 0.004 PHE S 40 TYR 0.049 0.003 TYR C 192 ARG 0.010 0.001 ARG K 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 392 time to evaluate : 2.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 PHE cc_start: 0.6502 (OUTLIER) cc_final: 0.5928 (m-80) REVERT: C 42 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6821 (mp) REVERT: C 125 ARG cc_start: 0.6766 (OUTLIER) cc_final: 0.6300 (mpp80) REVERT: C 130 ARG cc_start: 0.5758 (ttt-90) cc_final: 0.4976 (ttm170) REVERT: D 116 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7440 (tm-30) REVERT: E 26 LYS cc_start: 0.8729 (ptmm) cc_final: 0.8294 (pttm) REVERT: F 9 MET cc_start: 0.4842 (OUTLIER) cc_final: 0.4567 (pmm) REVERT: F 73 GLU cc_start: 0.5187 (tp30) cc_final: 0.4291 (tp30) REVERT: H 76 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8165 (pt0) REVERT: I 102 PHE cc_start: 0.6817 (m-10) cc_final: 0.6246 (m-80) REVERT: I 109 GLN cc_start: 0.8306 (pp30) cc_final: 0.8018 (pt0) REVERT: I 112 ARG cc_start: 0.7404 (ptm-80) cc_final: 0.6630 (ptm160) REVERT: I 118 ARG cc_start: 0.6063 (OUTLIER) cc_final: 0.4551 (ttm-80) REVERT: J 31 ARG cc_start: 0.4157 (OUTLIER) cc_final: 0.1800 (ptp-170) REVERT: K 69 ARG cc_start: 0.5487 (ptp90) cc_final: 0.5039 (ptm-80) REVERT: M 68 LEU cc_start: 0.4568 (pt) cc_final: 0.4105 (tp) REVERT: M 74 MET cc_start: 0.7473 (tmm) cc_final: 0.7272 (tmm) REVERT: N 6 LYS cc_start: 0.6362 (OUTLIER) cc_final: 0.6074 (pttt) REVERT: O 81 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8157 (mp) REVERT: P 1 MET cc_start: 0.7232 (pmm) cc_final: 0.6355 (pmm) REVERT: Q 37 PHE cc_start: 0.7587 (m-10) cc_final: 0.7324 (m-80) REVERT: R 73 ARG cc_start: 0.5889 (OUTLIER) cc_final: 0.5092 (mtm110) REVERT: S 80 ARG cc_start: 0.5445 (mmp80) cc_final: 0.4496 (mmm160) REVERT: T 78 ASN cc_start: 0.7745 (m-40) cc_final: 0.7485 (m-40) outliers start: 147 outliers final: 105 residues processed: 490 average time/residue: 0.7102 time to fit residues: 559.8305 Evaluate side-chains 483 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 367 time to evaluate : 2.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 125 ARG Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 116 GLN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain F residue 3 HIS Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain H residue 127 CYS Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 118 ARG Chi-restraints excluded: chain J residue 31 ARG Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 99 SER Chi-restraints excluded: chain O residue 3 LEU Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain Q residue 18 GLU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 39 LYS Chi-restraints excluded: chain Q residue 67 LEU Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 73 ARG Chi-restraints excluded: chain S residue 5 LYS Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 65 MET Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 80 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 314 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 185 optimal weight: 5.9990 chunk 238 optimal weight: 3.9990 chunk 184 optimal weight: 0.7980 chunk 274 optimal weight: 7.9990 chunk 182 optimal weight: 1.9990 chunk 324 optimal weight: 6.9990 chunk 203 optimal weight: 2.9990 chunk 198 optimal weight: 0.9980 chunk 149 optimal weight: 9.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 40 GLN D 74 ASN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 ASN T 61 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 52058 Z= 0.193 Angle : 0.652 10.175 77812 Z= 0.332 Chirality : 0.038 0.272 9933 Planarity : 0.005 0.048 4217 Dihedral : 23.674 177.202 25905 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.68 % Favored : 91.17 % Rotamer: Outliers : 6.64 % Allowed : 27.42 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.28 (0.18), residues: 1913 helix: -0.28 (0.19), residues: 702 sheet: -1.20 (0.27), residues: 335 loop : -2.72 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP F 42 HIS 0.005 0.001 HIS K 24 PHE 0.014 0.002 PHE R 13 TYR 0.025 0.002 TYR I 89 ARG 0.009 0.001 ARG K 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 384 time to evaluate : 3.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 PHE cc_start: 0.6543 (OUTLIER) cc_final: 0.5952 (m-80) REVERT: C 125 ARG cc_start: 0.6238 (OUTLIER) cc_final: 0.5608 (mpp80) REVERT: C 130 ARG cc_start: 0.5788 (ttt-90) cc_final: 0.4934 (ttm170) REVERT: D 105 MET cc_start: 0.7275 (OUTLIER) cc_final: 0.7045 (mmm) REVERT: D 116 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7425 (tm-30) REVERT: E 26 LYS cc_start: 0.8616 (ptmm) cc_final: 0.8200 (pttm) REVERT: E 121 HIS cc_start: 0.6955 (OUTLIER) cc_final: 0.5095 (m90) REVERT: H 76 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.7958 (pt0) REVERT: H 111 MET cc_start: 0.7114 (ptm) cc_final: 0.6813 (ptp) REVERT: I 84 ARG cc_start: 0.5613 (ttt180) cc_final: 0.5162 (ttt180) REVERT: J 31 ARG cc_start: 0.3740 (OUTLIER) cc_final: 0.0963 (ptp-170) REVERT: K 69 ARG cc_start: 0.5420 (ptp90) cc_final: 0.4906 (ptm-80) REVERT: M 10 ASP cc_start: 0.6142 (t70) cc_final: 0.5899 (t70) REVERT: N 6 LYS cc_start: 0.6133 (OUTLIER) cc_final: 0.5864 (pttt) REVERT: O 81 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8091 (mp) REVERT: O 88 ARG cc_start: 0.6787 (mmp80) cc_final: 0.6521 (mmp80) REVERT: P 1 MET cc_start: 0.7227 (pmm) cc_final: 0.6329 (pmm) REVERT: Q 37 PHE cc_start: 0.7512 (m-10) cc_final: 0.7213 (m-10) REVERT: R 73 ARG cc_start: 0.5944 (OUTLIER) cc_final: 0.5192 (mtm110) REVERT: S 35 ARG cc_start: 0.6825 (ptm-80) cc_final: 0.5974 (ptm160) REVERT: T 23 SER cc_start: 0.8924 (OUTLIER) cc_final: 0.8498 (m) REVERT: T 78 ASN cc_start: 0.7626 (m-40) cc_final: 0.7327 (m110) outliers start: 107 outliers final: 82 residues processed: 453 average time/residue: 0.6953 time to fit residues: 495.8316 Evaluate side-chains 455 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 362 time to evaluate : 2.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 HIS Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 125 ARG Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 116 GLN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 121 HIS Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 59 LYS Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 31 ARG Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain N residue 99 SER Chi-restraints excluded: chain O residue 3 LEU Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 39 LYS Chi-restraints excluded: chain Q residue 67 LEU Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 73 ARG Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain T residue 23 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 200 optimal weight: 7.9990 chunk 129 optimal weight: 10.0000 chunk 193 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 206 optimal weight: 10.0000 chunk 221 optimal weight: 5.9990 chunk 160 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 255 optimal weight: 10.0000 overall best weight: 8.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 GLN D 74 ASN J 64 GLN ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 ASN Q 9 GLN Q 45 HIS T 61 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.5936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.134 52058 Z= 0.569 Angle : 1.122 12.491 77812 Z= 0.547 Chirality : 0.056 0.471 9933 Planarity : 0.009 0.111 4217 Dihedral : 24.405 173.686 25905 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 23.14 Ramachandran Plot: Outliers : 0.26 % Allowed : 14.11 % Favored : 85.62 % Rotamer: Outliers : 9.00 % Allowed : 26.67 % Favored : 64.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.13 (0.17), residues: 1913 helix: -1.17 (0.18), residues: 686 sheet: -1.61 (0.27), residues: 338 loop : -3.04 (0.18), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.005 TRP F 42 HIS 0.008 0.002 HIS N 70 PHE 0.024 0.004 PHE C 22 TYR 0.051 0.004 TYR C 192 ARG 0.018 0.001 ARG K 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 394 time to evaluate : 3.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 PHE cc_start: 0.6662 (OUTLIER) cc_final: 0.5955 (m-80) REVERT: C 42 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6881 (mp) REVERT: C 130 ARG cc_start: 0.6158 (ttt-90) cc_final: 0.5114 (ttm170) REVERT: C 160 GLU cc_start: 0.6372 (OUTLIER) cc_final: 0.6156 (tm-30) REVERT: C 165 GLU cc_start: 0.5371 (mp0) cc_final: 0.5106 (mp0) REVERT: D 105 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.7258 (mmm) REVERT: D 116 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: E 26 LYS cc_start: 0.8764 (ptmm) cc_final: 0.8313 (pttm) REVERT: F 9 MET cc_start: 0.5189 (OUTLIER) cc_final: 0.4625 (pmm) REVERT: H 76 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8184 (pt0) REVERT: I 102 PHE cc_start: 0.6931 (m-10) cc_final: 0.6395 (m-80) REVERT: I 109 GLN cc_start: 0.8402 (pp30) cc_final: 0.7974 (pt0) REVERT: J 31 ARG cc_start: 0.4517 (OUTLIER) cc_final: 0.2112 (ptp-170) REVERT: K 14 LYS cc_start: 0.7400 (mmtm) cc_final: 0.7155 (mmtm) REVERT: K 69 ARG cc_start: 0.5501 (ptp90) cc_final: 0.5051 (ptm-80) REVERT: M 68 LEU cc_start: 0.4766 (pt) cc_final: 0.4279 (tp) REVERT: N 6 LYS cc_start: 0.6545 (OUTLIER) cc_final: 0.6293 (pttt) REVERT: O 81 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8196 (mp) REVERT: O 88 ARG cc_start: 0.6823 (mmp80) cc_final: 0.6400 (mmp80) REVERT: Q 37 PHE cc_start: 0.7615 (m-10) cc_final: 0.7303 (m-80) REVERT: Q 68 SER cc_start: 0.8683 (p) cc_final: 0.8472 (t) REVERT: R 73 ARG cc_start: 0.5999 (OUTLIER) cc_final: 0.5422 (mtm110) REVERT: S 43 MET cc_start: 0.6052 (tpp) cc_final: 0.5644 (tpp) REVERT: T 9 LYS cc_start: 0.7628 (ttpt) cc_final: 0.6964 (tptt) outliers start: 145 outliers final: 111 residues processed: 487 average time/residue: 0.6947 time to fit residues: 542.6109 Evaluate side-chains 503 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 381 time to evaluate : 2.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 116 GLN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain H residue 127 CYS Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 59 LYS Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 31 ARG Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 103 ASP Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 100 ARG Chi-restraints excluded: chain M residue 104 ASN Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 99 SER Chi-restraints excluded: chain O residue 3 LEU Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 46 HIS Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain Q residue 18 GLU Chi-restraints excluded: chain Q residue 39 LYS Chi-restraints excluded: chain Q residue 67 LEU Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 73 ARG Chi-restraints excluded: chain S residue 5 LYS Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 65 MET Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 80 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 295 optimal weight: 0.9980 chunk 311 optimal weight: 2.9990 chunk 283 optimal weight: 0.0670 chunk 302 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 chunk 237 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 chunk 273 optimal weight: 0.9980 chunk 286 optimal weight: 0.5980 chunk 301 optimal weight: 0.8980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN D 152 GLN H 16 ASN I 24 ASN J 64 GLN ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 45 HIS T 61 GLN T 78 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.5384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 52058 Z= 0.153 Angle : 0.645 11.278 77812 Z= 0.328 Chirality : 0.037 0.286 9933 Planarity : 0.005 0.069 4217 Dihedral : 23.730 179.820 25905 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.37 % Favored : 92.52 % Rotamer: Outliers : 4.22 % Allowed : 31.51 % Favored : 64.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 (0.18), residues: 1913 helix: -0.18 (0.19), residues: 688 sheet: -1.30 (0.27), residues: 337 loop : -2.59 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP F 42 HIS 0.007 0.001 HIS K 24 PHE 0.039 0.002 PHE M 62 TYR 0.026 0.001 TYR I 89 ARG 0.008 0.001 ARG K 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 402 time to evaluate : 2.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 PHE cc_start: 0.6676 (OUTLIER) cc_final: 0.6223 (m-80) REVERT: C 40 GLN cc_start: 0.7612 (tt0) cc_final: 0.7332 (tm-30) REVERT: C 130 ARG cc_start: 0.6287 (ttt-90) cc_final: 0.5075 (ttm170) REVERT: D 116 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7482 (tm-30) REVERT: E 26 LYS cc_start: 0.8593 (ptmm) cc_final: 0.8113 (pttm) REVERT: E 121 HIS cc_start: 0.6957 (OUTLIER) cc_final: 0.5250 (m90) REVERT: H 76 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.7938 (pt0) REVERT: H 111 MET cc_start: 0.7002 (ptm) cc_final: 0.6795 (ptp) REVERT: I 48 ARG cc_start: 0.6941 (ptp90) cc_final: 0.6131 (mmt-90) REVERT: I 84 ARG cc_start: 0.5513 (ttt180) cc_final: 0.5026 (ttm170) REVERT: I 102 PHE cc_start: 0.6671 (m-10) cc_final: 0.6374 (m-10) REVERT: J 71 LEU cc_start: 0.6507 (OUTLIER) cc_final: 0.6192 (mt) REVERT: K 70 CYS cc_start: 0.7097 (OUTLIER) cc_final: 0.6845 (p) REVERT: N 6 LYS cc_start: 0.6000 (OUTLIER) cc_final: 0.5754 (pttt) REVERT: P 1 MET cc_start: 0.7257 (pmm) cc_final: 0.6328 (pmm) REVERT: Q 37 PHE cc_start: 0.7443 (m-10) cc_final: 0.7151 (m-80) REVERT: Q 60 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.6743 (mp0) REVERT: R 73 ARG cc_start: 0.5935 (OUTLIER) cc_final: 0.5266 (mtm110) REVERT: T 23 SER cc_start: 0.8968 (t) cc_final: 0.8541 (m) REVERT: T 78 ASN cc_start: 0.7785 (m-40) cc_final: 0.7565 (m110) REVERT: T 80 THR cc_start: 0.7570 (m) cc_final: 0.7309 (m) outliers start: 68 outliers final: 49 residues processed: 441 average time/residue: 0.7083 time to fit residues: 489.4264 Evaluate side-chains 436 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 378 time to evaluate : 3.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 HIS Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain D residue 116 GLN Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 121 HIS Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 70 CYS Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 100 ARG Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain Q residue 18 GLU Chi-restraints excluded: chain Q residue 60 GLU Chi-restraints excluded: chain Q residue 67 LEU Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 73 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 198 optimal weight: 0.8980 chunk 320 optimal weight: 6.9990 chunk 195 optimal weight: 7.9990 chunk 151 optimal weight: 4.9990 chunk 222 optimal weight: 8.9990 chunk 335 optimal weight: 10.0000 chunk 309 optimal weight: 6.9990 chunk 267 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 206 optimal weight: 6.9990 chunk 163 optimal weight: 0.9980 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 GLN D 74 ASN D 131 ASN H 16 ASN ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.5650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 52058 Z= 0.304 Angle : 0.769 11.702 77812 Z= 0.385 Chirality : 0.042 0.297 9933 Planarity : 0.006 0.069 4217 Dihedral : 23.850 179.192 25905 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.08 % Favored : 87.77 % Rotamer: Outliers : 4.84 % Allowed : 31.45 % Favored : 63.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.44 (0.18), residues: 1913 helix: -0.37 (0.19), residues: 679 sheet: -1.39 (0.28), residues: 332 loop : -2.74 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.004 TRP F 42 HIS 0.006 0.001 HIS O 46 PHE 0.033 0.002 PHE M 62 TYR 0.029 0.002 TYR C 192 ARG 0.011 0.001 ARG K 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 378 time to evaluate : 2.841 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: C 28 PHE cc_start: 0.6642 (OUTLIER) cc_final: 0.6193 (m-80) REVERT: C 130 ARG cc_start: 0.6132 (ttt-90) cc_final: 0.5214 (ttm170) REVERT: D 116 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7269 (tm-30) REVERT: E 26 LYS cc_start: 0.8648 (ptmm) cc_final: 0.8211 (pttm) REVERT: E 88 VAL cc_start: 0.6901 (t) cc_final: 0.6663 (p) REVERT: E 121 HIS cc_start: 0.6971 (OUTLIER) cc_final: 0.5302 (m90) REVERT: H 76 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8004 (pt0) REVERT: I 102 PHE cc_start: 0.6817 (m-10) cc_final: 0.6475 (m-10) REVERT: J 31 ARG cc_start: 0.4573 (OUTLIER) cc_final: 0.3907 (ptt180) REVERT: K 70 CYS cc_start: 0.7171 (OUTLIER) cc_final: 0.6913 (p) REVERT: K 75 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.6585 (tppt) REVERT: N 6 LYS cc_start: 0.6248 (OUTLIER) cc_final: 0.5921 (pttt) REVERT: Q 37 PHE cc_start: 0.7644 (m-10) cc_final: 0.7391 (m-10) REVERT: Q 60 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.6147 (mp0) REVERT: R 73 ARG cc_start: 0.5900 (OUTLIER) cc_final: 0.5274 (mtm110) REVERT: S 43 MET cc_start: 0.6021 (tpp) cc_final: 0.5463 (tpp) REVERT: T 23 SER cc_start: 0.8938 (t) cc_final: 0.8472 (m) REVERT: T 57 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8271 (mp) REVERT: T 78 ASN cc_start: 0.7808 (m-40) cc_final: 0.7590 (m-40) outliers start: 78 outliers final: 57 residues processed: 428 average time/residue: 0.6887 time to fit residues: 464.4874 Evaluate side-chains 438 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 370 time to evaluate : 3.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain D residue 116 GLN Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 121 HIS Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 59 LYS Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 31 ARG Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 70 CYS Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 100 ARG Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain N residue 99 SER Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain Q residue 18 GLU Chi-restraints excluded: chain Q residue 60 GLU Chi-restraints excluded: chain Q residue 67 LEU Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 73 ARG Chi-restraints excluded: chain S residue 5 LYS Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 57 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 212 optimal weight: 4.9990 chunk 284 optimal weight: 0.0030 chunk 81 optimal weight: 10.0000 chunk 246 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 267 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 274 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 overall best weight: 4.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.144587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.135236 restraints weight = 143635.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.136746 restraints weight = 59954.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.137617 restraints weight = 31730.303| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.5664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 52058 Z= 0.333 Angle : 0.828 59.199 77812 Z= 0.431 Chirality : 0.042 0.304 9933 Planarity : 0.006 0.067 4217 Dihedral : 23.851 179.179 25905 Min Nonbonded Distance : 1.545 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.13 % Favored : 87.72 % Rotamer: Outliers : 5.27 % Allowed : 30.89 % Favored : 63.83 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.44 (0.18), residues: 1913 helix: -0.38 (0.19), residues: 679 sheet: -1.39 (0.28), residues: 332 loop : -2.74 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.004 TRP F 42 HIS 0.005 0.001 HIS O 46 PHE 0.032 0.002 PHE M 62 TYR 0.028 0.002 TYR C 192 ARG 0.059 0.001 ARG N 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9788.06 seconds wall clock time: 178 minutes 49.15 seconds (10729.15 seconds total)