Starting phenix.real_space_refine (version: dev) on Thu Dec 22 05:40:24 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w77_21569/12_2022/6w77_21569.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w77_21569/12_2022/6w77_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_21569/12_2022/6w77_21569.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w77_21569/12_2022/6w77_21569.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w77_21569/12_2022/6w77_21569.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w77_21569/12_2022/6w77_21569.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 25.92, 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: 24.69 Conformation dependent library (CDL) restraints added in 2.4 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: 18.12 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: 48.36 Time building geometry restraints manager: 26.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 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: 26847 35.82 - 71.64: 936 71.64 - 107.45: 83 107.45 - 143.27: 9 143.27 - 179.09: 12 Dihedral angle restraints: 27887 sinusoidal: 22306 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 27884 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 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. 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: 1.220 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: 0.030 Extract box with map and model: 10.120 Check model and map are aligned: 0.720 Convert atoms to be neutral: 0.380 Process input model: 159.010 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 175.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 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 : 14.955 179.089 24283 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.06 % Favored : 93.73 % Rotamer Outliers : 0.12 % 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 *********************** 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 : 2.842 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 outliers start: 2 outliers final: 0 residues processed: 575 average time/residue: 0.7012 time to fit residues: 617.0082 Evaluate side-chains 393 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 393 time to evaluate : 2.797 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9412 ------------------------------------------------------------------------------- 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: 10.0000 chunk 87 optimal weight: 10.0000 chunk 172 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 264 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 chunk 160 optimal weight: 30.0000 chunk 196 optimal weight: 5.9990 chunk 306 optimal weight: 6.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 ASN C 138 GLN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 ASN H 21 ASN I 49 GLN J 58 ASN ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 119 ASN L 5 ASN M 7 ASN O 40 GLN P 59 HIS R 31 ASN R 52 GLN T 21 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.097 52058 Z= 0.391 Angle : 0.856 10.732 77812 Z= 0.427 Chirality : 0.045 0.284 9933 Planarity : 0.007 0.071 4217 Dihedral : 15.519 174.343 20401 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.93 % Favored : 89.91 % Rotamer Outliers : 5.33 % 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: -3.00 (0.17), residues: 1913 helix: -1.22 (0.17), residues: 701 sheet: -1.37 (0.26), residues: 342 loop : -2.92 (0.18), residues: 870 *********************** 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 513 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 427 time to evaluate : 2.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 86 outliers final: 56 residues processed: 472 average time/residue: 0.6961 time to fit residues: 512.7575 Evaluate side-chains 440 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 384 time to evaluate : 3.116 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.4546 time to fit residues: 50.2946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 170 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 254 optimal weight: 5.9990 chunk 208 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 306 optimal weight: 6.9990 chunk 331 optimal weight: 2.9990 chunk 273 optimal weight: 0.6980 chunk 304 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 245 optimal weight: 0.9980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 GLN C 138 GLN D 41 HIS D 74 ASN D 131 ASN D 140 ASN D 164 GLN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 ASN H 16 ASN I 80 HIS J 70 HIS ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 13 HIS M 104 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 52058 Z= 0.228 Angle : 0.648 10.225 77812 Z= 0.329 Chirality : 0.037 0.274 9933 Planarity : 0.005 0.049 4217 Dihedral : 15.164 175.724 20401 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.05 % Favored : 91.79 % Rotamer Outliers : 3.04 % 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: -0.64 (0.19), residues: 698 sheet: -1.06 (0.27), residues: 338 loop : -2.70 (0.19), residues: 877 *********************** 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 453 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 404 time to evaluate : 2.833 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 outliers start: 49 outliers final: 20 residues processed: 431 average time/residue: 0.7530 time to fit residues: 510.3032 Evaluate side-chains 390 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 370 time to evaluate : 2.926 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.4625 time to fit residues: 20.5585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 302 optimal weight: 5.9990 chunk 230 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 205 optimal weight: 0.8980 chunk 307 optimal weight: 5.9990 chunk 325 optimal weight: 2.9990 chunk 160 optimal weight: 0.9980 chunk 291 optimal weight: 0.0040 chunk 87 optimal weight: 9.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 5 HIS D 40 GLN D 74 ASN D 140 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** N 3 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 52058 Z= 0.140 Angle : 0.548 9.622 77812 Z= 0.280 Chirality : 0.033 0.244 9933 Planarity : 0.004 0.042 4217 Dihedral : 14.777 178.412 20401 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.06 % Favored : 92.79 % Rotamer Outliers : 3.16 % 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: -1.90 (0.18), residues: 1913 helix: -0.03 (0.19), residues: 709 sheet: -0.90 (0.27), residues: 333 loop : -2.50 (0.19), residues: 871 *********************** 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 457 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 406 time to evaluate : 2.549 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 outliers start: 51 outliers final: 29 residues processed: 438 average time/residue: 0.6747 time to fit residues: 461.9468 Evaluate side-chains 393 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 364 time to evaluate : 2.746 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.4076 time to fit residues: 25.5355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 4 optimal weight: 10.0000 chunk 242 optimal weight: 7.9990 chunk 134 optimal weight: 9.9990 chunk 277 optimal weight: 2.9990 chunk 225 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 166 optimal weight: 7.9990 chunk 292 optimal weight: 0.0670 chunk 82 optimal weight: 10.0000 overall best weight: 3.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN D 131 ASN D 140 ASN D 164 GLN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 ASN ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 ASN N 34 ASN N 70 HIS ** O 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 78 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.095 52058 Z= 0.261 Angle : 0.690 11.738 77812 Z= 0.348 Chirality : 0.038 0.239 9933 Planarity : 0.005 0.047 4217 Dihedral : 15.236 175.104 20401 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.98 % Favored : 89.86 % Rotamer Outliers : 3.78 % 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: -2.12 (0.18), residues: 1913 helix: -0.20 (0.19), residues: 703 sheet: -0.99 (0.27), residues: 333 loop : -2.64 (0.19), residues: 877 *********************** 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 444 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 383 time to evaluate : 2.989 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 outliers start: 61 outliers final: 35 residues processed: 424 average time/residue: 0.6600 time to fit residues: 442.2072 Evaluate side-chains 398 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 363 time to evaluate : 2.741 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.4388 time to fit residues: 31.1827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 109 optimal weight: 10.0000 chunk 293 optimal weight: 0.5980 chunk 64 optimal weight: 10.0000 chunk 191 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 326 optimal weight: 0.9990 chunk 270 optimal weight: 7.9990 chunk 150 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 107 optimal weight: 8.9990 chunk 171 optimal weight: 6.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 ASN D 74 ASN D 164 GLN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 51 GLN M 104 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.070 52058 Z= 0.326 Angle : 0.807 11.843 77812 Z= 0.406 Chirality : 0.044 0.437 9933 Planarity : 0.007 0.060 4217 Dihedral : 15.973 173.940 20401 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.45 % Favored : 88.40 % Rotamer Outliers : 3.91 % 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: -2.49 (0.18), residues: 1913 helix: -0.56 (0.19), residues: 696 sheet: -1.19 (0.27), residues: 333 loop : -2.78 (0.19), residues: 884 *********************** 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 455 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 392 time to evaluate : 2.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 38 residues processed: 429 average time/residue: 0.6593 time to fit residues: 448.7909 Evaluate side-chains 401 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 363 time to evaluate : 3.055 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.4277 time to fit residues: 33.5556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 314 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 185 optimal weight: 10.0000 chunk 238 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 chunk 274 optimal weight: 9.9990 chunk 182 optimal weight: 0.8980 chunk 324 optimal weight: 7.9990 chunk 203 optimal weight: 0.9980 chunk 198 optimal weight: 1.9990 chunk 149 optimal weight: 10.0000 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN D 164 GLN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN T 61 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 52058 Z= 0.264 Angle : 0.715 12.101 77812 Z= 0.362 Chirality : 0.040 0.281 9933 Planarity : 0.005 0.048 4217 Dihedral : 15.756 177.413 20401 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.30 % Favored : 89.55 % Rotamer Outliers : 2.11 % 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: -2.39 (0.18), residues: 1913 helix: -0.43 (0.19), residues: 700 sheet: -1.22 (0.27), residues: 333 loop : -2.74 (0.19), residues: 880 *********************** 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 411 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 377 time to evaluate : 2.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 21 residues processed: 394 average time/residue: 0.6650 time to fit residues: 411.0553 Evaluate side-chains 387 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 366 time to evaluate : 2.601 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.4445 time to fit residues: 19.6626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 200 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 chunk 193 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 206 optimal weight: 9.9990 chunk 221 optimal weight: 0.9990 chunk 160 optimal weight: 0.0020 chunk 30 optimal weight: 10.0000 chunk 255 optimal weight: 4.9990 overall best weight: 4.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN T 61 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.5531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.077 52058 Z= 0.342 Angle : 0.827 12.165 77812 Z= 0.414 Chirality : 0.045 0.302 9933 Planarity : 0.007 0.060 4217 Dihedral : 16.193 177.700 20401 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.39 % Favored : 87.45 % Rotamer Outliers : 3.04 % 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: -2.61 (0.18), residues: 1913 helix: -0.62 (0.19), residues: 686 sheet: -1.32 (0.27), residues: 333 loop : -2.84 (0.19), residues: 894 *********************** 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 417 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 368 time to evaluate : 2.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 33 residues processed: 391 average time/residue: 0.6762 time to fit residues: 418.1660 Evaluate side-chains 389 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 356 time to evaluate : 3.099 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.4322 time to fit residues: 29.7364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 295 optimal weight: 2.9990 chunk 311 optimal weight: 0.2980 chunk 283 optimal weight: 0.2980 chunk 302 optimal weight: 7.9990 chunk 182 optimal weight: 1.9990 chunk 131 optimal weight: 10.0000 chunk 237 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 273 optimal weight: 0.0670 chunk 286 optimal weight: 0.8980 chunk 301 optimal weight: 0.0980 overall best weight: 0.3318 ------------------------------------------------------------------------------- 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 ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 ASN I 24 ASN J 64 GLN M 51 GLN P 9 HIS ** R 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.5165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.068 52058 Z= 0.144 Angle : 0.597 11.270 77812 Z= 0.303 Chirality : 0.034 0.300 9933 Planarity : 0.005 0.058 4217 Dihedral : 15.174 179.211 20401 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.53 % Favored : 93.31 % Rotamer Outliers : 0.31 % 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: -1.83 (0.18), residues: 1913 helix: 0.15 (0.20), residues: 702 sheet: -0.93 (0.28), residues: 331 loop : -2.52 (0.19), residues: 880 *********************** 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 405 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 400 time to evaluate : 2.832 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 outliers start: 5 outliers final: 2 residues processed: 403 average time/residue: 0.7098 time to fit residues: 443.4687 Evaluate side-chains 364 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 362 time to evaluate : 2.772 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3935 time to fit residues: 4.4928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 198 optimal weight: 0.9980 chunk 320 optimal weight: 7.9990 chunk 195 optimal weight: 1.9990 chunk 151 optimal weight: 0.0980 chunk 222 optimal weight: 3.9990 chunk 335 optimal weight: 5.9990 chunk 309 optimal weight: 0.9980 chunk 267 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 206 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN T 78 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.053 52058 Z= 0.148 Angle : 0.579 10.998 77812 Z= 0.292 Chirality : 0.033 0.306 9933 Planarity : 0.004 0.054 4217 Dihedral : 14.997 179.007 20401 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.26 % Favored : 91.58 % Rotamer Outliers : 0.50 % 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: -1.80 (0.18), residues: 1913 helix: 0.15 (0.19), residues: 715 sheet: -0.92 (0.28), residues: 331 loop : -2.52 (0.19), residues: 867 ********************** 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 387 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 379 time to evaluate : 2.899 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 outliers start: 8 outliers final: 5 residues processed: 382 average time/residue: 0.7052 time to fit residues: 419.1477 Evaluate side-chains 369 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 364 time to evaluate : 2.824 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4522 time to fit residues: 7.6616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 212 optimal weight: 0.7980 chunk 284 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 246 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 267 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 274 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 ASN I 24 ASN ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN M 51 GLN T 78 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.143900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.134584 restraints weight = 142806.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.136068 restraints weight = 59830.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.136954 restraints weight = 31674.149| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.5757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.085 52058 Z= 0.360 Angle : 0.844 11.969 77812 Z= 0.419 Chirality : 0.045 0.382 9933 Planarity : 0.007 0.062 4217 Dihedral : 16.009 176.584 20401 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.18 % Favored : 87.66 % Rotamer Outliers : 0.87 % 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: -2.34 (0.18), residues: 1913 helix: -0.45 (0.19), residues: 692 sheet: -1.13 (0.28), residues: 327 loop : -2.65 (0.19), residues: 894 =============================================================================== Job complete usr+sys time: 8699.97 seconds wall clock time: 158 minutes 47.80 seconds (9527.80 seconds total)