Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 18:48:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x8r_6710/04_2023/5x8r_6710.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x8r_6710/04_2023/5x8r_6710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x8r_6710/04_2023/5x8r_6710.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x8r_6710/04_2023/5x8r_6710.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x8r_6710/04_2023/5x8r_6710.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x8r_6710/04_2023/5x8r_6710.pdb" } resolution = 3.7 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= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1480 5.49 5 S 89 5.16 5 C 29036 2.51 5 N 10368 2.21 5 O 14439 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b ARG 25": "NH1" <-> "NH2" Residue "b ARG 30": "NH1" <-> "NH2" Residue "b ARG 49": "NH1" <-> "NH2" Residue "b ARG 52": "NH1" <-> "NH2" Residue "b ARG 67": "NH1" <-> "NH2" Residue "b ARG 86": "NH1" <-> "NH2" Residue "b ARG 90": "NH1" <-> "NH2" Residue "b ARG 92": "NH1" <-> "NH2" Residue "b ARG 114": "NH1" <-> "NH2" Residue "b ARG 119": "NH1" <-> "NH2" Residue "b ARG 122": "NH1" <-> "NH2" Residue "b ARG 129": "NH1" <-> "NH2" Residue "b ARG 132": "NH1" <-> "NH2" Residue "b ARG 136": "NH1" <-> "NH2" Residue "b ARG 143": "NH1" <-> "NH2" Residue "b ARG 178": "NH1" <-> "NH2" Residue "b ASP 209": "OD1" <-> "OD2" Residue "b ARG 215": "NH1" <-> "NH2" Residue "b ARG 229": "NH1" <-> "NH2" Residue "c ARG 11": "NH1" <-> "NH2" Residue "c ARG 40": "NH1" <-> "NH2" Residue "c ARG 88": "NH1" <-> "NH2" Residue "c ARG 108": "NH1" <-> "NH2" Residue "c ARG 116": "NH1" <-> "NH2" Residue "c ARG 167": "NH1" <-> "NH2" Residue "c ARG 175": "NH1" <-> "NH2" Residue "c ARG 183": "NH1" <-> "NH2" Residue "c ARG 190": "NH1" <-> "NH2" Residue "c ARG 201": "NH1" <-> "NH2" Residue "e TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 226": "NH1" <-> "NH2" Residue "e ARG 280": "NH1" <-> "NH2" Residue "e ARG 290": "NH1" <-> "NH2" Residue "e ARG 299": "NH1" <-> "NH2" Residue "f ARG 106": "NH1" <-> "NH2" Residue "f ARG 115": "NH1" <-> "NH2" Residue "f ARG 147": "NH1" <-> "NH2" Residue "f ARG 158": "NH1" <-> "NH2" Residue "f ARG 200": "NH1" <-> "NH2" Residue "g ARG 21": "NH1" <-> "NH2" Residue "g ARG 78": "NH1" <-> "NH2" Residue "g ARG 79": "NH1" <-> "NH2" Residue "g ARG 102": "NH1" <-> "NH2" Residue "g ARG 111": "NH1" <-> "NH2" Residue "g ARG 143": "NH1" <-> "NH2" Residue "h ARG 20": "NH1" <-> "NH2" Residue "h ARG 64": "NH1" <-> "NH2" Residue "h TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 77": "NH1" <-> "NH2" Residue "i ARG 99": "NH1" <-> "NH2" Residue "i ARG 152": "NH1" <-> "NH2" Residue "i ARG 173": "NH1" <-> "NH2" Residue "i ARG 176": "NH1" <-> "NH2" Residue "i ARG 189": "NH1" <-> "NH2" Residue "j ARG 155": "NH1" <-> "NH2" Residue "k PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 137": "NH1" <-> "NH2" Residue "l ARG 12": "NH1" <-> "NH2" Residue "l ARG 30": "NH1" <-> "NH2" Residue "l ARG 31": "NH1" <-> "NH2" Residue "l ARG 36": "NH1" <-> "NH2" Residue "l ARG 50": "NH1" <-> "NH2" Residue "l ARG 54": "NH1" <-> "NH2" Residue "l ARG 56": "NH1" <-> "NH2" Residue "l ARG 83": "NH1" <-> "NH2" Residue "l ARG 94": "NH1" <-> "NH2" Residue "l ARG 99": "NH1" <-> "NH2" Residue "l ARG 110": "NH1" <-> "NH2" Residue "l ARG 114": "NH1" <-> "NH2" Residue "m ARG 108": "NH1" <-> "NH2" Residue "m ARG 118": "NH1" <-> "NH2" Residue "m ARG 135": "NH1" <-> "NH2" Residue "o ARG 34": "NH1" <-> "NH2" Residue "o ARG 35": "NH1" <-> "NH2" Residue "o ARG 51": "NH1" <-> "NH2" Residue "o ARG 54": "NH1" <-> "NH2" Residue "o ARG 60": "NH1" <-> "NH2" Residue "o ARG 74": "NH1" <-> "NH2" Residue "p ARG 5": "NH1" <-> "NH2" Residue "p ARG 8": "NH1" <-> "NH2" Residue "p ARG 14": "NH1" <-> "NH2" Residue "p ARG 18": "NH1" <-> "NH2" Residue "p ARG 25": "NH1" <-> "NH2" Residue "p ARG 28": "NH1" <-> "NH2" Residue "p ARG 31": "NH1" <-> "NH2" Residue "p ARG 73": "NH1" <-> "NH2" Residue "r ARG 27": "NH1" <-> "NH2" Residue "r TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 38": "NH1" <-> "NH2" Residue "r ARG 49": "NH1" <-> "NH2" Residue "r ARG 50": "NH1" <-> "NH2" Residue "r ARG 53": "NH1" <-> "NH2" Residue "r ARG 60": "NH1" <-> "NH2" Residue "r ARG 70": "NH1" <-> "NH2" Residue "s ARG 17": "NH1" <-> "NH2" Residue "s ARG 55": "NH1" <-> "NH2" Residue "s ARG 65": "NH1" <-> "NH2" Residue "s ARG 81": "NH1" <-> "NH2" Residue "t ARG 84": "NH1" <-> "NH2" Residue "t ARG 103": "NH1" <-> "NH2" Residue "t ARG 105": "NH1" <-> "NH2" Residue "t ARG 150": "NH1" <-> "NH2" Residue "t ARG 162": "NH1" <-> "NH2" Residue "u ARG 104": "NH1" <-> "NH2" Residue "u ARG 109": "NH1" <-> "NH2" Residue "u ARG 120": "NH1" <-> "NH2" Residue "y ARG 91": "NH1" <-> "NH2" Residue "y ARG 110": "NH1" <-> "NH2" Residue "y ARG 115": "NH1" <-> "NH2" Residue "y ARG 130": "NH1" <-> "NH2" Residue "y ARG 131": "NH1" <-> "NH2" Residue "y ARG 140": "NH1" <-> "NH2" Residue "y ARG 166": "NH1" <-> "NH2" Residue "w ARG 98": "NH1" <-> "NH2" Residue "w GLU 107": "OE1" <-> "OE2" Residue "w ASP 115": "OD1" <-> "OD2" Residue "w ARG 134": "NH1" <-> "NH2" Residue "w ASP 136": "OD1" <-> "OD2" Residue "w GLU 140": "OE1" <-> "OE2" Residue "w GLU 146": "OE1" <-> "OE2" Residue "w ASP 165": "OD1" <-> "OD2" Residue "d ARG 3": "NH1" <-> "NH2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d ARG 14": "NH1" <-> "NH2" Residue "d ARG 25": "NH1" <-> "NH2" Residue "d ARG 45": "NH1" <-> "NH2" Residue "d ARG 47": "NH1" <-> "NH2" Residue "d ARG 55": "NH1" <-> "NH2" Residue "d ARG 63": "NH1" <-> "NH2" Residue "d ARG 70": "NH1" <-> "NH2" Residue "d ARG 97": "NH1" <-> "NH2" Residue "d ARG 108": "NH1" <-> "NH2" Residue "d ARG 114": "NH1" <-> "NH2" Residue "d ARG 121": "NH1" <-> "NH2" Residue "d ARG 129": "NH1" <-> "NH2" Residue "d ARG 139": "NH1" <-> "NH2" Residue "d ARG 157": "NH1" <-> "NH2" Residue "d TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 195": "OE1" <-> "OE2" Residue "v ASP 17": "OD1" <-> "OD2" Residue "v ARG 22": "NH1" <-> "NH2" Residue "v ARG 23": "NH1" <-> "NH2" Residue "v ARG 31": "NH1" <-> "NH2" Residue "v ASP 36": "OD1" <-> "OD2" Residue "v ARG 39": "NH1" <-> "NH2" Residue "v GLU 44": "OE1" <-> "OE2" Residue "v GLU 49": "OE1" <-> "OE2" Residue "v ARG 61": "NH1" <-> "NH2" Residue "v ARG 63": "NH1" <-> "NH2" Residue "v ARG 64": "NH1" <-> "NH2" Residue "v GLU 74": "OE1" <-> "OE2" Residue "v ASP 75": "OD1" <-> "OD2" Residue "v GLU 81": "OE1" <-> "OE2" Residue "v ASP 85": "OD1" <-> "OD2" Residue "v GLU 87": "OE1" <-> "OE2" Residue "v ARG 91": "NH1" <-> "NH2" Residue "v GLU 99": "OE1" <-> "OE2" Residue "v ASP 106": "OD1" <-> "OD2" Residue "v GLU 113": "OE1" <-> "OE2" Residue "v ASP 114": "OD1" <-> "OD2" Residue "v GLU 119": "OE1" <-> "OE2" Residue "v GLU 136": "OE1" <-> "OE2" Residue "v ASP 140": "OD1" <-> "OD2" Residue "v GLU 144": "OE1" <-> "OE2" Residue "v ARG 155": "NH1" <-> "NH2" Residue "v GLU 173": "OE1" <-> "OE2" Residue "v GLU 174": "OE1" <-> "OE2" Residue "v GLU 177": "OE1" <-> "OE2" Residue "v GLU 189": "OE1" <-> "OE2" Residue "v ARG 194": "NH1" <-> "NH2" Residue "n ARG 9": "NH1" <-> "NH2" Residue "n ARG 13": "NH1" <-> "NH2" Residue "n ARG 14": "NH1" <-> "NH2" Residue "n TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 24": "NH1" <-> "NH2" Residue "n ARG 25": "NH1" <-> "NH2" Residue "n ARG 32": "NH1" <-> "NH2" Residue "n ARG 61": "NH1" <-> "NH2" Residue "n ARG 62": "NH1" <-> "NH2" Residue "n ARG 70": "NH1" <-> "NH2" Residue "n ARG 74": "NH1" <-> "NH2" Residue "n ARG 84": "NH1" <-> "NH2" Residue "x ARG 75": "NH1" <-> "NH2" Residue "x PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 350": "OE1" <-> "OE2" Residue "8 PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 55412 Number of models: 1 Model: "" Number of chains: 26 Chain: "b" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1787 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 7, 'TRANS': 219} Chain: "c" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1719 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 7, 'TRANS': 205} Chain: "e" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1292 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 5, 'TRANS': 165} Chain: "f" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 886 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "g" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1161 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 5, 'TRANS': 143} Chain: "h" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1088 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "i" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1020 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 6, 'TRANS': 126} Chain: "j" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 796 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 90} Chain: "k" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 887 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain: "l" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 967 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 9, 'TRANS': 113} Chain: "m" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 898 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "o" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 525 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "p" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 664 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "q" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 635 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "r" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 518 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 62} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "s" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 627 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "t" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 832 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "u" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 393 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain: "y" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 845 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "a" Number of atoms: 31777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1480, 31777 Classifications: {'RNA': 1480} Modifications used: {'rna2p_pur': 118, 'rna2p_pyr': 77, 'rna3p_pur': 730, 'rna3p_pyr': 555} Link IDs: {'rna2p': 195, 'rna3p': 1284} Chain breaks: 2 Chain: "w" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 689 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 6, 'TRANS': 77} Chain: "d" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1633 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 11, 'TRANS': 187} Chain: "v" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1464 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain: "n" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 819 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "x" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 289 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 4, 'TRANS': 32} Chain: "8" Number of atoms: 1201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1201 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 7, 'TRANS': 146} Chain breaks: 1 Time building chain proxies: 22.43, per 1000 atoms: 0.40 Number of scatterers: 55412 At special positions: 0 Unit cell: (223.65, 219.45, 187.95, 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 89 16.00 P 1480 15.00 O 14439 8.00 N 10368 7.00 C 29036 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: 23.60 Conformation dependent library (CDL) restraints added in 3.5 seconds 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5508 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 30 sheets defined 39.2% alpha, 16.1% beta 510 base pairs and 824 stacking pairs defined. Time for finding SS restraints: 18.12 Creating SS restraints... Processing helix chain 'b' and resid 9 through 16 removed outlier: 3.859A pdb=" N MET b 13 " --> pdb=" O ASN b 9 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA b 16 " --> pdb=" O GLU b 12 " (cutoff:3.500A) Processing helix chain 'b' and resid 28 through 32 Processing helix chain 'b' and resid 46 through 68 removed outlier: 3.696A pdb=" N ALA b 64 " --> pdb=" O LEU b 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 80 through 90 removed outlier: 3.888A pdb=" N VAL b 84 " --> pdb=" O ALA b 80 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA b 85 " --> pdb=" O ALA b 81 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ARG b 90 " --> pdb=" O ARG b 86 " (cutoff:3.500A) Processing helix chain 'b' and resid 107 through 127 removed outlier: 3.518A pdb=" N THR b 111 " --> pdb=" O ASN b 107 " (cutoff:3.500A) Processing helix chain 'b' and resid 134 through 152 Processing helix chain 'b' and resid 173 through 184 Processing helix chain 'b' and resid 210 through 230 Processing helix chain 'c' and resid 6 through 11 Processing helix chain 'c' and resid 25 through 53 Processing helix chain 'c' and resid 80 through 84 Processing helix chain 'c' and resid 89 through 101 removed outlier: 3.608A pdb=" N GLU c 93 " --> pdb=" O PRO c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 123 through 137 Processing helix chain 'c' and resid 140 through 154 Processing helix chain 'c' and resid 188 through 191 Processing helix chain 'e' and resid 196 through 209 Processing helix chain 'e' and resid 250 through 259 Processing helix chain 'e' and resid 275 through 288 removed outlier: 3.715A pdb=" N THR e 288 " --> pdb=" O VAL e 284 " (cutoff:3.500A) Processing helix chain 'e' and resid 292 through 300 Processing helix chain 'f' and resid 124 through 137 Processing helix chain 'f' and resid 185 through 195 removed outlier: 3.722A pdb=" N ASP f 195 " --> pdb=" O ALA f 191 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 30 removed outlier: 3.611A pdb=" N MET g 25 " --> pdb=" O ARG g 21 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 54 removed outlier: 3.658A pdb=" N GLN g 52 " --> pdb=" O LYS g 48 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 68 removed outlier: 3.744A pdb=" N GLY g 68 " --> pdb=" O GLN g 64 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 109 Processing helix chain 'g' and resid 115 through 130 Processing helix chain 'g' and resid 133 through 146 removed outlier: 4.003A pdb=" N MET g 144 " --> pdb=" O GLU g 140 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA g 145 " --> pdb=" O THR g 141 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 18 removed outlier: 3.876A pdb=" N ILE h 9 " --> pdb=" O THR h 5 " (cutoff:3.500A) Processing helix chain 'h' and resid 29 through 41 removed outlier: 4.019A pdb=" N ARG h 41 " --> pdb=" O LYS h 37 " (cutoff:3.500A) Processing helix chain 'h' and resid 98 through 103 removed outlier: 3.964A pdb=" N MET h 103 " --> pdb=" O LEU h 100 " (cutoff:3.500A) Processing helix chain 'h' and resid 116 through 122 Processing helix chain 'i' and resid 101 through 105 Processing helix chain 'i' and resid 109 through 123 removed outlier: 3.988A pdb=" N GLN i 113 " --> pdb=" O PRO i 109 " (cutoff:3.500A) Proline residue: i 118 - end of helix removed outlier: 3.529A pdb=" N LEU i 122 " --> pdb=" O PRO i 118 " (cutoff:3.500A) Processing helix chain 'i' and resid 138 through 156 removed outlier: 3.576A pdb=" N LYS i 156 " --> pdb=" O ARG i 152 " (cutoff:3.500A) Processing helix chain 'i' and resid 157 through 160 removed outlier: 6.583A pdb=" N SER i 160 " --> pdb=" O VAL i 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 157 through 160' Processing helix chain 'i' and resid 161 through 168 removed outlier: 3.609A pdb=" N GLN i 167 " --> pdb=" O ALA i 163 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU i 168 " --> pdb=" O PRO i 164 " (cutoff:3.500A) Processing helix chain 'j' and resid 107 through 126 Processing helix chain 'j' and resid 173 through 181 Processing helix chain 'k' and resid 68 through 81 Processing helix chain 'k' and resid 82 through 84 No H-bonds generated for 'chain 'k' and resid 82 through 84' Processing helix chain 'k' and resid 101 through 113 removed outlier: 3.745A pdb=" N ALA k 105 " --> pdb=" O GLY k 101 " (cutoff:3.500A) Processing helix chain 'm' and resid 44 through 51 Processing helix chain 'm' and resid 56 through 64 Processing helix chain 'm' and resid 79 through 93 removed outlier: 3.780A pdb=" N SER m 93 " --> pdb=" O THR m 89 " (cutoff:3.500A) Processing helix chain 'm' and resid 95 through 113 removed outlier: 4.116A pdb=" N LEU m 100 " --> pdb=" O GLU m 96 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG m 113 " --> pdb=" O VAL m 109 " (cutoff:3.500A) Processing helix chain 'm' and resid 115 through 123 removed outlier: 3.605A pdb=" N ILE m 123 " --> pdb=" O CYS m 119 " (cutoff:3.500A) Processing helix chain 'o' and resid 22 through 41 Processing helix chain 'o' and resid 48 through 71 removed outlier: 3.961A pdb=" N GLY o 52 " --> pdb=" O SER o 48 " (cutoff:3.500A) Processing helix chain 'o' and resid 72 through 82 removed outlier: 3.725A pdb=" N LEU o 82 " --> pdb=" O LEU o 78 " (cutoff:3.500A) Processing helix chain 'p' and resid 49 through 60 Processing helix chain 'p' and resid 64 through 74 removed outlier: 3.504A pdb=" N ALA p 74 " --> pdb=" O ILE p 70 " (cutoff:3.500A) Processing helix chain 'r' and resid 48 through 53 Processing helix chain 'r' and resid 55 through 72 Processing helix chain 's' and resid 12 through 23 Processing helix chain 's' and resid 41 through 45 removed outlier: 3.591A pdb=" N ILE s 45 " --> pdb=" O PRO s 42 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 74 removed outlier: 3.553A pdb=" N GLU s 73 " --> pdb=" O LYS s 70 " (cutoff:3.500A) Processing helix chain 't' and resid 82 through 120 Processing helix chain 't' and resid 127 through 148 removed outlier: 3.983A pdb=" N LEU t 131 " --> pdb=" O PRO t 127 " (cutoff:3.500A) Processing helix chain 't' and resid 155 through 171 Processing helix chain 'u' and resid 100 through 106 Processing helix chain 'u' and resid 107 through 113 removed outlier: 7.595A pdb=" N ALA u 110 " --> pdb=" O VAL u 107 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLY u 111 " --> pdb=" O MET u 108 " (cutoff:3.500A) Processing helix chain 'u' and resid 122 through 137 removed outlier: 3.688A pdb=" N ALA u 137 " --> pdb=" O HIS u 133 " (cutoff:3.500A) Processing helix chain 'y' and resid 87 through 102 removed outlier: 3.869A pdb=" N ARG y 91 " --> pdb=" O SER y 87 " (cutoff:3.500A) Processing helix chain 'y' and resid 152 through 175 Processing helix chain 'w' and resid 137 through 148 Processing helix chain 'w' and resid 152 through 176 Processing helix chain 'd' and resid 8 through 16 Processing helix chain 'd' and resid 42 through 59 removed outlier: 3.791A pdb=" N HIS d 57 " --> pdb=" O LYS d 53 " (cutoff:3.500A) Processing helix chain 'd' and resid 61 through 75 Processing helix chain 'd' and resid 78 through 87 removed outlier: 4.167A pdb=" N LEU d 84 " --> pdb=" O GLY d 80 " (cutoff:3.500A) Processing helix chain 'd' and resid 90 through 98 Processing helix chain 'd' and resid 103 through 113 Processing helix chain 'd' and resid 139 through 144 removed outlier: 3.716A pdb=" N LYS d 143 " --> pdb=" O ASP d 140 " (cutoff:3.500A) Processing helix chain 'd' and resid 146 through 155 Processing helix chain 'd' and resid 189 through 197 removed outlier: 3.508A pdb=" N VAL d 193 " --> pdb=" O ASN d 189 " (cutoff:3.500A) Processing helix chain 'v' and resid 10 through 20 Processing helix chain 'v' and resid 34 through 44 removed outlier: 3.853A pdb=" N GLU v 44 " --> pdb=" O THR v 40 " (cutoff:3.500A) Processing helix chain 'v' and resid 72 through 84 removed outlier: 3.869A pdb=" N ASN v 84 " --> pdb=" O ILE v 80 " (cutoff:3.500A) Processing helix chain 'v' and resid 105 through 116 Processing helix chain 'v' and resid 134 through 145 Processing helix chain 'v' and resid 172 through 184 Processing helix chain 'n' and resid 3 through 32 removed outlier: 3.877A pdb=" N ILE n 7 " --> pdb=" O ARG n 3 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN n 8 " --> pdb=" O LYS n 4 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR n 20 " --> pdb=" O LEU n 16 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU n 22 " --> pdb=" O GLN n 18 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE n 23 " --> pdb=" O LYS n 19 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU n 30 " --> pdb=" O SER n 26 " (cutoff:3.500A) Processing helix chain 'n' and resid 43 through 49 Processing helix chain 'n' and resid 80 through 86 removed outlier: 3.866A pdb=" N ARG n 84 " --> pdb=" O GLY n 80 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU n 85 " --> pdb=" O HIS n 81 " (cutoff:3.500A) Processing helix chain 'x' and resid 61 through 69 removed outlier: 3.751A pdb=" N LYS x 65 " --> pdb=" O THR x 61 " (cutoff:3.500A) Processing helix chain '8' and resid 51 through 66 Processing helix chain '8' and resid 250 through 257 Processing helix chain '8' and resid 289 through 292 Processing helix chain '8' and resid 319 through 323 removed outlier: 4.123A pdb=" N ARG 8 323 " --> pdb=" O GLU 8 320 " (cutoff:3.500A) Processing helix chain '8' and resid 341 through 359 removed outlier: 3.670A pdb=" N GLU 8 347 " --> pdb=" O LYS 8 343 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'b' and resid 37 through 39 Processing sheet with id=AA2, first strand: chain 'b' and resid 94 through 95 removed outlier: 3.507A pdb=" N ILE b 73 " --> pdb=" O HIS b 94 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU b 72 " --> pdb=" O ILE b 166 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'b' and resid 190 through 191 Processing sheet with id=AA4, first strand: chain 'c' and resid 20 through 21 removed outlier: 3.698A pdb=" N LYS c 67 " --> pdb=" O LEU c 21 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG c 62 " --> pdb=" O HIS c 77 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'c' and resid 20 through 21 removed outlier: 3.698A pdb=" N LYS c 67 " --> pdb=" O LEU c 21 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG c 62 " --> pdb=" O HIS c 77 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N THR c 115 " --> pdb=" O VAL c 74 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE c 76 " --> pdb=" O THR c 115 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'c' and resid 177 through 181 Processing sheet with id=AA7, first strand: chain 'e' and resid 153 through 165 removed outlier: 5.517A pdb=" N GLU e 154 " --> pdb=" O GLY e 181 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N GLY e 181 " --> pdb=" O GLU e 154 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL e 156 " --> pdb=" O VAL e 179 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL e 179 " --> pdb=" O VAL e 156 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN e 158 " --> pdb=" O ILE e 177 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'e' and resid 153 through 165 removed outlier: 5.517A pdb=" N GLU e 154 " --> pdb=" O GLY e 181 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N GLY e 181 " --> pdb=" O GLU e 154 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL e 156 " --> pdb=" O VAL e 179 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL e 179 " --> pdb=" O VAL e 156 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN e 158 " --> pdb=" O ILE e 177 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN e 186 " --> pdb=" O ASP e 182 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'e' and resid 227 through 228 removed outlier: 6.767A pdb=" N ILE e 248 " --> pdb=" O GLY e 267 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N GLN e 269 " --> pdb=" O ILE e 248 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'f' and resid 106 through 107 Processing sheet with id=AB2, first strand: chain 'f' and resid 146 through 155 removed outlier: 5.392A pdb=" N ASN f 146 " --> pdb=" O LEU f 175 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU f 175 " --> pdb=" O ASN f 146 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N GLY f 148 " --> pdb=" O TYR f 173 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N TYR f 173 " --> pdb=" O GLY f 148 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE f 150 " --> pdb=" O GLY f 171 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY f 171 " --> pdb=" O ILE f 150 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU f 169 " --> pdb=" O LEU f 152 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE f 172 " --> pdb=" O LEU f 114 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL f 113 " --> pdb=" O ARG f 200 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ARG f 200 " --> pdb=" O VAL f 113 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'g' and resid 74 through 75 removed outlier: 3.755A pdb=" N ALA g 74 " --> pdb=" O ILE g 89 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'g' and resid 78 through 80 Processing sheet with id=AB5, first strand: chain 'h' and resid 24 through 27 removed outlier: 6.240A pdb=" N PHE h 58 " --> pdb=" O LYS h 50 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS h 50 " --> pdb=" O PHE h 58 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL h 60 " --> pdb=" O ALA h 48 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ALA h 48 " --> pdb=" O VAL h 60 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N THR h 62 " --> pdb=" O GLU h 46 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'h' and resid 114 through 115 removed outlier: 3.562A pdb=" N LEU h 108 " --> pdb=" O MET h 115 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE h 105 " --> pdb=" O TYR h 132 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR h 132 " --> pdb=" O ILE h 105 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE h 107 " --> pdb=" O LEU h 130 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU h 128 " --> pdb=" O SER h 109 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'i' and resid 73 through 78 removed outlier: 3.551A pdb=" N HIS i 135 " --> pdb=" O ILE i 82 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'i' and resid 95 through 96 Processing sheet with id=AB9, first strand: chain 'j' and resid 130 through 134 removed outlier: 4.871A pdb=" N GLY j 131 " --> pdb=" O ASP j 168 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASP j 168 " --> pdb=" O GLY j 131 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'j' and resid 130 through 134 removed outlier: 4.871A pdb=" N GLY j 131 " --> pdb=" O ASP j 168 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASP j 168 " --> pdb=" O GLY j 131 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'k' and resid 50 through 55 removed outlier: 6.235A pdb=" N GLY k 28 " --> pdb=" O GLU k 92 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N MET k 94 " --> pdb=" O GLY k 28 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE k 30 " --> pdb=" O MET k 94 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LYS k 96 " --> pdb=" O ILE k 30 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL k 32 " --> pdb=" O LYS k 96 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ALA k 91 " --> pdb=" O SER k 117 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL k 119 " --> pdb=" O ALA k 91 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL k 93 " --> pdb=" O VAL k 119 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ASP k 121 " --> pdb=" O VAL k 93 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE k 95 " --> pdb=" O ASP k 121 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'l' and resid 39 through 40 removed outlier: 4.390A pdb=" N TYR l 95 " --> pdb=" O THR l 64 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ARG l 54 " --> pdb=" O THR l 35 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'p' and resid 2 through 8 removed outlier: 4.042A pdb=" N ILE p 22 " --> pdb=" O LYS p 3 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'q' and resid 61 through 64 removed outlier: 3.793A pdb=" N ASP q 115 " --> pdb=" O LEU q 127 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU q 127 " --> pdb=" O ASP q 115 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE q 126 " --> pdb=" O GLN q 98 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 's' and resid 48 through 52 Processing sheet with id=AC7, first strand: chain 'y' and resid 76 through 82 removed outlier: 6.109A pdb=" N LYS y 76 " --> pdb=" O VAL y 112 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL y 114 " --> pdb=" O LYS y 76 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE y 78 " --> pdb=" O VAL y 114 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LEU y 116 " --> pdb=" O ILE y 78 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLN y 80 " --> pdb=" O LEU y 116 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ALA y 118 " --> pdb=" O GLN y 80 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ARG y 82 " --> pdb=" O ALA y 118 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'w' and resid 100 through 106 Processing sheet with id=AC9, first strand: chain 'd' and resid 117 through 118 Processing sheet with id=AD1, first strand: chain 'v' and resid 48 through 53 removed outlier: 3.714A pdb=" N THR v 86 " --> pdb=" O ILE v 93 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'v' and resid 148 through 154 removed outlier: 3.923A pdb=" N PHE v 165 " --> pdb=" O GLN v 154 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS v 123 " --> pdb=" O ALA v 198 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '8' and resid 309 through 310 removed outlier: 7.097A pdb=" N PHE 8 277 " --> pdb=" O GLN 8 269 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU 8 271 " --> pdb=" O GLY 8 275 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N GLY 8 275 " --> pdb=" O LEU 8 271 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N LEU 8 326 " --> pdb=" O ASN 8 284 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU 8 286 " --> pdb=" O LEU 8 326 " (cutoff:3.500A) 1015 hydrogen bonds defined for protein. 2910 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1289 hydrogen bonds 2036 hydrogen bond angles 0 basepair planarities 510 basepair parallelities 824 stacking parallelities Total time for adding SS restraints: 41.89 Time building geometry restraints manager: 25.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.17: 13 1.17 - 1.34: 13199 1.34 - 1.50: 28462 1.50 - 1.66: 17764 1.66 - 1.83: 147 Bond restraints: 59585 Sorted by residual: bond pdb=" CZ ARG h 67 " pdb=" NH2 ARG h 67 " ideal model delta sigma weight residual 1.330 1.127 0.203 1.30e-02 5.92e+03 2.45e+02 bond pdb=" CB ARG h 67 " pdb=" CG ARG h 67 " ideal model delta sigma weight residual 1.520 1.127 0.393 3.00e-02 1.11e+03 1.72e+02 bond pdb=" CE1 PHE v 142 " pdb=" CZ PHE v 142 " ideal model delta sigma weight residual 1.382 1.008 0.374 3.00e-02 1.11e+03 1.55e+02 bond pdb=" CE2 PHE v 142 " pdb=" CZ PHE v 142 " ideal model delta sigma weight residual 1.382 1.030 0.352 3.00e-02 1.11e+03 1.38e+02 bond pdb=" CG ASN b 7 " pdb=" ND2 ASN b 7 " ideal model delta sigma weight residual 1.328 1.084 0.244 2.10e-02 2.27e+03 1.35e+02 ... (remaining 59580 not shown) Histogram of bond angle deviations from ideal: 85.27 - 97.33: 9 97.33 - 109.39: 22095 109.39 - 121.45: 50762 121.45 - 133.51: 14816 133.51 - 145.57: 56 Bond angle restraints: 87738 Sorted by residual: angle pdb=" NE ARG h 67 " pdb=" CZ ARG h 67 " pdb=" NH1 ARG h 67 " ideal model delta sigma weight residual 121.50 145.57 -24.07 1.00e+00 1.00e+00 5.79e+02 angle pdb=" CA ASP b 201 " pdb=" CB ASP b 201 " pdb=" CG ASP b 201 " ideal model delta sigma weight residual 112.60 126.79 -14.19 1.00e+00 1.00e+00 2.01e+02 angle pdb=" NH1 ARG h 67 " pdb=" CZ ARG h 67 " pdb=" NH2 ARG h 67 " ideal model delta sigma weight residual 119.30 101.21 18.09 1.30e+00 5.92e-01 1.94e+02 angle pdb=" CD ARG h 67 " pdb=" NE ARG h 67 " pdb=" CZ ARG h 67 " ideal model delta sigma weight residual 124.40 143.78 -19.38 1.40e+00 5.10e-01 1.92e+02 angle pdb=" CB ARG h 67 " pdb=" CG ARG h 67 " pdb=" CD ARG h 67 " ideal model delta sigma weight residual 111.30 143.04 -31.74 2.30e+00 1.89e-01 1.90e+02 ... (remaining 87733 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 31455 35.46 - 70.92: 1090 70.92 - 106.38: 106 106.38 - 141.85: 9 141.85 - 177.31: 5 Dihedral angle restraints: 32665 sinusoidal: 24136 harmonic: 8529 Sorted by residual: dihedral pdb=" CA THR 8 302 " pdb=" C THR 8 302 " pdb=" N VAL 8 303 " pdb=" CA VAL 8 303 " ideal model delta harmonic sigma weight residual 180.00 -103.83 -76.17 0 5.00e+00 4.00e-02 2.32e+02 dihedral pdb=" CA MET 8 72 " pdb=" C MET 8 72 " pdb=" N GLU 8 73 " pdb=" CA GLU 8 73 " ideal model delta harmonic sigma weight residual 180.00 110.70 69.30 0 5.00e+00 4.00e-02 1.92e+02 dihedral pdb=" CA ARG 8 359 " pdb=" C ARG 8 359 " pdb=" N ILE 8 360 " pdb=" CA ILE 8 360 " ideal model delta harmonic sigma weight residual 180.00 120.01 59.99 0 5.00e+00 4.00e-02 1.44e+02 ... (remaining 32662 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.238: 10924 0.238 - 0.477: 58 0.477 - 0.715: 9 0.715 - 0.953: 2 0.953 - 1.192: 1 Chirality restraints: 10994 Sorted by residual: chirality pdb=" CB ILE 8 280 " pdb=" CA ILE 8 280 " pdb=" CG1 ILE 8 280 " pdb=" CG2 ILE 8 280 " both_signs ideal model delta sigma weight residual False 2.64 1.45 1.19 2.00e-01 2.50e+01 3.55e+01 chirality pdb=" CG LEU 8 315 " pdb=" CB LEU 8 315 " pdb=" CD1 LEU 8 315 " pdb=" CD2 LEU 8 315 " both_signs ideal model delta sigma weight residual False -2.59 -1.71 -0.88 2.00e-01 2.50e+01 1.92e+01 chirality pdb=" CG LEU b 60 " pdb=" CB LEU b 60 " pdb=" CD1 LEU b 60 " pdb=" CD2 LEU b 60 " both_signs ideal model delta sigma weight residual False -2.59 -1.84 -0.75 2.00e-01 2.50e+01 1.41e+01 ... (remaining 10991 not shown) Planarity restraints: 5617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE u 103 " -0.122 2.00e-02 2.50e+03 8.62e-02 1.30e+02 pdb=" CG PHE u 103 " 0.085 2.00e-02 2.50e+03 pdb=" CD1 PHE u 103 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 PHE u 103 " 0.078 2.00e-02 2.50e+03 pdb=" CE1 PHE u 103 " 0.036 2.00e-02 2.50e+03 pdb=" CE2 PHE u 103 " 0.017 2.00e-02 2.50e+03 pdb=" CZ PHE u 103 " -0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 8 346 " -0.034 2.00e-02 2.50e+03 7.76e-02 1.05e+02 pdb=" CG PHE 8 346 " 0.157 2.00e-02 2.50e+03 pdb=" CD1 PHE 8 346 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE 8 346 " -0.108 2.00e-02 2.50e+03 pdb=" CE1 PHE 8 346 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 PHE 8 346 " 0.034 2.00e-02 2.50e+03 pdb=" CZ PHE 8 346 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE v 165 " 0.113 2.00e-02 2.50e+03 7.37e-02 9.50e+01 pdb=" CG PHE v 165 " -0.129 2.00e-02 2.50e+03 pdb=" CD1 PHE v 165 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE v 165 " -0.042 2.00e-02 2.50e+03 pdb=" CE1 PHE v 165 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE v 165 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE v 165 " 0.082 2.00e-02 2.50e+03 ... (remaining 5614 not shown) Histogram of nonbonded interaction distances: 1.25 - 1.98: 21 1.98 - 2.71: 5724 2.71 - 3.44: 74922 3.44 - 4.17: 171935 4.17 - 4.90: 237432 Nonbonded interactions: 490034 Sorted by model distance: nonbonded pdb=" ND1 HIS d 163 " pdb=" CD1 ILE d 179 " model vdw 1.255 3.540 nonbonded pdb=" O PHE u 103 " pdb=" CE2 TRP w 138 " model vdw 1.356 3.260 nonbonded pdb=" NZ LYS d 51 " pdb=" OH TYR d 197 " model vdw 1.471 2.520 nonbonded pdb=" OP1 U a 75 " pdb=" CZ ARG v 194 " model vdw 1.522 3.270 nonbonded pdb=" O PHE u 103 " pdb=" CD2 TRP w 138 " model vdw 1.548 3.260 ... (remaining 490029 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: 2.090 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: 14.440 Check model and map are aligned: 0.640 Set scattering table: 0.390 Process input model: 149.900 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.130 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 171.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 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 : 0.012 0.393 59585 Z= 0.719 Angle : 1.321 31.737 87738 Z= 0.674 Chirality : 0.063 1.192 10994 Planarity : 0.011 0.166 5617 Dihedral : 14.799 177.307 27157 Min Nonbonded Distance : 1.255 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 1.10 % Allowed : 12.14 % Favored : 86.77 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.83 % Twisted General : 1.56 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.16 (0.13), residues: 2917 helix: -2.57 (0.12), residues: 1059 sheet: -2.44 (0.21), residues: 443 loop : -3.00 (0.14), residues: 1415 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1218 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1192 time to evaluate : 2.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 4 residues processed: 1208 average time/residue: 0.6490 time to fit residues: 1226.8934 Evaluate side-chains 880 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 876 time to evaluate : 2.995 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3806 time to fit residues: 6.3526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 365 optimal weight: 0.8980 chunk 328 optimal weight: 1.9990 chunk 182 optimal weight: 0.0050 chunk 112 optimal weight: 0.9980 chunk 221 optimal weight: 3.9990 chunk 175 optimal weight: 0.3980 chunk 339 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 206 optimal weight: 0.9990 chunk 252 optimal weight: 6.9990 chunk 393 optimal weight: 8.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 94 HIS c 34 GLN c 134 GLN c 187 GLN ** e 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 24 ASN g 86 GLN ** h 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 19 ASN h 51 HIS h 78 HIS i 127 ASN ** i 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 151 HIS k 31 HIS k 127 HIS ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 125 HIS r 68 GLN r 83 GLN u 124 ASN ** u 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 34 ASN d 57 HIS d 64 GLN ** d 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 93 ASN ** d 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 96 ASN v 135 ASN v 163 ASN n 8 GLN ** n 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 269 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 59585 Z= 0.190 Angle : 0.725 16.646 87738 Z= 0.371 Chirality : 0.039 0.699 10994 Planarity : 0.006 0.101 5617 Dihedral : 14.812 176.562 21067 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.72 % Allowed : 9.05 % Favored : 90.23 % Rotamer Outliers : 4.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.57 % 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: -2.98 (0.14), residues: 2917 helix: -1.05 (0.14), residues: 1088 sheet: -1.54 (0.23), residues: 456 loop : -2.94 (0.15), residues: 1373 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1082 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 959 time to evaluate : 3.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 123 outliers final: 65 residues processed: 1008 average time/residue: 0.6080 time to fit residues: 979.5542 Evaluate side-chains 898 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 833 time to evaluate : 2.928 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 0 residues processed: 65 average time/residue: 0.4135 time to fit residues: 53.6541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 218 optimal weight: 7.9990 chunk 122 optimal weight: 0.7980 chunk 327 optimal weight: 9.9990 chunk 267 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 393 optimal weight: 3.9990 chunk 425 optimal weight: 30.0000 chunk 350 optimal weight: 10.0000 chunk 390 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 316 optimal weight: 6.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 125 ASN c 134 GLN ** e 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 65 HIS ** i 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 142 GLN ** i 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 117 GLN ** j 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 149 HIS ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 111 GLN m 68 HIS ** m 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 75 ASN r 52 ASN r 68 GLN r 83 GLN u 101 ASN ** u 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 162 GLN ** w 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 172 GLN d 64 GLN ** d 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 116 GLN n 29 GLN n 44 HIS 8 58 GLN ** 8 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.111 59585 Z= 0.435 Angle : 0.825 12.589 87738 Z= 0.417 Chirality : 0.043 0.280 10994 Planarity : 0.007 0.097 5617 Dihedral : 15.009 174.736 21067 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 22.24 Ramachandran Plot: Outliers : 0.51 % Allowed : 11.93 % Favored : 87.56 % Rotamer Outliers : 5.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.50 % 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: -2.72 (0.15), residues: 2917 helix: -0.71 (0.15), residues: 1110 sheet: -1.63 (0.23), residues: 479 loop : -2.86 (0.15), residues: 1328 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1002 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 866 time to evaluate : 2.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 136 outliers final: 94 residues processed: 932 average time/residue: 0.6131 time to fit residues: 927.4660 Evaluate side-chains 894 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 800 time to evaluate : 2.974 Switching outliers to nearest non-outliers outliers start: 94 outliers final: 0 residues processed: 94 average time/residue: 0.4183 time to fit residues: 77.7763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 389 optimal weight: 5.9990 chunk 296 optimal weight: 5.9990 chunk 204 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 187 optimal weight: 1.9990 chunk 264 optimal weight: 4.9990 chunk 395 optimal weight: 6.9990 chunk 418 optimal weight: 5.9990 chunk 206 optimal weight: 2.9990 chunk 374 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 125 ASN c 134 GLN ** e 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 33 HIS ** h 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 34 ASN ** i 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 142 GLN ** i 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 117 GLN ** m 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 62 GLN q 70 ASN r 52 ASN r 68 GLN u 114 GLN ** u 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 116 GLN ** n 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 29 GLN ** x 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 59585 Z= 0.205 Angle : 0.672 12.383 87738 Z= 0.343 Chirality : 0.037 0.398 10994 Planarity : 0.006 0.089 5617 Dihedral : 14.675 175.662 21067 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.55 % Allowed : 10.08 % Favored : 89.37 % Rotamer Outliers : 3.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.35 % 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: -2.35 (0.15), residues: 2917 helix: -0.34 (0.15), residues: 1108 sheet: -1.22 (0.24), residues: 459 loop : -2.79 (0.16), residues: 1350 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 969 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 875 time to evaluate : 3.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 94 outliers final: 39 residues processed: 911 average time/residue: 0.6050 time to fit residues: 894.1947 Evaluate side-chains 841 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 802 time to evaluate : 2.974 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.4346 time to fit residues: 34.6607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 348 optimal weight: 8.9990 chunk 237 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 311 optimal weight: 7.9990 chunk 172 optimal weight: 5.9990 chunk 357 optimal weight: 6.9990 chunk 289 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 213 optimal weight: 4.9990 chunk 375 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 94 HIS ** c 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 125 ASN ** e 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 264 ASN e 277 ASN g 142 HIS h 34 ASN h 65 HIS i 127 ASN ** i 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 46 ASN ** m 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 138 ASN ** o 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 52 ASN r 58 GLN ** s 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 114 GLN ** y 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 81 GLN ** d 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 116 GLN v 163 ASN v 181 GLN ** n 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.095 59585 Z= 0.601 Angle : 0.954 14.365 87738 Z= 0.476 Chirality : 0.048 0.318 10994 Planarity : 0.007 0.085 5617 Dihedral : 15.359 173.361 21067 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 27.31 Ramachandran Plot: Outliers : 0.58 % Allowed : 13.47 % Favored : 85.94 % Rotamer Outliers : 6.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.35 % 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: -2.85 (0.14), residues: 2917 helix: -0.86 (0.14), residues: 1121 sheet: -1.52 (0.23), residues: 484 loop : -2.98 (0.16), residues: 1312 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 977 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 824 time to evaluate : 3.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 153 outliers final: 98 residues processed: 890 average time/residue: 0.5985 time to fit residues: 867.4606 Evaluate side-chains 891 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 793 time to evaluate : 3.520 Switching outliers to nearest non-outliers outliers start: 98 outliers final: 0 residues processed: 98 average time/residue: 0.4488 time to fit residues: 85.1851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 140 optimal weight: 0.6980 chunk 376 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 245 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 418 optimal weight: 6.9990 chunk 347 optimal weight: 6.9990 chunk 193 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 138 optimal weight: 10.0000 chunk 219 optimal weight: 10.0000 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 125 ASN ** e 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 86 GLN g 142 HIS h 15 ASN i 127 ASN i 135 HIS ** i 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 111 GLN m 68 HIS ** m 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 138 ASN o 50 GLN q 70 ASN ** s 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 114 GLN ** y 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 163 ASN ** n 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 59585 Z= 0.205 Angle : 0.684 13.442 87738 Z= 0.349 Chirality : 0.038 0.236 10994 Planarity : 0.005 0.085 5617 Dihedral : 14.752 175.233 21067 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.08 % Favored : 89.44 % Rotamer Outliers : 3.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.35 % 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: -2.36 (0.15), residues: 2917 helix: -0.38 (0.15), residues: 1110 sheet: -1.17 (0.24), residues: 464 loop : -2.79 (0.16), residues: 1343 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 940 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 863 time to evaluate : 3.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 41 residues processed: 895 average time/residue: 0.6030 time to fit residues: 875.3509 Evaluate side-chains 851 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 810 time to evaluate : 3.044 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.4274 time to fit residues: 36.1228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 403 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 238 optimal weight: 5.9990 chunk 305 optimal weight: 10.0000 chunk 237 optimal weight: 5.9990 chunk 352 optimal weight: 10.0000 chunk 233 optimal weight: 7.9990 chunk 417 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 254 optimal weight: 8.9990 chunk 192 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 125 ASN ** e 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 144 GLN ** i 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 114 GLN ** y 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.084 59585 Z= 0.537 Angle : 0.886 14.723 87738 Z= 0.444 Chirality : 0.046 0.382 10994 Planarity : 0.007 0.112 5617 Dihedral : 15.124 174.276 21067 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 25.46 Ramachandran Plot: Outliers : 0.45 % Allowed : 13.68 % Favored : 85.88 % Rotamer Outliers : 3.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.32 % 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: -2.67 (0.15), residues: 2917 helix: -0.66 (0.15), residues: 1113 sheet: -1.42 (0.24), residues: 464 loop : -2.91 (0.16), residues: 1340 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 920 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 822 time to evaluate : 3.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 98 outliers final: 65 residues processed: 857 average time/residue: 0.5971 time to fit residues: 833.4717 Evaluate side-chains 864 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 799 time to evaluate : 2.978 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 0 residues processed: 65 average time/residue: 0.4211 time to fit residues: 54.6157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 258 optimal weight: 3.9990 chunk 166 optimal weight: 0.0570 chunk 249 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 265 optimal weight: 7.9990 chunk 284 optimal weight: 4.9990 chunk 206 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 328 optimal weight: 3.9990 overall best weight: 1.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 135 HIS ** i 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 111 GLN ** m 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 GLN ** y 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 77 ASN ** v 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 181 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 59585 Z= 0.242 Angle : 0.705 16.045 87738 Z= 0.361 Chirality : 0.039 0.315 10994 Planarity : 0.006 0.084 5617 Dihedral : 14.788 175.791 21067 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.45 % Allowed : 11.62 % Favored : 87.93 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.32 % 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 (0.15), residues: 2917 helix: -0.40 (0.15), residues: 1108 sheet: -1.08 (0.25), residues: 443 loop : -2.84 (0.16), residues: 1366 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 820 time to evaluate : 3.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 29 residues processed: 834 average time/residue: 0.6185 time to fit residues: 834.4056 Evaluate side-chains 819 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 790 time to evaluate : 2.991 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.4471 time to fit residues: 27.0842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 379 optimal weight: 6.9990 chunk 399 optimal weight: 0.9990 chunk 364 optimal weight: 4.9990 chunk 388 optimal weight: 8.9990 chunk 234 optimal weight: 7.9990 chunk 169 optimal weight: 8.9990 chunk 305 optimal weight: 10.0000 chunk 119 optimal weight: 0.2980 chunk 351 optimal weight: 10.0000 chunk 367 optimal weight: 2.9990 chunk 387 optimal weight: 8.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 9 ASN ** b 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 111 GLN ** m 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 GLN u 114 GLN ** y 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.064 59585 Z= 0.347 Angle : 0.763 15.691 87738 Z= 0.388 Chirality : 0.041 0.292 10994 Planarity : 0.006 0.113 5617 Dihedral : 14.818 175.623 21067 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 21.61 Ramachandran Plot: Outliers : 0.38 % Allowed : 13.34 % Favored : 86.29 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.25 % 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: -2.41 (0.15), residues: 2917 helix: -0.38 (0.15), residues: 1113 sheet: -1.14 (0.25), residues: 447 loop : -2.88 (0.16), residues: 1357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 814 time to evaluate : 3.008 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 outliers start: 45 outliers final: 30 residues processed: 828 average time/residue: 0.5943 time to fit residues: 800.6476 Evaluate side-chains 822 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 792 time to evaluate : 3.003 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.4593 time to fit residues: 28.2633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 255 optimal weight: 10.0000 chunk 411 optimal weight: 7.9990 chunk 251 optimal weight: 7.9990 chunk 195 optimal weight: 1.9990 chunk 285 optimal weight: 7.9990 chunk 431 optimal weight: 10.0000 chunk 397 optimal weight: 2.9990 chunk 343 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 265 optimal weight: 8.9990 chunk 210 optimal weight: 0.6980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 291 GLN ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 65 HIS ** i 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 GLN u 114 GLN ** y 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 45 HIS ** v 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 59585 Z= 0.300 Angle : 0.741 16.702 87738 Z= 0.378 Chirality : 0.040 0.339 10994 Planarity : 0.006 0.084 5617 Dihedral : 14.731 175.748 21067 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.41 % Allowed : 12.34 % Favored : 87.25 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.25 % 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: -2.42 (0.15), residues: 2917 helix: -0.36 (0.15), residues: 1110 sheet: -1.22 (0.25), residues: 452 loop : -2.88 (0.16), residues: 1355 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 829 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 801 time to evaluate : 3.261 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: 28 outliers final: 19 residues processed: 805 average time/residue: 0.5995 time to fit residues: 789.4570 Evaluate side-chains 796 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 777 time to evaluate : 3.055 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.4126 time to fit residues: 18.4541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 272 optimal weight: 7.9990 chunk 365 optimal weight: 0.0470 chunk 105 optimal weight: 6.9990 chunk 316 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 344 optimal weight: 7.9990 chunk 143 optimal weight: 4.9990 chunk 353 optimal weight: 8.9990 chunk 43 optimal weight: 0.0050 chunk 63 optimal weight: 4.9990 overall best weight: 2.2096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 65 HIS ** i 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 171 HIS u 114 GLN ** y 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.108387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.086656 restraints weight = 158633.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.089091 restraints weight = 54672.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.090506 restraints weight = 30876.347| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 59585 Z= 0.266 Angle : 0.724 16.390 87738 Z= 0.368 Chirality : 0.039 0.283 10994 Planarity : 0.006 0.094 5617 Dihedral : 14.610 176.022 21067 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 19.81 Ramachandran Plot: Outliers : 0.38 % Allowed : 12.48 % Favored : 87.14 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.21 % 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: -2.36 (0.15), residues: 2917 helix: -0.28 (0.15), residues: 1118 sheet: -1.23 (0.25), residues: 439 loop : -2.85 (0.16), residues: 1360 =============================================================================== Job complete usr+sys time: 13044.17 seconds wall clock time: 230 minutes 9.66 seconds (13809.66 seconds total)