Starting phenix.real_space_refine (version: dev) on Tue Feb 21 06:29:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k78_22696/02_2023/7k78_22696.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k78_22696/02_2023/7k78_22696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k78_22696/02_2023/7k78_22696.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k78_22696/02_2023/7k78_22696.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k78_22696/02_2023/7k78_22696.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k78_22696/02_2023/7k78_22696.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A GLU 136": "OE1" <-> "OE2" Residue "A GLU 141": "OE1" <-> "OE2" Residue "A GLU 164": "OE1" <-> "OE2" Residue "A ASP 173": "OD1" <-> "OD2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C GLU 66": "OE1" <-> "OE2" Residue "C ASP 92": "OD1" <-> "OD2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D ASP 55": "OD1" <-> "OD2" Residue "D ASP 72": "OD1" <-> "OD2" Residue "D GLU 80": "OE1" <-> "OE2" Residue "D TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 97": "OE1" <-> "OE2" Residue "D GLU 109": "OE1" <-> "OE2" Residue "D GLU 117": "OE1" <-> "OE2" Residue "E GLU 141": "OE1" <-> "OE2" Residue "E ASP 150": "OD1" <-> "OD2" Residue "E PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 175": "OD1" <-> "OD2" Residue "E PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 25": "OD1" <-> "OD2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "F ARG 96": "NH1" <-> "NH2" Residue "G ARG 34": "NH1" <-> "NH2" Residue "G TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "H GLU 39": "OE1" <-> "OE2" Residue "H ASP 55": "OD1" <-> "OD2" Residue "H GLU 109": "OE1" <-> "OE2" Residue "H GLU 117": "OE1" <-> "OE2" Residue "K GLU 23": "OE1" <-> "OE2" Residue "K GLU 32": "OE1" <-> "OE2" Residue "K TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 68": "OE1" <-> "OE2" Residue "K TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 104": "OE1" <-> "OE2" Residue "K ASP 112": "OD1" <-> "OD2" Residue "K TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 130": "OD1" <-> "OD2" Residue "K TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 175": "OE1" <-> "OE2" Residue "K ARG 176": "NH1" <-> "NH2" Residue "K ASP 186": "OD1" <-> "OD2" Residue "K TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 219": "NH1" <-> "NH2" Residue "K ASP 228": "OD1" <-> "OD2" Residue "K PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 239": "OD1" <-> "OD2" Residue "K TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 251": "OE1" <-> "OE2" Residue "K PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 263": "OE1" <-> "OE2" Residue "L GLU 23": "OE1" <-> "OE2" Residue "L GLU 32": "OE1" <-> "OE2" Residue "L ASP 95": "OD1" <-> "OD2" Residue "L GLU 104": "OE1" <-> "OE2" Residue "L TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 130": "OD1" <-> "OD2" Residue "L TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 176": "NH1" <-> "NH2" Residue "L TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 214": "OD1" <-> "OD2" Residue "L ARG 219": "NH1" <-> "NH2" Residue "L ASP 228": "OD1" <-> "OD2" Residue "L ASP 239": "OD1" <-> "OD2" Residue "L ASP 240": "OD1" <-> "OD2" Residue "L PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 263": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 14125 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 1, 'TRANS': 93} Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 771 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 802 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 95} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 632 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 722 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 2397 Classifications: {'DNA': 116} Link IDs: {'rna3p': 115} Chain: "J" Number of atoms: 2359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 2359 Classifications: {'DNA': 116} Link IDs: {'rna3p': 115} Chain: "K" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1779 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1766 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 7.89, per 1000 atoms: 0.56 Number of scatterers: 14125 At special positions: 0 Unit cell: (116.6, 145.22, 115.54, 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 27 16.00 P 232 15.00 O 3184 8.00 N 2472 7.00 C 8210 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS K 44 " - pdb=" SG CYS K 118 " distance=2.03 Simple disulfide: pdb=" SG CYS K 181 " - pdb=" SG CYS K 246 " distance=2.04 Simple disulfide: pdb=" SG CYS L 44 " - pdb=" SG CYS L 118 " distance=2.03 Simple disulfide: pdb=" SG CYS L 181 " - pdb=" SG CYS L 246 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.10 Conformation dependent library (CDL) restraints added in 1.4 seconds 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2236 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 22 sheets defined 46.7% alpha, 21.8% beta 68 base pairs and 219 stacking pairs defined. Time for finding SS restraints: 5.17 Creating SS restraints... Processing helix chain 'A' and resid 134 through 148 removed outlier: 4.177A pdb=" N LEU A 139 " --> pdb=" O SER A 135 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 147 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER A 148 " --> pdb=" O LYS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 168 removed outlier: 3.690A pdb=" N PHE A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP A 167 " --> pdb=" O LYS A 163 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 208 Processing helix chain 'A' and resid 214 through 226 Processing helix chain 'B' and resid 26 through 30 Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 50 through 77 removed outlier: 3.735A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B 77 " --> pdb=" O TYR B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 removed outlier: 3.706A pdb=" N VAL B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 24 Processing helix chain 'C' and resid 28 through 38 Processing helix chain 'C' and resid 47 through 75 removed outlier: 4.456A pdb=" N VAL C 51 " --> pdb=" O SER C 47 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 91 removed outlier: 3.551A pdb=" N LEU C 85 " --> pdb=" O ILE C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 99 Processing helix chain 'D' and resid 41 through 53 removed outlier: 3.745A pdb=" N LYS D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN D 51 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR D 52 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 88 removed outlier: 3.512A pdb=" N ASN D 88 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 106 removed outlier: 3.536A pdb=" N ILE D 98 " --> pdb=" O SER D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 129 removed outlier: 3.780A pdb=" N LYS D 112 " --> pdb=" O GLY D 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 148 removed outlier: 3.539A pdb=" N SER E 148 " --> pdb=" O LYS E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 168 removed outlier: 3.649A pdb=" N PHE E 158 " --> pdb=" O SER E 154 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU E 168 " --> pdb=" O GLU E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 208 Processing helix chain 'E' and resid 214 through 225 removed outlier: 3.685A pdb=" N MET E 218 " --> pdb=" O MET E 214 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 30 Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 50 through 77 removed outlier: 3.753A pdb=" N GLU F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA F 77 " --> pdb=" O TYR F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 removed outlier: 3.640A pdb=" N VAL F 87 " --> pdb=" O THR F 83 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL F 88 " --> pdb=" O SER F 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 24 Processing helix chain 'G' and resid 28 through 38 removed outlier: 3.584A pdb=" N VAL G 32 " --> pdb=" O PRO G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 75 removed outlier: 3.540A pdb=" N ASN G 75 " --> pdb=" O ALA G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 91 Processing helix chain 'H' and resid 41 through 53 removed outlier: 3.629A pdb=" N LYS H 47 " --> pdb=" O SER H 43 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN H 51 " --> pdb=" O LYS H 47 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR H 52 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 88 Processing helix chain 'H' and resid 94 through 106 Processing helix chain 'H' and resid 108 through 129 removed outlier: 3.513A pdb=" N ALA H 121 " --> pdb=" O GLU H 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 52 No H-bonds generated for 'chain 'K' and resid 50 through 52' Processing helix chain 'K' and resid 109 through 113 Processing helix chain 'L' and resid 50 through 52 No H-bonds generated for 'chain 'L' and resid 50 through 52' Processing helix chain 'L' and resid 84 through 87 Processing helix chain 'L' and resid 109 through 113 removed outlier: 3.562A pdb=" N SER L 113 " --> pdb=" O SER L 110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 178 removed outlier: 6.944A pdb=" N ARG A 177 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 212 through 213 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AA4, first strand: chain 'C' and resid 44 through 45 removed outlier: 7.186A pdb=" N ARG C 44 " --> pdb=" O ILE D 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 79 through 80 Processing sheet with id=AA6, first strand: chain 'C' and resid 102 through 104 Processing sheet with id=AA7, first strand: chain 'E' and resid 177 through 178 removed outlier: 7.145A pdb=" N ARG E 177 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 212 through 213 Processing sheet with id=AA9, first strand: chain 'G' and resid 44 through 45 removed outlier: 7.184A pdb=" N ARG G 44 " --> pdb=" O ILE H 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 79 through 80 Processing sheet with id=AB2, first strand: chain 'K' and resid 25 through 27 Processing sheet with id=AB3, first strand: chain 'K' and resid 32 through 34 removed outlier: 3.773A pdb=" N THR K 139 " --> pdb=" O GLU K 32 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N TYR K 54 " --> pdb=" O TYR K 74 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N TYR K 74 " --> pdb=" O TYR K 54 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE K 56 " --> pdb=" O TYR K 72 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR K 72 " --> pdb=" O ILE K 56 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N TRP K 58 " --> pdb=" O ILE K 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 32 through 34 removed outlier: 3.773A pdb=" N THR K 139 " --> pdb=" O GLU K 32 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR K 131 " --> pdb=" O ARG K 120 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N SER K 122 " --> pdb=" O LEU K 129 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU K 129 " --> pdb=" O SER K 122 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 162 through 164 removed outlier: 3.602A pdb=" N PHE K 229 " --> pdb=" O CYS K 181 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLN K 227 " --> pdb=" O ALA K 183 " (cutoff:3.500A) removed outlier: 10.630A pdb=" N GLN K 185 " --> pdb=" O SER K 225 " (cutoff:3.500A) removed outlier: 10.154A pdb=" N SER K 225 " --> pdb=" O GLN K 185 " (cutoff:3.500A) removed outlier: 11.601A pdb=" N ILE K 187 " --> pdb=" O SER K 223 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N SER K 223 " --> pdb=" O ILE K 187 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 168 through 170 removed outlier: 6.017A pdb=" N MET K 169 " --> pdb=" O GLU K 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'K' and resid 211 through 212 removed outlier: 6.565A pdb=" N TRP K 193 " --> pdb=" O LEU K 205 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N TYR K 207 " --> pdb=" O LEU K 191 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU K 191 " --> pdb=" O TYR K 207 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR K 255 " --> pdb=" O GLN K 248 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 25 through 28 removed outlier: 3.560A pdb=" N THR L 100 " --> pdb=" O ASP L 95 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 32 through 34 removed outlier: 3.566A pdb=" N VAL L 34 " --> pdb=" O THR L 139 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N TYR L 54 " --> pdb=" O TYR L 74 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N TYR L 74 " --> pdb=" O TYR L 54 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE L 56 " --> pdb=" O TYR L 72 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TYR L 72 " --> pdb=" O ILE L 56 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N TRP L 58 " --> pdb=" O ILE L 70 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 32 through 34 removed outlier: 3.566A pdb=" N VAL L 34 " --> pdb=" O THR L 139 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR L 131 " --> pdb=" O ARG L 120 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N SER L 122 " --> pdb=" O LEU L 129 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LEU L 129 " --> pdb=" O SER L 122 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 162 through 164 removed outlier: 3.850A pdb=" N ASP L 228 " --> pdb=" O SER L 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 168 through 171 removed outlier: 3.849A pdb=" N ALA L 242 " --> pdb=" O LEU L 262 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU L 191 " --> pdb=" O TYR L 207 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N TYR L 207 " --> pdb=" O LEU L 191 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N TRP L 193 " --> pdb=" O LEU L 205 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 168 through 171 removed outlier: 3.849A pdb=" N ALA L 242 " --> pdb=" O LEU L 262 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN L 248 " --> pdb=" O THR L 255 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR L 255 " --> pdb=" O GLN L 248 " (cutoff:3.500A) 530 hydrogen bonds defined for protein. 1482 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 147 hydrogen bonds 294 hydrogen bond angles 0 basepair planarities 68 basepair parallelities 219 stacking parallelities Total time for adding SS restraints: 5.17 Time building geometry restraints manager: 6.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3489 1.34 - 1.46: 4289 1.46 - 1.58: 6578 1.58 - 1.70: 462 1.70 - 1.82: 46 Bond restraints: 14864 Sorted by residual: bond pdb=" CA CYS K 181 " pdb=" CB CYS K 181 " ideal model delta sigma weight residual 1.527 1.553 -0.026 1.75e-02 3.27e+03 2.20e+00 bond pdb=" C3' DA J 225 " pdb=" O3' DA J 225 " ideal model delta sigma weight residual 1.422 1.464 -0.042 3.00e-02 1.11e+03 2.01e+00 bond pdb=" CB ASN C 101 " pdb=" CG ASN C 101 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.81e+00 bond pdb=" CG LEU E 204 " pdb=" CD1 LEU E 204 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.61e+00 bond pdb=" C4' DA J 273 " pdb=" C3' DA J 273 " ideal model delta sigma weight residual 1.523 1.499 0.024 2.00e-02 2.50e+03 1.41e+00 ... (remaining 14859 not shown) Histogram of bond angle deviations from ideal: 97.91 - 105.16: 1076 105.16 - 112.41: 8138 112.41 - 119.65: 4693 119.65 - 126.90: 6416 126.90 - 134.15: 776 Bond angle restraints: 21099 Sorted by residual: angle pdb=" N ASP A 173 " pdb=" CA ASP A 173 " pdb=" C ASP A 173 " ideal model delta sigma weight residual 114.56 107.21 7.35 1.27e+00 6.20e-01 3.35e+01 angle pdb=" C TYR L 208 " pdb=" N ALA L 209 " pdb=" CA ALA L 209 " ideal model delta sigma weight residual 121.54 129.33 -7.79 1.91e+00 2.74e-01 1.66e+01 angle pdb=" C TYR K 208 " pdb=" N ALA K 209 " pdb=" CA ALA K 209 " ideal model delta sigma weight residual 121.54 129.01 -7.47 1.91e+00 2.74e-01 1.53e+01 angle pdb=" N LEU G 95 " pdb=" CA LEU G 95 " pdb=" C LEU G 95 " ideal model delta sigma weight residual 113.88 109.88 4.00 1.23e+00 6.61e-01 1.06e+01 angle pdb=" C ASN C 101 " pdb=" CA ASN C 101 " pdb=" CB ASN C 101 " ideal model delta sigma weight residual 111.73 116.67 -4.94 1.55e+00 4.16e-01 1.01e+01 ... (remaining 21094 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.09: 6636 32.09 - 64.18: 1420 64.18 - 96.26: 54 96.26 - 128.35: 0 128.35 - 160.44: 2 Dihedral angle restraints: 8112 sinusoidal: 4625 harmonic: 3487 Sorted by residual: dihedral pdb=" CB CYS K 181 " pdb=" SG CYS K 181 " pdb=" SG CYS K 246 " pdb=" CB CYS K 246 " ideal model delta sinusoidal sigma weight residual -86.00 -8.78 -77.22 1 1.00e+01 1.00e-02 7.48e+01 dihedral pdb=" CB CYS L 181 " pdb=" SG CYS L 181 " pdb=" SG CYS L 246 " pdb=" CB CYS L 246 " ideal model delta sinusoidal sigma weight residual 93.00 29.98 63.02 1 1.00e+01 1.00e-02 5.24e+01 dihedral pdb=" C4' DA J 225 " pdb=" C3' DA J 225 " pdb=" O3' DA J 225 " pdb=" P DT J 226 " ideal model delta sinusoidal sigma weight residual 220.00 59.56 160.44 1 3.50e+01 8.16e-04 1.52e+01 ... (remaining 8109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1619 0.033 - 0.065: 581 0.065 - 0.098: 123 0.098 - 0.131: 64 0.131 - 0.163: 9 Chirality restraints: 2396 Sorted by residual: chirality pdb=" CA ILE L 206 " pdb=" N ILE L 206 " pdb=" C ILE L 206 " pdb=" CB ILE L 206 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" CB ILE K 206 " pdb=" CA ILE K 206 " pdb=" CG1 ILE K 206 " pdb=" CG2 ILE K 206 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.38e-01 chirality pdb=" CB THR K 50 " pdb=" CA THR K 50 " pdb=" OG1 THR K 50 " pdb=" CG2 THR K 50 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.21e-01 ... (remaining 2393 not shown) Planarity restraints: 1855 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET K 42 " 0.038 5.00e-02 4.00e+02 5.79e-02 5.37e+00 pdb=" N PRO K 43 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO K 43 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO K 43 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS H 53 " 0.033 5.00e-02 4.00e+02 5.10e-02 4.17e+00 pdb=" N PRO H 54 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO H 54 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO H 54 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 272 " -0.023 2.00e-02 2.50e+03 1.19e-02 3.89e+00 pdb=" N9 DA J 272 " 0.026 2.00e-02 2.50e+03 pdb=" C8 DA J 272 " 0.007 2.00e-02 2.50e+03 pdb=" N7 DA J 272 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA J 272 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DA J 272 " -0.005 2.00e-02 2.50e+03 pdb=" N6 DA J 272 " -0.011 2.00e-02 2.50e+03 pdb=" N1 DA J 272 " 0.011 2.00e-02 2.50e+03 pdb=" C2 DA J 272 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA J 272 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DA J 272 " -0.006 2.00e-02 2.50e+03 ... (remaining 1852 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 640 2.70 - 3.25: 12284 3.25 - 3.80: 24033 3.80 - 4.35: 32266 4.35 - 4.90: 49096 Nonbonded interactions: 118319 Sorted by model distance: nonbonded pdb=" O ASN C 101 " pdb=" ND2 ASN C 101 " model vdw 2.149 2.520 nonbonded pdb=" OE1 GLN K 61 " pdb=" OH TYR K 117 " model vdw 2.158 2.440 nonbonded pdb=" OD2 ASP L 95 " pdb=" OG SER L 98 " model vdw 2.181 2.440 nonbonded pdb=" OH TYR C 52 " pdb=" OE1 GLN D 99 " model vdw 2.217 2.440 nonbonded pdb=" OE1 GLN L 61 " pdb=" OH TYR L 117 " model vdw 2.223 2.440 ... (remaining 118314 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 134 through 171 or (resid 172 and (name N or name CA or na \ me C or name O or name CB )) or resid 173 through 228)) selection = (chain 'E' and resid 134 through 228) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 25 through 103) } ncs_group { reference = (chain 'C' and (resid 16 through 72 or (resid 73 and (name N or name CA or name \ C or name O or name CB )) or resid 74 through 115)) selection = chain 'G' } ncs_group { reference = (chain 'D' and (resid 37 or (resid 38 and (name N or name CA or name C or name O \ or name CB )) or resid 39 through 129)) selection = chain 'H' } ncs_group { reference = (chain 'K' and (resid 23 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 86 or (resid 87 and (name N or nam \ e CA or name C or name O or name CB )) or resid 88 or (resid 89 through 90 and ( \ name N or name CA or name C or name O or name CB )) or resid 91 through 157 or ( \ resid 158 and (name N or name CA or name C or name O or name CB )) or resid 159 \ through 265)) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 232 5.49 5 S 27 5.16 5 C 8210 2.51 5 N 2472 2.21 5 O 3184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.260 Check model and map are aligned: 0.190 Process input model: 42.030 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.120 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 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 : 0.004 0.044 14864 Z= 0.263 Angle : 0.693 7.791 21099 Z= 0.425 Chirality : 0.038 0.163 2396 Planarity : 0.005 0.058 1855 Dihedral : 27.089 160.440 5864 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.24), residues: 1174 helix: 1.41 (0.23), residues: 522 sheet: 0.39 (0.33), residues: 238 loop : -1.62 (0.26), residues: 414 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 169 time to evaluate : 1.263 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 170 average time/residue: 0.3864 time to fit residues: 86.3232 Evaluate side-chains 151 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.409 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 57 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 ASN H 67 ASN K 170 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 14864 Z= 0.202 Angle : 0.587 6.248 21099 Z= 0.347 Chirality : 0.036 0.151 2396 Planarity : 0.005 0.056 1855 Dihedral : 29.784 160.341 3644 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.24), residues: 1174 helix: 2.32 (0.23), residues: 528 sheet: 0.88 (0.33), residues: 236 loop : -1.43 (0.27), residues: 410 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 165 time to evaluate : 1.365 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 167 average time/residue: 0.3686 time to fit residues: 82.2742 Evaluate side-chains 155 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 151 time to evaluate : 1.359 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2768 time to fit residues: 3.1502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 110 optimal weight: 0.9990 chunk 123 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 ASN K 170 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 14864 Z= 0.260 Angle : 0.581 5.540 21099 Z= 0.342 Chirality : 0.036 0.150 2396 Planarity : 0.005 0.052 1855 Dihedral : 29.639 159.322 3644 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.25), residues: 1174 helix: 2.54 (0.22), residues: 529 sheet: 0.85 (0.34), residues: 238 loop : -1.39 (0.27), residues: 407 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 158 time to evaluate : 1.327 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 167 average time/residue: 0.3691 time to fit residues: 82.6528 Evaluate side-chains 163 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 154 time to evaluate : 1.260 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1338 time to fit residues: 3.8260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 123 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 83 optimal weight: 8.9990 chunk 125 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 ASN K 170 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 14864 Z= 0.213 Angle : 0.559 5.481 21099 Z= 0.331 Chirality : 0.035 0.144 2396 Planarity : 0.004 0.046 1855 Dihedral : 29.531 160.254 3644 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.25), residues: 1174 helix: 2.77 (0.22), residues: 530 sheet: 0.86 (0.34), residues: 238 loop : -1.30 (0.28), residues: 406 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 160 time to evaluate : 1.340 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 167 average time/residue: 0.3693 time to fit residues: 82.2920 Evaluate side-chains 164 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 155 time to evaluate : 1.251 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1314 time to fit residues: 3.7716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 110 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 0 optimal weight: 0.9990 chunk 67 optimal weight: 0.0980 chunk 118 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN K 170 HIS L 25 GLN L 170 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 14864 Z= 0.310 Angle : 0.593 5.613 21099 Z= 0.347 Chirality : 0.037 0.147 2396 Planarity : 0.005 0.052 1855 Dihedral : 29.553 158.666 3644 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.25), residues: 1174 helix: 2.65 (0.22), residues: 529 sheet: 0.91 (0.33), residues: 236 loop : -1.44 (0.27), residues: 409 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 152 time to evaluate : 1.190 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 157 average time/residue: 0.3653 time to fit residues: 76.6499 Evaluate side-chains 152 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 143 time to evaluate : 1.327 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1316 time to fit residues: 3.8949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 44 optimal weight: 1.9990 chunk 119 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 0.0170 chunk 11 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 overall best weight: 1.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN K 170 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 14864 Z= 0.197 Angle : 0.552 5.701 21099 Z= 0.326 Chirality : 0.035 0.138 2396 Planarity : 0.004 0.047 1855 Dihedral : 29.433 161.042 3644 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.25), residues: 1174 helix: 2.88 (0.22), residues: 530 sheet: 0.86 (0.34), residues: 240 loop : -1.35 (0.28), residues: 404 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 145 time to evaluate : 1.302 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 148 average time/residue: 0.3865 time to fit residues: 76.0064 Evaluate side-chains 156 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 152 time to evaluate : 1.215 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1376 time to fit residues: 2.6962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 127 optimal weight: 0.0000 chunk 14 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 96 optimal weight: 0.0970 chunk 74 optimal weight: 8.9990 chunk 111 optimal weight: 20.0000 chunk 132 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN L 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.054 14864 Z= 0.361 Angle : 0.609 5.792 21099 Z= 0.355 Chirality : 0.038 0.163 2396 Planarity : 0.005 0.051 1855 Dihedral : 29.571 158.482 3644 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.25), residues: 1174 helix: 2.61 (0.22), residues: 529 sheet: 0.80 (0.34), residues: 240 loop : -1.56 (0.27), residues: 405 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 154 time to evaluate : 1.245 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 159 average time/residue: 0.3533 time to fit residues: 75.7363 Evaluate side-chains 158 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 152 time to evaluate : 1.236 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1315 time to fit residues: 2.9935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 52 optimal weight: 0.7980 chunk 78 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 83 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN K 170 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 14864 Z= 0.185 Angle : 0.555 8.581 21099 Z= 0.327 Chirality : 0.034 0.140 2396 Planarity : 0.004 0.044 1855 Dihedral : 29.448 161.538 3644 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.25), residues: 1174 helix: 2.91 (0.22), residues: 530 sheet: 0.83 (0.34), residues: 240 loop : -1.36 (0.28), residues: 404 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 153 time to evaluate : 1.385 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 155 average time/residue: 0.4025 time to fit residues: 83.8448 Evaluate side-chains 153 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 152 time to evaluate : 1.298 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1301 time to fit residues: 1.8172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 53 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 37 optimal weight: 0.0000 chunk 111 optimal weight: 9.9990 chunk 116 optimal weight: 30.0000 chunk 122 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 overall best weight: 3.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN K 170 HIS L 170 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.054 14864 Z= 0.385 Angle : 0.620 7.970 21099 Z= 0.360 Chirality : 0.039 0.160 2396 Planarity : 0.005 0.050 1855 Dihedral : 29.602 158.385 3644 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.25), residues: 1174 helix: 2.58 (0.22), residues: 529 sheet: 0.73 (0.34), residues: 240 loop : -1.58 (0.27), residues: 405 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 150 time to evaluate : 1.150 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 153 average time/residue: 0.3625 time to fit residues: 74.3094 Evaluate side-chains 152 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 150 time to evaluate : 1.255 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1360 time to fit residues: 2.0761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 130 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN K 170 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.064 14864 Z= 0.364 Angle : 0.616 10.131 21099 Z= 0.357 Chirality : 0.038 0.155 2396 Planarity : 0.005 0.051 1855 Dihedral : 29.608 159.754 3644 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.24), residues: 1174 helix: 2.50 (0.22), residues: 529 sheet: 0.74 (0.33), residues: 240 loop : -1.63 (0.27), residues: 405 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 1.358 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 150 average time/residue: 0.3677 time to fit residues: 74.0954 Evaluate side-chains 149 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 1.258 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1215 time to fit residues: 1.8709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN K 170 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.170517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.117552 restraints weight = 15661.843| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.15 r_work: 0.2967 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 14864 Z= 0.185 Angle : 0.571 16.152 21099 Z= 0.334 Chirality : 0.035 0.140 2396 Planarity : 0.004 0.045 1855 Dihedral : 29.520 161.729 3644 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.25), residues: 1174 helix: 2.87 (0.22), residues: 530 sheet: 0.83 (0.34), residues: 240 loop : -1.41 (0.28), residues: 404 =============================================================================== Job complete usr+sys time: 2768.73 seconds wall clock time: 50 minutes 51.05 seconds (3051.05 seconds total)