Starting phenix.real_space_refine on Fri Feb 16 02:42:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k78_22696/02_2024/7k78_22696.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k78_22696/02_2024/7k78_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_2024/7k78_22696.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k78_22696/02_2024/7k78_22696.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k78_22696/02_2024/7k78_22696.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k78_22696/02_2024/7k78_22696.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 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. 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-5238/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: 7.65, per 1000 atoms: 0.54 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: 6.82 Conformation dependent library (CDL) restraints added in 1.8 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: 5.77 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: 5.45 Time building geometry restraints manager: 7.27 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: 6931 32.09 - 64.18: 1537 64.18 - 96.26: 54 96.26 - 128.35: 0 128.35 - 160.44: 2 Dihedral angle restraints: 8524 sinusoidal: 5037 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 8521 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 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: 0.990 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: 3.940 Check model and map are aligned: 0.230 Set scattering table: 0.120 Process input model: 45.240 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 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 : 27.106 160.440 6276 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 % Allowed : 0.99 % Favored : 98.82 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 132 HIS 0.006 0.001 HIS C 84 PHE 0.014 0.002 PHE A 169 TYR 0.022 0.002 TYR L 117 ARG 0.013 0.001 ARG C 79 *********************** 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 : 1.278 Fit side-chains REVERT: A 174 GLN cc_start: 0.7283 (tt0) cc_final: 0.7060 (tt0) REVERT: B 75 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7377 (mt-10) REVERT: E 177 ARG cc_start: 0.8566 (mtp85) cc_final: 0.8256 (mtp85) REVERT: F 80 LYS cc_start: 0.8424 (mttm) cc_final: 0.8119 (mttt) REVERT: K 188 ARG cc_start: 0.7516 (mtm180) cc_final: 0.7113 (mtm110) REVERT: K 251 GLU cc_start: 0.7254 (mm-30) cc_final: 0.7036 (mp0) REVERT: L 65 GLN cc_start: 0.7690 (mp10) cc_final: 0.7270 (mp10) outliers start: 2 outliers final: 0 residues processed: 170 average time/residue: 0.3976 time to fit residues: 88.6577 Evaluate side-chains 158 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.416 ------------------------------------------------------------------------------- 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: 6.9990 chunk 41 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 79 optimal weight: 8.9990 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: 0.8097 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14864 Z= 0.201 Angle : 0.586 6.188 21099 Z= 0.347 Chirality : 0.036 0.151 2396 Planarity : 0.005 0.056 1855 Dihedral : 29.257 160.605 4056 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.79 % Allowed : 8.29 % Favored : 90.92 % 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: 1.18 (0.24), residues: 1174 helix: 2.34 (0.23), residues: 528 sheet: 0.88 (0.33), residues: 236 loop : -1.44 (0.27), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 132 HIS 0.003 0.001 HIS B 76 PHE 0.010 0.001 PHE A 169 TYR 0.013 0.001 TYR G 52 ARG 0.004 0.000 ARG C 79 *********************** 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 171 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 163 time to evaluate : 1.375 Fit side-chains REVERT: A 174 GLN cc_start: 0.7201 (tt0) cc_final: 0.6896 (tt0) REVERT: B 75 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7306 (mt-10) REVERT: K 84 GLU cc_start: 0.7551 (tp30) cc_final: 0.7293 (mm-30) REVERT: K 160 ILE cc_start: 0.8678 (mt) cc_final: 0.8151 (mp) REVERT: L 65 GLN cc_start: 0.7649 (mp10) cc_final: 0.7325 (mm-40) outliers start: 8 outliers final: 4 residues processed: 165 average time/residue: 0.3598 time to fit residues: 79.5533 Evaluate side-chains 148 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 144 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain K residue 261 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 84 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 chunk 123 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 99 optimal weight: 0.0970 overall best weight: 2.1984 ------------------------------------------------------------------------------- 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: 0.8131 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14864 Z= 0.277 Angle : 0.590 5.575 21099 Z= 0.346 Chirality : 0.037 0.152 2396 Planarity : 0.005 0.053 1855 Dihedral : 29.116 159.405 4056 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.88 % Allowed : 11.94 % Favored : 86.18 % 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: 1.29 (0.25), residues: 1174 helix: 2.52 (0.23), residues: 529 sheet: 0.83 (0.33), residues: 238 loop : -1.48 (0.27), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 132 HIS 0.005 0.001 HIS L 249 PHE 0.010 0.001 PHE A 169 TYR 0.011 0.002 TYR K 117 ARG 0.008 0.000 ARG C 79 *********************** 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 168 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 149 time to evaluate : 1.267 Fit side-chains REVERT: K 84 GLU cc_start: 0.7599 (tp30) cc_final: 0.7367 (mm-30) REVERT: L 65 GLN cc_start: 0.7672 (mp10) cc_final: 0.7339 (mm-40) REVERT: L 111 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7107 (pm20) outliers start: 19 outliers final: 14 residues processed: 159 average time/residue: 0.3734 time to fit residues: 80.0195 Evaluate side-chains 166 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 151 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 25 GLN Chi-restraints excluded: chain K residue 130 ASP Chi-restraints excluded: chain K residue 261 LYS Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain L residue 170 HIS Chi-restraints excluded: chain L residue 180 THR 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: 8.9990 chunk 64 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 83 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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: 0.8112 moved from start: 0.1510 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= 0.229 Angle : 0.557 5.681 21099 Z= 0.330 Chirality : 0.035 0.145 2396 Planarity : 0.004 0.050 1855 Dihedral : 28.863 160.605 4056 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.37 % Allowed : 12.64 % Favored : 85.00 % 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: 1.48 (0.25), residues: 1174 helix: 2.70 (0.22), residues: 530 sheet: 0.88 (0.34), residues: 238 loop : -1.40 (0.27), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 132 HIS 0.004 0.001 HIS L 249 PHE 0.008 0.001 PHE A 169 TYR 0.010 0.001 TYR K 117 ARG 0.007 0.000 ARG C 79 *********************** 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 180 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 156 time to evaluate : 1.287 Fit side-chains REVERT: F 80 LYS cc_start: 0.8446 (mttm) cc_final: 0.8117 (mttt) REVERT: K 84 GLU cc_start: 0.7535 (tp30) cc_final: 0.7333 (mm-30) REVERT: L 65 GLN cc_start: 0.7660 (mp10) cc_final: 0.7339 (mm-40) REVERT: L 111 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7103 (pm20) outliers start: 24 outliers final: 18 residues processed: 169 average time/residue: 0.3534 time to fit residues: 79.9773 Evaluate side-chains 166 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 147 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 25 GLN Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 130 ASP Chi-restraints excluded: chain K residue 261 LYS Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain L residue 170 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 110 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 0 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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: 0.8135 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14864 Z= 0.288 Angle : 0.576 5.591 21099 Z= 0.338 Chirality : 0.037 0.148 2396 Planarity : 0.004 0.049 1855 Dihedral : 28.851 159.772 4056 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.76 % Allowed : 13.82 % Favored : 83.42 % 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: 1.40 (0.25), residues: 1174 helix: 2.67 (0.22), residues: 529 sheet: 0.83 (0.33), residues: 238 loop : -1.48 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 132 HIS 0.005 0.001 HIS L 249 PHE 0.010 0.001 PHE A 169 TYR 0.012 0.001 TYR K 117 ARG 0.007 0.000 ARG C 79 *********************** 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 181 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 153 time to evaluate : 1.310 Fit side-chains REVERT: F 94 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8517 (mp10) REVERT: K 84 GLU cc_start: 0.7607 (tp30) cc_final: 0.7389 (mm-30) REVERT: L 111 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7102 (pm20) REVERT: L 173 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7928 (tt) outliers start: 28 outliers final: 22 residues processed: 169 average time/residue: 0.3495 time to fit residues: 79.2039 Evaluate side-chains 174 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 149 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 94 GLN Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 25 GLN Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 130 ASP Chi-restraints excluded: chain K residue 261 LYS Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain L residue 160 ILE Chi-restraints excluded: chain L residue 170 HIS Chi-restraints excluded: chain L residue 173 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 44 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 L 25 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1656 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= 0.246 Angle : 0.559 5.590 21099 Z= 0.330 Chirality : 0.035 0.144 2396 Planarity : 0.004 0.049 1855 Dihedral : 28.772 160.881 4056 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.06 % Allowed : 14.61 % Favored : 82.33 % 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: 1.52 (0.25), residues: 1174 helix: 2.78 (0.22), residues: 530 sheet: 0.85 (0.33), residues: 238 loop : -1.43 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 132 HIS 0.004 0.001 HIS L 249 PHE 0.008 0.001 PHE A 169 TYR 0.011 0.001 TYR A 145 ARG 0.004 0.000 ARG C 79 *********************** 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 184 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 153 time to evaluate : 1.295 Fit side-chains REVERT: F 94 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8575 (mp10) REVERT: H 67 ASN cc_start: 0.8777 (OUTLIER) cc_final: 0.8471 (m-40) REVERT: K 84 GLU cc_start: 0.7583 (tp30) cc_final: 0.7376 (mm-30) REVERT: L 111 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7104 (pm20) outliers start: 31 outliers final: 25 residues processed: 172 average time/residue: 0.3433 time to fit residues: 79.6110 Evaluate side-chains 179 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 151 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 94 GLN Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 25 GLN Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 130 ASP Chi-restraints excluded: chain K residue 261 LYS Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 25 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 160 ILE Chi-restraints excluded: chain L residue 170 HIS Chi-restraints excluded: chain L residue 221 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 127 optimal weight: 0.0370 chunk 14 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 96 optimal weight: 0.5980 chunk 74 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 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: 2.7264 ------------------------------------------------------------------------------- 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: 0.8143 moved from start: 0.1648 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= 0.317 Angle : 0.584 5.633 21099 Z= 0.341 Chirality : 0.037 0.147 2396 Planarity : 0.004 0.050 1855 Dihedral : 28.810 160.284 4056 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.96 % Allowed : 15.99 % Favored : 81.05 % 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: 1.31 (0.25), residues: 1174 helix: 2.66 (0.22), residues: 529 sheet: 0.74 (0.33), residues: 240 loop : -1.60 (0.27), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 132 HIS 0.005 0.001 HIS L 249 PHE 0.010 0.002 PHE A 169 TYR 0.013 0.002 TYR K 117 ARG 0.004 0.000 ARG C 38 *********************** 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 182 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 152 time to evaluate : 1.305 Fit side-chains REVERT: F 94 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8507 (mp10) outliers start: 30 outliers final: 26 residues processed: 171 average time/residue: 0.3345 time to fit residues: 77.6423 Evaluate side-chains 167 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 140 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 94 GLN Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 130 ASP Chi-restraints excluded: chain K residue 261 LYS Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 160 ILE Chi-restraints excluded: chain L residue 170 HIS Chi-restraints excluded: chain L residue 173 LEU Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 221 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 52 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 120 optimal weight: 0.0060 chunk 126 optimal weight: 10.0000 overall best weight: 1.1200 ------------------------------------------------------------------------------- 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 L 170 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14864 Z= 0.193 Angle : 0.544 5.904 21099 Z= 0.322 Chirality : 0.034 0.139 2396 Planarity : 0.004 0.045 1855 Dihedral : 28.693 161.990 4056 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.76 % Allowed : 17.18 % Favored : 80.06 % 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: 1.61 (0.25), residues: 1174 helix: 2.92 (0.22), residues: 530 sheet: 0.83 (0.34), residues: 240 loop : -1.44 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 132 HIS 0.007 0.001 HIS L 170 PHE 0.007 0.001 PHE A 169 TYR 0.013 0.001 TYR A 145 ARG 0.004 0.000 ARG C 38 *********************** 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 179 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 151 time to evaluate : 1.226 Fit side-chains REVERT: F 94 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8556 (mp10) REVERT: H 67 ASN cc_start: 0.8717 (OUTLIER) cc_final: 0.8417 (m-40) REVERT: K 84 GLU cc_start: 0.7559 (tp30) cc_final: 0.7254 (mm-30) REVERT: L 162 MET cc_start: 0.8001 (mmm) cc_final: 0.7208 (mmm) outliers start: 28 outliers final: 24 residues processed: 169 average time/residue: 0.3451 time to fit residues: 78.2866 Evaluate side-chains 176 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 150 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 94 GLN Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 25 GLN Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 130 ASP Chi-restraints excluded: chain K residue 261 LYS Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 160 ILE Chi-restraints excluded: chain L residue 170 HIS Chi-restraints excluded: chain L residue 173 LEU Chi-restraints excluded: chain L residue 221 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 126 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 53 optimal weight: 0.4980 chunk 96 optimal weight: 0.9990 chunk 37 optimal weight: 0.0010 chunk 111 optimal weight: 20.0000 chunk 116 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 overall best weight: 1.2590 ------------------------------------------------------------------------------- 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: 0.8097 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14864 Z= 0.196 Angle : 0.538 6.732 21099 Z= 0.319 Chirality : 0.034 0.137 2396 Planarity : 0.004 0.041 1855 Dihedral : 28.577 162.131 4056 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.67 % Allowed : 17.18 % Favored : 80.16 % 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: 1.73 (0.25), residues: 1174 helix: 3.01 (0.22), residues: 530 sheet: 0.92 (0.34), residues: 240 loop : -1.40 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 132 HIS 0.010 0.001 HIS L 170 PHE 0.006 0.001 PHE A 169 TYR 0.016 0.001 TYR H 46 ARG 0.004 0.000 ARG C 38 *********************** 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 180 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 153 time to evaluate : 1.360 Fit side-chains REVERT: F 94 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8549 (mp10) REVERT: K 84 GLU cc_start: 0.7575 (tp30) cc_final: 0.7275 (mm-30) REVERT: L 162 MET cc_start: 0.7919 (mmm) cc_final: 0.7538 (mmm) outliers start: 27 outliers final: 22 residues processed: 172 average time/residue: 0.3419 time to fit residues: 79.9531 Evaluate side-chains 173 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 150 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 94 GLN Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 25 GLN Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 130 ASP Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 170 HIS Chi-restraints excluded: chain L residue 173 LEU Chi-restraints excluded: chain L residue 221 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 130 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 136 optimal weight: 0.8980 chunk 125 optimal weight: 0.0980 chunk 108 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 L 170 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 14864 Z= 0.288 Angle : 0.568 6.470 21099 Z= 0.333 Chirality : 0.036 0.144 2396 Planarity : 0.004 0.057 1855 Dihedral : 28.661 161.646 4056 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.57 % Allowed : 17.18 % Favored : 80.26 % 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: 1.54 (0.25), residues: 1174 helix: 2.83 (0.22), residues: 530 sheet: 0.89 (0.33), residues: 240 loop : -1.49 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 132 HIS 0.004 0.001 HIS L 249 PHE 0.009 0.001 PHE A 169 TYR 0.012 0.001 TYR K 117 ARG 0.010 0.000 ARG C 79 ********************** 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 177 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 151 time to evaluate : 1.302 Fit side-chains REVERT: F 94 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8546 (mp10) REVERT: L 162 MET cc_start: 0.7931 (mmm) cc_final: 0.7490 (mmm) outliers start: 26 outliers final: 24 residues processed: 168 average time/residue: 0.3474 time to fit residues: 79.2108 Evaluate side-chains 174 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 149 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 94 GLN Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 25 GLN Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 130 ASP Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 170 HIS Chi-restraints excluded: chain L residue 173 LEU Chi-restraints excluded: chain L residue 221 SER 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: 2.9990 chunk 100 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 111 optimal weight: 9.9990 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 170 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.165545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.115029 restraints weight = 15911.010| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.38 r_work: 0.2981 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 14864 Z= 0.288 Angle : 0.771 59.198 21099 Z= 0.467 Chirality : 0.036 0.339 2396 Planarity : 0.005 0.096 1855 Dihedral : 28.667 161.636 4056 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.37 % Allowed : 17.47 % Favored : 80.16 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.56 (0.25), residues: 1174 helix: 2.85 (0.22), residues: 530 sheet: 0.88 (0.33), residues: 240 loop : -1.48 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 132 HIS 0.100 0.004 HIS L 170 PHE 0.009 0.001 PHE A 169 TYR 0.012 0.001 TYR K 117 ARG 0.008 0.000 ARG C 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2827.81 seconds wall clock time: 52 minutes 7.13 seconds (3127.13 seconds total)