Starting phenix.real_space_refine on Wed Feb 14 05:39:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdh_31918/02_2024/7vdh_31918_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdh_31918/02_2024/7vdh_31918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdh_31918/02_2024/7vdh_31918.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdh_31918/02_2024/7vdh_31918.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdh_31918/02_2024/7vdh_31918_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdh_31918/02_2024/7vdh_31918_updated.pdb" } resolution = 2.9 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= 0.001 sd= 0.006 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: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 5592 2.51 5 N 1457 2.21 5 O 1597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 138": "NH1" <-> "NH2" Residue "R ARG 140": "NH1" <-> "NH2" Residue "R ARG 141": "NH1" <-> "NH2" Residue "R PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 208": "NH1" <-> "NH2" Residue "R ARG 220": "NH1" <-> "NH2" Residue "R TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 254": "OD1" <-> "OD2" Residue "R TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A GLU 25": "OE1" <-> "OE2" Residue "A ASP 26": "OD1" <-> "OD2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A GLU 43": "OE1" <-> "OE2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 200": "OD1" <-> "OD2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 350": "OD1" <-> "OD2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B ASP 5": "OD1" <-> "OD2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ASP 38": "OD1" <-> "OD2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "S PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 89": "OE1" <-> "OE2" Residue "S ASP 90": "OD1" <-> "OD2" Residue "S TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 125": "OD1" <-> "OD2" Residue "S ARG 148": "NH1" <-> "NH2" Residue "S GLU 222": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8710 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2131 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 8, 'TRANS': 258} Chain: "A" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1751 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2590 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 415 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1757 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "R" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'6IB': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.26, per 1000 atoms: 0.60 Number of scatterers: 8710 At special positions: 0 Unit cell: (119.928, 112.564, 102.044, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 1597 8.00 N 1457 7.00 C 5592 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 26 " - pdb=" SG CYS R 258 " distance=2.03 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " distance=2.02 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.08 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.05 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: 3.25 Conformation dependent library (CDL) restraints added in 1.8 seconds 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2062 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 13 sheets defined 33.5% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'R' and resid 28 through 56 removed outlier: 3.994A pdb=" N LEU R 31 " --> pdb=" O LYS R 28 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE R 32 " --> pdb=" O GLU R 29 " (cutoff:3.500A) Proline residue: R 33 - end of helix removed outlier: 3.604A pdb=" N PHE R 39 " --> pdb=" O LEU R 36 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE R 40 " --> pdb=" O ILE R 37 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA R 41 " --> pdb=" O LEU R 38 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY R 44 " --> pdb=" O ALA R 41 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN R 48 " --> pdb=" O LEU R 45 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY R 49 " --> pdb=" O VAL R 46 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL R 51 " --> pdb=" O ASN R 48 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP R 53 " --> pdb=" O PHE R 50 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU R 55 " --> pdb=" O LEU R 52 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLY R 56 " --> pdb=" O TRP R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 93 removed outlier: 4.312A pdb=" N TYR R 67 " --> pdb=" O ALA R 63 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 132 Processing helix chain 'R' and resid 134 through 138 Processing helix chain 'R' and resid 143 through 166 removed outlier: 4.294A pdb=" N SER R 146 " --> pdb=" O ARG R 143 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL R 149 " --> pdb=" O SER R 146 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL R 151 " --> pdb=" O VAL R 148 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU R 153 " --> pdb=" O CYS R 150 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP R 154 " --> pdb=" O VAL R 151 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU R 156 " --> pdb=" O LEU R 153 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU R 160 " --> pdb=" O SER R 157 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE R 162 " --> pdb=" O LEU R 159 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU R 163 " --> pdb=" O LEU R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 212 removed outlier: 4.135A pdb=" N THR R 182 " --> pdb=" O GLY R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 234 Processing helix chain 'R' and resid 237 through 244 Processing helix chain 'R' and resid 246 through 249 No H-bonds generated for 'chain 'R' and resid 246 through 249' Processing helix chain 'R' and resid 257 through 279 Proline residue: R 262 - end of helix Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 281 through 284 No H-bonds generated for 'chain 'R' and resid 281 through 284' Processing helix chain 'A' and resid 7 through 31 removed outlier: 3.777A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 208 through 215 removed outlier: 4.933A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.810A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 23 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 7.094A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.817A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.715A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.692A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 220 through 223 removed outlier: 4.316A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.662A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.664A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.513A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.920A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.741A pdb=" N LYS S 232 " --> pdb=" O VAL S 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'S' and resid 143 through 148 Processing sheet with id= M, first strand: chain 'S' and resid 214 through 219 removed outlier: 6.215A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) 378 hydrogen bonds defined for protein. 1020 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.46 Time building geometry restraints manager: 3.43 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: 2688 1.34 - 1.47: 2451 1.47 - 1.60: 3676 1.60 - 1.74: 1 1.74 - 1.87: 88 Bond restraints: 8904 Sorted by residual: bond pdb=" C17 CLR R 401 " pdb=" C20 CLR R 401 " ideal model delta sigma weight residual 1.535 1.672 -0.137 2.00e-02 2.50e+03 4.70e+01 bond pdb=" C ALA S 40 " pdb=" N PRO S 41 " ideal model delta sigma weight residual 1.335 1.392 -0.058 1.28e-02 6.10e+03 2.03e+01 bond pdb=" CG1 ILE B 232 " pdb=" CD1 ILE B 232 " ideal model delta sigma weight residual 1.513 1.367 0.146 3.90e-02 6.57e+02 1.41e+01 bond pdb=" N THR B 143 " pdb=" CA THR B 143 " ideal model delta sigma weight residual 1.457 1.500 -0.042 1.29e-02 6.01e+03 1.07e+01 bond pdb=" C31 6IB R 402 " pdb=" N5 6IB R 402 " ideal model delta sigma weight residual 1.447 1.503 -0.056 2.00e-02 2.50e+03 7.87e+00 ... (remaining 8899 not shown) Histogram of bond angle deviations from ideal: 93.48 - 102.39: 33 102.39 - 111.31: 3442 111.31 - 120.22: 4928 120.22 - 129.13: 3584 129.13 - 138.04: 83 Bond angle restraints: 12070 Sorted by residual: angle pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta sigma weight residual 121.54 138.04 -16.50 1.91e+00 2.74e-01 7.46e+01 angle pdb=" CA CYS B 149 " pdb=" CB CYS B 149 " pdb=" SG CYS B 149 " ideal model delta sigma weight residual 114.40 129.91 -15.51 2.30e+00 1.89e-01 4.55e+01 angle pdb=" CA GLY B 144 " pdb=" C GLY B 144 " pdb=" N TYR B 145 " ideal model delta sigma weight residual 114.58 119.87 -5.29 8.60e-01 1.35e+00 3.78e+01 angle pdb=" CA ARG A 208 " pdb=" CB ARG A 208 " pdb=" CG ARG A 208 " ideal model delta sigma weight residual 114.10 125.10 -11.00 2.00e+00 2.50e-01 3.02e+01 angle pdb=" C GLY S 197 " pdb=" N THR S 198 " pdb=" CA THR S 198 " ideal model delta sigma weight residual 124.31 133.10 -8.79 1.67e+00 3.59e-01 2.77e+01 ... (remaining 12065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4814 17.93 - 35.86: 386 35.86 - 53.79: 58 53.79 - 71.72: 21 71.72 - 89.65: 7 Dihedral angle restraints: 5286 sinusoidal: 2088 harmonic: 3198 Sorted by residual: dihedral pdb=" CA ASP B 290 " pdb=" C ASP B 290 " pdb=" N ASP B 291 " pdb=" CA ASP B 291 " ideal model delta harmonic sigma weight residual 180.00 149.89 30.11 0 5.00e+00 4.00e-02 3.63e+01 dihedral pdb=" CA PHE R 172 " pdb=" C PHE R 172 " pdb=" N SER R 173 " pdb=" CA SER R 173 " ideal model delta harmonic sigma weight residual 180.00 156.15 23.85 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA GLU S 210 " pdb=" C GLU S 210 " pdb=" N ASP S 211 " pdb=" CA ASP S 211 " ideal model delta harmonic sigma weight residual 180.00 156.81 23.19 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 5283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 1268 0.131 - 0.261: 91 0.261 - 0.392: 8 0.392 - 0.523: 0 0.523 - 0.653: 3 Chirality restraints: 1370 Sorted by residual: chirality pdb=" CG LEU A 310 " pdb=" CB LEU A 310 " pdb=" CD1 LEU A 310 " pdb=" CD2 LEU A 310 " both_signs ideal model delta sigma weight residual False -2.59 -1.94 -0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CG LEU S 162 " pdb=" CB LEU S 162 " pdb=" CD1 LEU S 162 " pdb=" CD2 LEU S 162 " both_signs ideal model delta sigma weight residual False -2.59 -2.01 -0.58 2.00e-01 2.50e+01 8.44e+00 chirality pdb=" CG LEU S 117 " pdb=" CB LEU S 117 " pdb=" CD1 LEU S 117 " pdb=" CD2 LEU S 117 " both_signs ideal model delta sigma weight residual False -2.59 -2.01 -0.58 2.00e-01 2.50e+01 8.36e+00 ... (remaining 1367 not shown) Planarity restraints: 1506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 119 " 0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" CG ASN B 119 " -0.059 2.00e-02 2.50e+03 pdb=" OD1 ASN B 119 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN B 119 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 105 " 0.007 2.00e-02 2.50e+03 2.00e-02 7.96e+00 pdb=" CG TYR B 105 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR B 105 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR B 105 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR B 105 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR B 105 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 105 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 105 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " -0.046 5.00e-02 4.00e+02 6.95e-02 7.73e+00 pdb=" N PRO B 194 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " -0.038 5.00e-02 4.00e+02 ... (remaining 1503 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1583 2.77 - 3.30: 7505 3.30 - 3.83: 15277 3.83 - 4.37: 17746 4.37 - 4.90: 30933 Nonbonded interactions: 73044 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.232 2.440 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.273 2.440 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.291 2.440 nonbonded pdb=" OH TYR R 113 " pdb=" O GLY R 236 " model vdw 2.313 2.440 nonbonded pdb=" O THR R 107 " pdb=" OG SER R 161 " model vdw 2.313 2.440 ... (remaining 73039 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.150 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: 1.300 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 26.310 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:11.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 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 : 0.011 0.146 8904 Z= 0.744 Angle : 1.387 16.498 12070 Z= 0.735 Chirality : 0.078 0.653 1370 Planarity : 0.008 0.069 1506 Dihedral : 13.914 89.652 3212 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.38 (0.22), residues: 1093 helix: -2.07 (0.20), residues: 365 sheet: -0.54 (0.29), residues: 295 loop : -1.68 (0.26), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 82 HIS 0.017 0.002 HIS B 311 PHE 0.032 0.004 PHE R 104 TYR 0.045 0.004 TYR B 59 ARG 0.041 0.002 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.063 Fit side-chains REVERT: R 58 ARG cc_start: 0.6054 (ttm-80) cc_final: 0.4767 (ttt180) REVERT: A 273 LEU cc_start: 0.8839 (mm) cc_final: 0.8545 (mm) REVERT: A 331 ASN cc_start: 0.8399 (m110) cc_final: 0.8179 (m110) REVERT: A 333 GLN cc_start: 0.8664 (tp40) cc_final: 0.8149 (mm-40) REVERT: A 337 ASP cc_start: 0.8492 (m-30) cc_final: 0.8114 (m-30) REVERT: B 12 GLU cc_start: 0.7968 (pp20) cc_final: 0.7759 (pp20) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 1.3995 time to fit residues: 292.5766 Evaluate side-chains 151 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 43 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 91 HIS B 119 ASN B 259 GLN S 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8904 Z= 0.213 Angle : 0.655 9.142 12070 Z= 0.327 Chirality : 0.044 0.189 1370 Planarity : 0.004 0.041 1506 Dihedral : 7.352 74.495 1283 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.02 % Allowed : 10.83 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.24), residues: 1093 helix: -0.06 (0.25), residues: 365 sheet: -0.45 (0.30), residues: 288 loop : -1.32 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.005 0.001 HIS B 142 PHE 0.014 0.001 PHE A 189 TYR 0.010 0.001 TYR S 103 ARG 0.007 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 168 time to evaluate : 1.046 Fit side-chains revert: symmetry clash REVERT: R 58 ARG cc_start: 0.6065 (ttm-80) cc_final: 0.5014 (ttt180) REVERT: A 273 LEU cc_start: 0.8771 (mm) cc_final: 0.8562 (mm) REVERT: A 308 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: B 12 GLU cc_start: 0.7901 (pp20) cc_final: 0.7642 (pp20) REVERT: B 111 TYR cc_start: 0.9051 (m-80) cc_final: 0.8833 (m-80) REVERT: B 304 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7793 (ttp80) outliers start: 19 outliers final: 3 residues processed: 173 average time/residue: 1.2077 time to fit residues: 222.7979 Evaluate side-chains 149 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 144 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 241 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain S residue 84 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 82 GLN A 269 ASN A 304 GLN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8904 Z= 0.297 Angle : 0.651 10.189 12070 Z= 0.324 Chirality : 0.044 0.166 1370 Planarity : 0.003 0.035 1506 Dihedral : 6.638 71.305 1283 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.40 % Allowed : 13.69 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.25), residues: 1093 helix: 0.74 (0.27), residues: 363 sheet: -0.30 (0.30), residues: 273 loop : -1.13 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS B 142 PHE 0.014 0.001 PHE A 189 TYR 0.010 0.002 TYR S 103 ARG 0.006 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 152 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: R 45 LEU cc_start: 0.7745 (mt) cc_final: 0.7500 (mt) REVERT: R 234 LEU cc_start: 0.8597 (mt) cc_final: 0.8359 (mm) REVERT: A 193 ASP cc_start: 0.7243 (t0) cc_final: 0.7001 (t0) REVERT: A 273 LEU cc_start: 0.8764 (mm) cc_final: 0.8544 (mm) REVERT: A 304 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7467 (mt0) REVERT: A 308 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: B 12 GLU cc_start: 0.7918 (pp20) cc_final: 0.7610 (pp20) REVERT: B 101 MET cc_start: 0.8741 (mtp) cc_final: 0.8394 (mtp) REVERT: B 111 TYR cc_start: 0.9099 (m-80) cc_final: 0.8855 (m-80) REVERT: B 153 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7499 (p0) outliers start: 32 outliers final: 9 residues processed: 164 average time/residue: 1.1754 time to fit residues: 205.5041 Evaluate side-chains 157 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 145 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain S residue 84 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 98 optimal weight: 0.0470 chunk 104 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 333 GLN B 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8904 Z= 0.254 Angle : 0.628 9.954 12070 Z= 0.309 Chirality : 0.043 0.163 1370 Planarity : 0.003 0.032 1506 Dihedral : 6.383 68.735 1283 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.97 % Allowed : 15.92 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.25), residues: 1093 helix: 1.10 (0.28), residues: 363 sheet: -0.30 (0.30), residues: 270 loop : -0.93 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS B 142 PHE 0.013 0.001 PHE A 189 TYR 0.008 0.001 TYR S 103 ARG 0.007 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 156 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: R 45 LEU cc_start: 0.7824 (mt) cc_final: 0.7458 (mt) REVERT: R 48 ASN cc_start: 0.7754 (m-40) cc_final: 0.7424 (t0) REVERT: R 50 PHE cc_start: 0.7234 (t80) cc_final: 0.6993 (t80) REVERT: R 58 ARG cc_start: 0.5854 (ttm-80) cc_final: 0.4892 (ttt180) REVERT: R 234 LEU cc_start: 0.8603 (mt) cc_final: 0.8336 (mm) REVERT: A 193 ASP cc_start: 0.7237 (t0) cc_final: 0.6891 (t0) REVERT: B 12 GLU cc_start: 0.7927 (pp20) cc_final: 0.7638 (pp20) REVERT: B 101 MET cc_start: 0.8689 (mtp) cc_final: 0.8353 (mtp) REVERT: B 111 TYR cc_start: 0.9076 (m-80) cc_final: 0.8852 (m-80) REVERT: B 153 ASP cc_start: 0.7835 (m-30) cc_final: 0.7492 (p0) REVERT: B 228 ASP cc_start: 0.7888 (p0) cc_final: 0.7659 (p0) outliers start: 28 outliers final: 8 residues processed: 168 average time/residue: 1.1053 time to fit residues: 198.4361 Evaluate side-chains 158 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 150 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 89 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 77 optimal weight: 9.9990 chunk 43 optimal weight: 0.0980 chunk 89 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 75 GLN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8904 Z= 0.163 Angle : 0.595 10.082 12070 Z= 0.287 Chirality : 0.041 0.165 1370 Planarity : 0.003 0.033 1506 Dihedral : 6.038 68.243 1283 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.55 % Allowed : 17.62 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.26), residues: 1093 helix: 1.33 (0.28), residues: 367 sheet: -0.19 (0.31), residues: 265 loop : -0.76 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.000 HIS B 311 PHE 0.011 0.001 PHE A 189 TYR 0.009 0.001 TYR S 178 ARG 0.009 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 163 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: R 32 ILE cc_start: 0.7416 (OUTLIER) cc_final: 0.6932 (tp) REVERT: R 50 PHE cc_start: 0.7226 (t80) cc_final: 0.6997 (t80) REVERT: R 58 ARG cc_start: 0.6078 (ttm-80) cc_final: 0.5016 (ttt180) REVERT: A 193 ASP cc_start: 0.7271 (t0) cc_final: 0.6894 (t0) REVERT: B 12 GLU cc_start: 0.7963 (pp20) cc_final: 0.7656 (pp20) REVERT: B 101 MET cc_start: 0.8667 (mtp) cc_final: 0.8278 (mtp) REVERT: B 111 TYR cc_start: 0.8977 (m-80) cc_final: 0.8720 (m-80) REVERT: B 228 ASP cc_start: 0.7685 (p0) cc_final: 0.7404 (p0) REVERT: S 148 ARG cc_start: 0.7542 (mtp85) cc_final: 0.7323 (mtp85) outliers start: 24 outliers final: 7 residues processed: 172 average time/residue: 1.1112 time to fit residues: 204.7487 Evaluate side-chains 157 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 149 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 89 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.0040 chunk 94 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 104 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 304 GLN A 333 GLN B 75 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8904 Z= 0.160 Angle : 0.595 9.932 12070 Z= 0.286 Chirality : 0.041 0.168 1370 Planarity : 0.003 0.043 1506 Dihedral : 5.908 68.435 1283 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.76 % Allowed : 17.62 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.26), residues: 1093 helix: 1.49 (0.28), residues: 367 sheet: -0.06 (0.32), residues: 263 loop : -0.67 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.000 HIS B 311 PHE 0.022 0.001 PHE R 239 TYR 0.011 0.001 TYR B 59 ARG 0.010 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 157 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: R 31 LEU cc_start: 0.7299 (tp) cc_final: 0.6976 (mt) REVERT: R 32 ILE cc_start: 0.7741 (OUTLIER) cc_final: 0.7422 (tp) REVERT: R 48 ASN cc_start: 0.7800 (m-40) cc_final: 0.7467 (t0) REVERT: R 50 PHE cc_start: 0.7263 (t80) cc_final: 0.7021 (t80) REVERT: R 58 ARG cc_start: 0.6086 (ttm-80) cc_final: 0.4909 (tmt90) REVERT: A 193 ASP cc_start: 0.7282 (t0) cc_final: 0.6888 (t0) REVERT: B 12 GLU cc_start: 0.7979 (pp20) cc_final: 0.7694 (pp20) REVERT: B 101 MET cc_start: 0.8658 (mtp) cc_final: 0.8272 (mtp) REVERT: B 111 TYR cc_start: 0.8942 (m-80) cc_final: 0.8680 (m-80) REVERT: B 228 ASP cc_start: 0.7673 (p0) cc_final: 0.7355 (p0) outliers start: 26 outliers final: 3 residues processed: 167 average time/residue: 1.1617 time to fit residues: 207.1290 Evaluate side-chains 149 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 145 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain S residue 84 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 6.9990 chunk 11 optimal weight: 0.0050 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 304 GLN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8904 Z= 0.237 Angle : 0.641 11.058 12070 Z= 0.308 Chirality : 0.043 0.170 1370 Planarity : 0.003 0.049 1506 Dihedral : 6.001 68.197 1283 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.02 % Allowed : 19.64 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.26), residues: 1093 helix: 1.66 (0.28), residues: 363 sheet: -0.14 (0.30), residues: 280 loop : -0.66 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.009 0.001 HIS B 142 PHE 0.021 0.001 PHE R 39 TYR 0.008 0.001 TYR B 124 ARG 0.012 0.001 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 149 time to evaluate : 1.153 Fit side-chains revert: symmetry clash REVERT: R 31 LEU cc_start: 0.7341 (tp) cc_final: 0.7026 (mt) REVERT: R 32 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7409 (tp) REVERT: R 48 ASN cc_start: 0.7740 (m-40) cc_final: 0.7415 (t0) REVERT: R 50 PHE cc_start: 0.7334 (t80) cc_final: 0.7085 (t80) REVERT: R 58 ARG cc_start: 0.6083 (ttm-80) cc_final: 0.5172 (ttt180) REVERT: A 193 ASP cc_start: 0.7237 (t0) cc_final: 0.6808 (t0) REVERT: B 12 GLU cc_start: 0.7956 (pp20) cc_final: 0.7719 (pp20) REVERT: B 101 MET cc_start: 0.8655 (mtp) cc_final: 0.8269 (mtp) REVERT: B 111 TYR cc_start: 0.9032 (m-80) cc_final: 0.8811 (m-80) outliers start: 19 outliers final: 6 residues processed: 156 average time/residue: 1.1544 time to fit residues: 192.3006 Evaluate side-chains 153 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 146 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 84 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 304 GLN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8904 Z= 0.198 Angle : 0.633 11.256 12070 Z= 0.303 Chirality : 0.042 0.169 1370 Planarity : 0.003 0.054 1506 Dihedral : 5.936 68.498 1283 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.80 % Allowed : 20.38 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.26), residues: 1093 helix: 1.62 (0.28), residues: 369 sheet: -0.02 (0.31), residues: 272 loop : -0.57 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.000 HIS B 311 PHE 0.013 0.001 PHE R 239 TYR 0.008 0.001 TYR B 124 ARG 0.013 0.001 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 150 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: R 31 LEU cc_start: 0.7346 (tp) cc_final: 0.7021 (mt) REVERT: R 32 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7414 (tp) REVERT: R 48 ASN cc_start: 0.7774 (m-40) cc_final: 0.7461 (t0) REVERT: R 50 PHE cc_start: 0.7347 (t80) cc_final: 0.7069 (t80) REVERT: R 58 ARG cc_start: 0.6058 (ttm-80) cc_final: 0.5120 (ttt180) REVERT: A 193 ASP cc_start: 0.7232 (t0) cc_final: 0.6846 (t0) REVERT: A 205 ARG cc_start: 0.7148 (mpp-170) cc_final: 0.6918 (pmm150) REVERT: B 12 GLU cc_start: 0.8025 (pp20) cc_final: 0.7721 (pp20) REVERT: B 101 MET cc_start: 0.8647 (mtp) cc_final: 0.8258 (mtp) REVERT: B 111 TYR cc_start: 0.9017 (m-80) cc_final: 0.8798 (m-80) outliers start: 17 outliers final: 7 residues processed: 156 average time/residue: 1.1256 time to fit residues: 187.3616 Evaluate side-chains 153 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 145 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain S residue 84 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 91 optimal weight: 0.5980 chunk 96 optimal weight: 10.0000 chunk 63 optimal weight: 0.5980 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 304 GLN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8904 Z= 0.351 Angle : 0.701 11.450 12070 Z= 0.341 Chirality : 0.045 0.170 1370 Planarity : 0.004 0.059 1506 Dihedral : 6.249 67.426 1283 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.23 % Allowed : 20.49 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.26), residues: 1093 helix: 1.47 (0.28), residues: 371 sheet: -0.13 (0.30), residues: 279 loop : -0.71 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS B 54 PHE 0.012 0.001 PHE A 189 TYR 0.012 0.002 TYR B 59 ARG 0.013 0.001 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 147 time to evaluate : 1.088 Fit side-chains revert: symmetry clash REVERT: R 31 LEU cc_start: 0.7185 (tp) cc_final: 0.6815 (mt) REVERT: R 32 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7479 (tp) REVERT: R 50 PHE cc_start: 0.7470 (t80) cc_final: 0.7165 (t80) REVERT: R 58 ARG cc_start: 0.6036 (ttm-80) cc_final: 0.5152 (ttt180) REVERT: A 193 ASP cc_start: 0.7327 (t0) cc_final: 0.6892 (t0) REVERT: B 12 GLU cc_start: 0.8050 (pp20) cc_final: 0.7722 (pp20) REVERT: B 59 TYR cc_start: 0.8755 (m-80) cc_final: 0.8550 (m-80) REVERT: B 101 MET cc_start: 0.8668 (mtp) cc_final: 0.8351 (mtp) REVERT: B 111 TYR cc_start: 0.9097 (m-80) cc_final: 0.8861 (m-80) REVERT: B 217 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7463 (pmt) REVERT: S 13 GLN cc_start: 0.8638 (mm110) cc_final: 0.8378 (mm-40) outliers start: 21 outliers final: 9 residues processed: 156 average time/residue: 1.2265 time to fit residues: 203.6917 Evaluate side-chains 151 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 140 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 84 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 107 optimal weight: 7.9990 chunk 99 optimal weight: 0.7980 chunk 85 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 66 optimal weight: 0.0670 chunk 52 optimal weight: 3.9990 chunk 68 optimal weight: 0.3980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 304 GLN S 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8904 Z= 0.168 Angle : 0.644 12.670 12070 Z= 0.307 Chirality : 0.042 0.170 1370 Planarity : 0.003 0.054 1506 Dihedral : 5.872 68.534 1283 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.06 % Allowed : 21.97 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.26), residues: 1093 helix: 1.62 (0.28), residues: 373 sheet: -0.01 (0.31), residues: 272 loop : -0.47 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.000 HIS B 54 PHE 0.026 0.001 PHE R 39 TYR 0.011 0.001 TYR B 124 ARG 0.014 0.001 ARG A 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 151 time to evaluate : 0.966 Fit side-chains REVERT: R 31 LEU cc_start: 0.7353 (tp) cc_final: 0.7004 (mt) REVERT: R 32 ILE cc_start: 0.7779 (OUTLIER) cc_final: 0.7520 (tp) REVERT: R 48 ASN cc_start: 0.7713 (m-40) cc_final: 0.7426 (t0) REVERT: R 58 ARG cc_start: 0.6045 (ttm-80) cc_final: 0.5147 (ttt180) REVERT: A 193 ASP cc_start: 0.7235 (t0) cc_final: 0.6859 (t0) REVERT: A 331 ASN cc_start: 0.7155 (m110) cc_final: 0.6810 (m110) REVERT: B 12 GLU cc_start: 0.8025 (pp20) cc_final: 0.7673 (pp20) REVERT: B 101 MET cc_start: 0.8689 (mtp) cc_final: 0.8306 (mtp) REVERT: B 111 TYR cc_start: 0.8984 (m-80) cc_final: 0.8760 (m-80) REVERT: B 217 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7759 (ppp) REVERT: S 13 GLN cc_start: 0.8563 (mm110) cc_final: 0.8197 (mm-40) REVERT: S 89 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7727 (pm20) outliers start: 10 outliers final: 2 residues processed: 153 average time/residue: 1.2477 time to fit residues: 203.6686 Evaluate side-chains 151 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 146 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 89 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.0670 chunk 26 optimal weight: 0.1980 chunk 79 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 0.0060 chunk 85 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 75 optimal weight: 0.0030 overall best weight: 0.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 304 GLN S 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.138749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.101164 restraints weight = 12630.289| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.33 r_work: 0.3146 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8904 Z= 0.155 Angle : 0.629 10.680 12070 Z= 0.300 Chirality : 0.041 0.174 1370 Planarity : 0.003 0.060 1506 Dihedral : 5.716 69.725 1283 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.96 % Allowed : 22.29 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.26), residues: 1093 helix: 1.77 (0.28), residues: 372 sheet: 0.15 (0.30), residues: 277 loop : -0.40 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.002 0.000 HIS S 35 PHE 0.010 0.001 PHE A 189 TYR 0.010 0.001 TYR S 178 ARG 0.014 0.001 ARG A 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3864.29 seconds wall clock time: 69 minutes 16.69 seconds (4156.69 seconds total)