Starting phenix.real_space_refine on Wed Feb 14 06:24:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpf_0744/02_2024/6kpf_0744_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpf_0744/02_2024/6kpf_0744.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/6kpf_0744/02_2024/6kpf_0744.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpf_0744/02_2024/6kpf_0744.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpf_0744/02_2024/6kpf_0744_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpf_0744/02_2024/6kpf_0744_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= 0.000 sd= 0.005 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 66 5.16 5 C 5599 2.51 5 N 1493 2.21 5 O 1617 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A ASP 9": "OD1" <-> "OD2" Residue "A GLU 25": "OE1" <-> "OE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A ASP 261": "OD1" <-> "OD2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B ASP 27": "OD1" <-> "OD2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "R ARG 65": "NH1" <-> "NH2" Residue "R ARG 66": "NH1" <-> "NH2" Residue "R ASP 80": "OD1" <-> "OD2" Residue "R ARG 131": "NH1" <-> "NH2" Residue "R ARG 136": "NH1" <-> "NH2" Residue "R ARG 147": "NH1" <-> "NH2" Residue "R ARG 149": "NH1" <-> "NH2" Residue "R PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 189": "OD1" <-> "OD2" Residue "R ARG 238": "NH1" <-> "NH2" Residue "R ARG 302": "NH1" <-> "NH2" Residue "S ARG 98": "NH1" <-> "NH2" Residue "S ARG 148": "NH1" <-> "NH2" Residue "S TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 206": "NH1" <-> "NH2" Residue "S GLU 208": "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: 8775 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1708 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2590 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2250 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 278} Chain breaks: 1 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: "S" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1760 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'E3R': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.52, per 1000 atoms: 0.63 Number of scatterers: 8775 At special positions: 0 Unit cell: (118.56, 100.88, 120.64, 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 66 16.00 O 1617 8.00 N 1493 7.00 C 5599 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 174 " - pdb=" SG CYS R 179 " distance=2.05 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 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: 3.35 Conformation dependent library (CDL) restraints added in 1.8 seconds 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 13 sheets defined 30.7% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 7 through 31 removed outlier: 3.514A pdb=" N ALA A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 278 removed outlier: 3.919A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 307 removed outlier: 3.936A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'B' and resid 4 through 23 removed outlier: 3.757A pdb=" N ASN B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.731A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 8 through 23 removed outlier: 3.724A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 removed outlier: 3.717A pdb=" N TYR C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 60 removed outlier: 4.424A pdb=" N LEU R 39 " --> pdb=" O ALA R 35 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU R 46 " --> pdb=" O LEU R 42 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL R 52 " --> pdb=" O ALA R 48 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU R 59 " --> pdb=" O LEU R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 65 No H-bonds generated for 'chain 'R' and resid 62 through 65' Processing helix chain 'R' and resid 70 through 85 Processing helix chain 'R' and resid 87 through 95 removed outlier: 3.638A pdb=" N VAL R 92 " --> pdb=" O ALA R 88 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE R 94 " --> pdb=" O SER R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 132 removed outlier: 3.840A pdb=" N THR R 116 " --> pdb=" O SER R 112 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER R 120 " --> pdb=" O THR R 116 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 144 No H-bonds generated for 'chain 'R' and resid 141 through 144' Processing helix chain 'R' and resid 147 through 163 removed outlier: 3.522A pdb=" N THR R 153 " --> pdb=" O ARG R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 215 removed outlier: 3.811A pdb=" N SER R 193 " --> pdb=" O ASP R 189 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU R 196 " --> pdb=" O LEU R 192 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE R 197 " --> pdb=" O SER R 193 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE R 200 " --> pdb=" O LEU R 196 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR R 207 " --> pdb=" O SER R 203 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 220 through 223 No H-bonds generated for 'chain 'R' and resid 220 through 223' Processing helix chain 'R' and resid 239 through 244 Processing helix chain 'R' and resid 246 through 253 removed outlier: 3.674A pdb=" N LEU R 251 " --> pdb=" O LEU R 247 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL R 253 " --> pdb=" O LEU R 249 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 268 removed outlier: 5.346A pdb=" N LEU R 264 " --> pdb=" O PRO R 260 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET R 265 " --> pdb=" O VAL R 261 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER R 268 " --> pdb=" O LEU R 264 " (cutoff:3.500A) Processing helix chain 'R' and resid 278 through 290 removed outlier: 4.458A pdb=" N ALA R 282 " --> pdb=" O LYS R 278 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET R 286 " --> pdb=" O ALA R 282 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU R 287 " --> pdb=" O PHE R 283 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N CYS R 288 " --> pdb=" O CYS R 284 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU R 289 " --> pdb=" O SER R 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 299 Processing helix chain 'R' and resid 304 through 315 removed outlier: 3.531A pdb=" N SER R 309 " --> pdb=" O GLU R 305 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU R 314 " --> pdb=" O ALA R 310 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ALA R 315 " --> pdb=" O HIS R 311 " (cutoff:3.500A) 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 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing helix chain 'S' and resid 209 through 211 No H-bonds generated for 'chain 'S' and resid 209 through 211' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.726A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.718A 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: 6.750A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.793A 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: 6.853A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.971A 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: 6.677A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.898A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.602A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 307 through 309 removed outlier: 4.159A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.490A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.646A 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: 5.996A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.641A 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: 6.596A 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 213 through 219 removed outlier: 6.075A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ARG S 168 " --> pdb=" O PRO S 173 " (cutoff:3.500A) 337 hydrogen bonds defined for protein. 966 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: 2.67 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1401 1.29 - 1.43: 2404 1.43 - 1.57: 5061 1.57 - 1.70: 1 1.70 - 1.84: 95 Bond restraints: 8962 Sorted by residual: bond pdb=" CA ILE R 186 " pdb=" CB ILE R 186 " ideal model delta sigma weight residual 1.537 1.565 -0.028 1.29e-02 6.01e+03 4.74e+00 bond pdb=" N THR A 4 " pdb=" CA THR A 4 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.29e-02 6.01e+03 4.22e+00 bond pdb=" CG1 ILE B 81 " pdb=" CD1 ILE B 81 " ideal model delta sigma weight residual 1.513 1.433 0.080 3.90e-02 6.57e+02 4.17e+00 bond pdb=" C LEU R 167 " pdb=" N PRO R 168 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.40e+00 bond pdb=" C4 E3R R 401 " pdb=" C5 E3R R 401 " ideal model delta sigma weight residual 1.399 1.435 -0.036 2.00e-02 2.50e+03 3.28e+00 ... (remaining 8957 not shown) Histogram of bond angle deviations from ideal: 99.21 - 114.91: 5591 114.91 - 130.61: 6506 130.61 - 146.32: 51 146.32 - 162.02: 0 162.02 - 177.72: 1 Bond angle restraints: 12149 Sorted by residual: angle pdb=" CA CYS R 179 " pdb=" CB CYS R 179 " pdb=" SG CYS R 179 " ideal model delta sigma weight residual 114.40 126.55 -12.15 2.30e+00 1.89e-01 2.79e+01 angle pdb=" C PRO R 178 " pdb=" N CYS R 179 " pdb=" CA CYS R 179 " ideal model delta sigma weight residual 121.54 130.54 -9.00 1.91e+00 2.74e-01 2.22e+01 angle pdb=" C11 E3R R 401 " pdb=" C10 E3R R 401 " pdb=" C7 E3R R 401 " ideal model delta sigma weight residual 111.05 124.27 -13.22 3.00e+00 1.11e-01 1.94e+01 angle pdb=" C TYR S 178 " pdb=" N ARG S 179 " pdb=" CA ARG S 179 " ideal model delta sigma weight residual 122.03 113.59 8.44 2.01e+00 2.48e-01 1.76e+01 angle pdb=" C3 E3R R 401 " pdb=" C4 E3R R 401 " pdb=" O3 E3R R 401 " ideal model delta sigma weight residual 120.37 108.10 12.27 3.00e+00 1.11e-01 1.67e+01 ... (remaining 12144 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.06: 4759 18.06 - 36.12: 469 36.12 - 54.18: 84 54.18 - 72.24: 12 72.24 - 90.30: 9 Dihedral angle restraints: 5333 sinusoidal: 2049 harmonic: 3284 Sorted by residual: dihedral pdb=" CA PRO R 178 " pdb=" C PRO R 178 " pdb=" N CYS R 179 " pdb=" CA CYS R 179 " ideal model delta harmonic sigma weight residual 180.00 124.09 55.91 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CB CYS R 174 " pdb=" SG CYS R 174 " pdb=" SG CYS R 179 " pdb=" CB CYS R 179 " ideal model delta sinusoidal sigma weight residual -86.00 -6.95 -79.05 1 1.00e+01 1.00e-02 7.78e+01 dihedral pdb=" CA TRP B 332 " pdb=" C TRP B 332 " pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta harmonic sigma weight residual 180.00 150.43 29.57 0 5.00e+00 4.00e-02 3.50e+01 ... (remaining 5330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1126 0.063 - 0.126: 229 0.126 - 0.189: 27 0.189 - 0.252: 6 0.252 - 0.315: 2 Chirality restraints: 1390 Sorted by residual: chirality pdb=" C11 E3R R 401 " pdb=" C10 E3R R 401 " pdb=" C12 E3R R 401 " pdb=" C14 E3R R 401 " both_signs ideal model delta sigma weight residual False -2.57 -2.89 0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" C8 E3R R 401 " pdb=" C13 E3R R 401 " pdb=" C7 E3R R 401 " pdb=" C9 E3R R 401 " both_signs ideal model delta sigma weight residual False 2.42 2.73 -0.31 2.00e-01 2.50e+01 2.47e+00 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 -2.35 -0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 1387 not shown) Planarity restraints: 1521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 167 " -0.060 5.00e-02 4.00e+02 9.14e-02 1.34e+01 pdb=" N PRO R 168 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO R 168 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO R 168 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE R 259 " -0.046 5.00e-02 4.00e+02 6.83e-02 7.47e+00 pdb=" N PRO R 260 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO R 260 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO R 260 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE R 186 " -0.043 5.00e-02 4.00e+02 6.56e-02 6.88e+00 pdb=" N PRO R 187 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO R 187 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO R 187 " -0.036 5.00e-02 4.00e+02 ... (remaining 1518 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1271 2.75 - 3.29: 7806 3.29 - 3.83: 15167 3.83 - 4.36: 18614 4.36 - 4.90: 31687 Nonbonded interactions: 74545 Sorted by model distance: nonbonded pdb=" OG1 THR B 128 " pdb=" O ARG B 129 " model vdw 2.215 2.440 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.235 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.241 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.245 2.440 nonbonded pdb=" O SER R 161 " pdb=" OG SER R 165 " model vdw 2.258 2.440 ... (remaining 74540 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: 0.810 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: 0.000 Extract box with map and model: 4.220 Check model and map are aligned: 0.150 Set scattering table: 0.080 Process input model: 28.330 Find NCS groups from input model: 0.260 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: 0.010 Load rotamer database and sin/cos tables:13.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 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 : 0.007 0.080 8962 Z= 0.451 Angle : 0.909 13.222 12149 Z= 0.468 Chirality : 0.054 0.315 1390 Planarity : 0.007 0.091 1521 Dihedral : 14.925 90.302 3206 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.39 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -4.46 (0.20), residues: 1117 helix: -4.64 (0.09), residues: 384 sheet: -1.43 (0.28), residues: 285 loop : -2.14 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 63 HIS 0.005 0.001 HIS A 188 PHE 0.020 0.002 PHE S 27 TYR 0.032 0.002 TYR S 178 ARG 0.004 0.000 ARG S 179 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.924 Fit side-chains REVERT: A 35 LYS cc_start: 0.8564 (mttp) cc_final: 0.8236 (mtmt) REVERT: B 325 MET cc_start: 0.8453 (tpp) cc_final: 0.8207 (tpp) REVERT: C 20 LYS cc_start: 0.8482 (ttmt) cc_final: 0.8273 (mtmm) REVERT: C 47 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7797 (mt-10) REVERT: C 53 PRO cc_start: 0.7155 (Cg_exo) cc_final: 0.6937 (Cg_endo) REVERT: R 33 LYS cc_start: 0.4799 (ptpt) cc_final: 0.4578 (pttm) REVERT: R 115 MET cc_start: 0.7393 (ttp) cc_final: 0.7078 (ttm) REVERT: R 147 ARG cc_start: 0.6376 (ttt-90) cc_final: 0.5990 (ttt180) REVERT: R 157 MET cc_start: 0.6415 (tpp) cc_final: 0.6183 (tpp) REVERT: R 245 LYS cc_start: 0.6932 (mmpt) cc_final: 0.6726 (mmpt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 1.3764 time to fit residues: 231.7039 Evaluate side-chains 131 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.6980 chunk 84 optimal weight: 8.9990 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 0.2980 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 269 ASN A 322 HIS B 32 GLN B 62 HIS B 91 HIS B 175 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN R 295 ASN S 3 GLN S 182 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8962 Z= 0.191 Angle : 0.566 10.709 12149 Z= 0.296 Chirality : 0.042 0.159 1390 Planarity : 0.005 0.068 1521 Dihedral : 5.902 58.907 1264 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.78 % Favored : 97.05 % Rotamer: Outliers : 2.23 % Allowed : 18.51 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.88 (0.22), residues: 1117 helix: -2.61 (0.20), residues: 376 sheet: -1.01 (0.29), residues: 267 loop : -1.65 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.003 0.001 HIS R 95 PHE 0.015 0.001 PHE A 189 TYR 0.017 0.001 TYR S 178 ARG 0.005 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 143 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8508 (mttp) cc_final: 0.8170 (mtmt) REVERT: A 198 MET cc_start: 0.7422 (mtm) cc_final: 0.7217 (ttp) REVERT: B 23 LYS cc_start: 0.8467 (ttmt) cc_final: 0.8210 (tptt) REVERT: B 46 ARG cc_start: 0.7758 (mmt-90) cc_final: 0.7463 (tpp-160) REVERT: B 161 SER cc_start: 0.9138 (p) cc_final: 0.8915 (p) REVERT: C 46 LYS cc_start: 0.8554 (mmtm) cc_final: 0.8125 (mmtt) REVERT: C 47 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7745 (mt-10) REVERT: S 39 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8237 (tt0) outliers start: 21 outliers final: 6 residues processed: 155 average time/residue: 1.3681 time to fit residues: 224.5339 Evaluate side-chains 138 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 131 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 39 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 0.0980 chunk 99 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS A 304 GLN A 322 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN S 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8962 Z= 0.197 Angle : 0.552 10.773 12149 Z= 0.283 Chirality : 0.041 0.143 1390 Planarity : 0.004 0.064 1521 Dihedral : 5.433 58.295 1264 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.49 % Favored : 96.42 % Rotamer: Outliers : 3.40 % Allowed : 19.89 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.00 (0.23), residues: 1117 helix: -1.41 (0.24), residues: 386 sheet: -0.87 (0.29), residues: 260 loop : -1.34 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.002 0.001 HIS R 95 PHE 0.014 0.001 PHE A 189 TYR 0.019 0.001 TYR S 178 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 135 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8527 (mttp) cc_final: 0.8182 (mtmt) REVERT: B 23 LYS cc_start: 0.8457 (ttmt) cc_final: 0.8197 (tptt) REVERT: B 46 ARG cc_start: 0.7767 (mmt-90) cc_final: 0.7512 (tpp-160) REVERT: B 134 ARG cc_start: 0.7511 (ptt-90) cc_final: 0.7249 (ptt-90) REVERT: B 161 SER cc_start: 0.9149 (p) cc_final: 0.8929 (p) REVERT: C 20 LYS cc_start: 0.8420 (ttpt) cc_final: 0.8206 (mtmm) REVERT: C 47 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7763 (mt-10) REVERT: R 245 LYS cc_start: 0.6973 (mmpt) cc_final: 0.6706 (mmpt) outliers start: 32 outliers final: 12 residues processed: 152 average time/residue: 1.2876 time to fit residues: 207.9283 Evaluate side-chains 141 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 67 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 96 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8962 Z= 0.243 Angle : 0.561 10.935 12149 Z= 0.289 Chirality : 0.042 0.143 1390 Planarity : 0.004 0.061 1521 Dihedral : 5.387 57.640 1264 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.22 % Favored : 96.69 % Rotamer: Outliers : 4.26 % Allowed : 20.64 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.55 (0.24), residues: 1117 helix: -0.77 (0.26), residues: 386 sheet: -0.91 (0.27), residues: 281 loop : -1.13 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS A 244 PHE 0.014 0.001 PHE A 189 TYR 0.022 0.001 TYR S 178 ARG 0.003 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 139 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8568 (mttp) cc_final: 0.8212 (mtmt) REVERT: B 23 LYS cc_start: 0.8466 (ttmt) cc_final: 0.8207 (tptt) REVERT: B 46 ARG cc_start: 0.7780 (mmt-90) cc_final: 0.7418 (tpp-160) REVERT: B 161 SER cc_start: 0.9147 (p) cc_final: 0.8928 (p) REVERT: B 234 PHE cc_start: 0.9458 (OUTLIER) cc_final: 0.8723 (m-80) REVERT: C 20 LYS cc_start: 0.8450 (ttpt) cc_final: 0.8206 (mtmm) REVERT: C 47 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7740 (mt-10) REVERT: R 169 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7365 (pt) REVERT: R 245 LYS cc_start: 0.7003 (mmpt) cc_final: 0.6742 (mmpt) REVERT: S 19 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8501 (tttt) outliers start: 40 outliers final: 21 residues processed: 164 average time/residue: 1.1902 time to fit residues: 208.3238 Evaluate side-chains 157 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 211 HIS Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN A 322 HIS ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8962 Z= 0.244 Angle : 0.564 11.488 12149 Z= 0.287 Chirality : 0.042 0.178 1390 Planarity : 0.004 0.060 1521 Dihedral : 5.382 55.456 1264 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.67 % Favored : 96.15 % Rotamer: Outliers : 4.57 % Allowed : 21.91 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.14 (0.25), residues: 1117 helix: -0.30 (0.27), residues: 380 sheet: -0.84 (0.27), residues: 282 loop : -0.90 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS A 244 PHE 0.014 0.001 PHE A 189 TYR 0.021 0.001 TYR S 178 ARG 0.002 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 135 time to evaluate : 1.056 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8554 (mttp) cc_final: 0.8190 (mtmt) REVERT: A 243 MET cc_start: 0.8264 (ttp) cc_final: 0.8015 (mtm) REVERT: B 23 LYS cc_start: 0.8447 (ttmt) cc_final: 0.8202 (tptt) REVERT: B 46 ARG cc_start: 0.7817 (mmt-90) cc_final: 0.7434 (tpp-160) REVERT: B 161 SER cc_start: 0.9128 (p) cc_final: 0.8902 (p) REVERT: B 234 PHE cc_start: 0.9457 (OUTLIER) cc_final: 0.8795 (m-80) REVERT: C 20 LYS cc_start: 0.8454 (ttpt) cc_final: 0.8226 (mtmm) REVERT: C 47 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7733 (mt-10) REVERT: R 245 LYS cc_start: 0.7019 (mmpt) cc_final: 0.6773 (mmpt) REVERT: R 286 MET cc_start: 0.4483 (OUTLIER) cc_final: 0.4237 (mtp) REVERT: S 19 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8502 (tttt) REVERT: S 207 LEU cc_start: 0.8666 (tt) cc_final: 0.8230 (pp) outliers start: 43 outliers final: 27 residues processed: 164 average time/residue: 1.2285 time to fit residues: 214.6194 Evaluate side-chains 161 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 131 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain R residue 211 HIS Chi-restraints excluded: chain R residue 286 MET Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 56 optimal weight: 0.0050 chunk 103 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN A 331 ASN B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8962 Z= 0.211 Angle : 0.558 10.971 12149 Z= 0.281 Chirality : 0.042 0.190 1390 Planarity : 0.004 0.060 1521 Dihedral : 5.280 53.350 1264 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.04 % Favored : 96.78 % Rotamer: Outliers : 4.68 % Allowed : 22.98 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.94 (0.25), residues: 1117 helix: -0.04 (0.27), residues: 383 sheet: -0.71 (0.29), residues: 256 loop : -0.92 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS B 62 PHE 0.014 0.001 PHE A 189 TYR 0.019 0.001 TYR S 178 ARG 0.006 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 136 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8562 (mttp) cc_final: 0.8224 (mtmt) REVERT: B 23 LYS cc_start: 0.8438 (ttmt) cc_final: 0.8190 (tptt) REVERT: B 46 ARG cc_start: 0.7809 (mmt-90) cc_final: 0.7430 (tpp-160) REVERT: B 161 SER cc_start: 0.9124 (p) cc_final: 0.8894 (p) REVERT: B 234 PHE cc_start: 0.9452 (OUTLIER) cc_final: 0.8786 (m-80) REVERT: C 20 LYS cc_start: 0.8441 (ttpt) cc_final: 0.8214 (mtmm) REVERT: C 47 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7750 (mt-10) REVERT: R 245 LYS cc_start: 0.6986 (mmpt) cc_final: 0.6760 (mmpt) REVERT: R 286 MET cc_start: 0.4433 (OUTLIER) cc_final: 0.4152 (mtp) REVERT: S 19 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8515 (tttt) outliers start: 44 outliers final: 29 residues processed: 165 average time/residue: 1.1568 time to fit residues: 203.9690 Evaluate side-chains 167 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 135 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 211 HIS Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 286 MET Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 187 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 0.0270 chunk 66 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.5444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 304 GLN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8962 Z= 0.211 Angle : 0.558 10.971 12149 Z= 0.281 Chirality : 0.042 0.190 1390 Planarity : 0.004 0.060 1521 Dihedral : 5.280 53.350 1264 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.04 % Favored : 96.78 % Rotamer: Outliers : 3.51 % Allowed : 24.04 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.94 (0.25), residues: 1117 helix: -0.04 (0.27), residues: 383 sheet: -0.71 (0.29), residues: 256 loop : -0.92 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS B 62 PHE 0.014 0.001 PHE A 189 TYR 0.019 0.001 TYR S 178 ARG 0.006 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 135 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8565 (mttp) cc_final: 0.8224 (mtmt) REVERT: B 23 LYS cc_start: 0.8438 (ttmt) cc_final: 0.8190 (tptt) REVERT: B 46 ARG cc_start: 0.7807 (mmt-90) cc_final: 0.7430 (tpp-160) REVERT: B 161 SER cc_start: 0.9124 (p) cc_final: 0.8894 (p) REVERT: B 234 PHE cc_start: 0.9453 (OUTLIER) cc_final: 0.8786 (m-80) REVERT: C 20 LYS cc_start: 0.8441 (ttpt) cc_final: 0.8214 (mtmm) REVERT: C 47 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7750 (mt-10) REVERT: R 245 LYS cc_start: 0.6985 (mmpt) cc_final: 0.6760 (mmpt) REVERT: R 286 MET cc_start: 0.4420 (OUTLIER) cc_final: 0.4152 (mtp) REVERT: S 19 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8521 (tttt) outliers start: 33 outliers final: 29 residues processed: 155 average time/residue: 1.2185 time to fit residues: 201.4996 Evaluate side-chains 167 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 135 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 211 HIS Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 286 MET Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 187 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8962 Z= 0.211 Angle : 0.558 10.971 12149 Z= 0.281 Chirality : 0.042 0.190 1390 Planarity : 0.004 0.060 1521 Dihedral : 5.280 53.350 1264 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.04 % Favored : 96.78 % Rotamer: Outliers : 3.51 % Allowed : 24.04 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.94 (0.25), residues: 1117 helix: -0.04 (0.27), residues: 383 sheet: -0.71 (0.29), residues: 256 loop : -0.92 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS B 62 PHE 0.014 0.001 PHE A 189 TYR 0.019 0.001 TYR S 178 ARG 0.006 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 135 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8565 (mttp) cc_final: 0.8224 (mtmt) REVERT: B 23 LYS cc_start: 0.8438 (ttmt) cc_final: 0.8190 (tptt) REVERT: B 46 ARG cc_start: 0.7807 (mmt-90) cc_final: 0.7430 (tpp-160) REVERT: B 161 SER cc_start: 0.9124 (p) cc_final: 0.8894 (p) REVERT: B 234 PHE cc_start: 0.9453 (OUTLIER) cc_final: 0.8786 (m-80) REVERT: C 20 LYS cc_start: 0.8441 (ttpt) cc_final: 0.8214 (mtmm) REVERT: C 47 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7750 (mt-10) REVERT: R 245 LYS cc_start: 0.6985 (mmpt) cc_final: 0.6760 (mmpt) REVERT: R 286 MET cc_start: 0.4420 (OUTLIER) cc_final: 0.4152 (mtp) REVERT: S 19 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8521 (tttt) outliers start: 33 outliers final: 29 residues processed: 155 average time/residue: 1.1861 time to fit residues: 196.2645 Evaluate side-chains 167 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 135 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 211 HIS Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 286 MET Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 187 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8962 Z= 0.211 Angle : 0.558 10.971 12149 Z= 0.281 Chirality : 0.042 0.190 1390 Planarity : 0.004 0.060 1521 Dihedral : 5.280 53.350 1264 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.04 % Favored : 96.78 % Rotamer: Outliers : 3.51 % Allowed : 24.04 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.94 (0.25), residues: 1117 helix: -0.04 (0.27), residues: 383 sheet: -0.71 (0.29), residues: 256 loop : -0.92 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS B 62 PHE 0.014 0.001 PHE A 189 TYR 0.019 0.001 TYR S 178 ARG 0.006 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 135 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8565 (mttp) cc_final: 0.8224 (mtmt) REVERT: B 23 LYS cc_start: 0.8438 (ttmt) cc_final: 0.8190 (tptt) REVERT: B 46 ARG cc_start: 0.7807 (mmt-90) cc_final: 0.7430 (tpp-160) REVERT: B 161 SER cc_start: 0.9124 (p) cc_final: 0.8894 (p) REVERT: B 234 PHE cc_start: 0.9453 (OUTLIER) cc_final: 0.8786 (m-80) REVERT: C 20 LYS cc_start: 0.8441 (ttpt) cc_final: 0.8214 (mtmm) REVERT: C 47 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7750 (mt-10) REVERT: R 245 LYS cc_start: 0.6985 (mmpt) cc_final: 0.6760 (mmpt) REVERT: R 286 MET cc_start: 0.4420 (OUTLIER) cc_final: 0.4152 (mtp) REVERT: S 19 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8521 (tttt) outliers start: 33 outliers final: 29 residues processed: 155 average time/residue: 1.1898 time to fit residues: 197.0573 Evaluate side-chains 167 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 135 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 211 HIS Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 286 MET Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 187 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 53 optimal weight: 0.1980 chunk 69 optimal weight: 0.7980 chunk 93 optimal weight: 0.2980 chunk 26 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8962 Z= 0.211 Angle : 0.558 10.971 12149 Z= 0.281 Chirality : 0.042 0.190 1390 Planarity : 0.004 0.060 1521 Dihedral : 5.280 53.350 1264 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.04 % Favored : 96.78 % Rotamer: Outliers : 3.51 % Allowed : 24.04 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.94 (0.25), residues: 1117 helix: -0.04 (0.27), residues: 383 sheet: -0.71 (0.29), residues: 256 loop : -0.92 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS B 62 PHE 0.014 0.001 PHE A 189 TYR 0.019 0.001 TYR S 178 ARG 0.006 0.000 ARG A 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 135 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8565 (mttp) cc_final: 0.8224 (mtmt) REVERT: B 23 LYS cc_start: 0.8438 (ttmt) cc_final: 0.8190 (tptt) REVERT: B 46 ARG cc_start: 0.7807 (mmt-90) cc_final: 0.7430 (tpp-160) REVERT: B 161 SER cc_start: 0.9124 (p) cc_final: 0.8894 (p) REVERT: B 234 PHE cc_start: 0.9453 (OUTLIER) cc_final: 0.8786 (m-80) REVERT: C 20 LYS cc_start: 0.8441 (ttpt) cc_final: 0.8214 (mtmm) REVERT: C 47 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7750 (mt-10) REVERT: R 245 LYS cc_start: 0.6985 (mmpt) cc_final: 0.6760 (mmpt) REVERT: R 286 MET cc_start: 0.4420 (OUTLIER) cc_final: 0.4152 (mtp) REVERT: S 19 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8521 (tttt) outliers start: 33 outliers final: 29 residues processed: 155 average time/residue: 1.2286 time to fit residues: 203.2827 Evaluate side-chains 167 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 135 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 211 HIS Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 286 MET Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 187 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 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 304 GLN A 333 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.159719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.105236 restraints weight = 9808.243| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.12 r_work: 0.2949 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8962 Z= 0.203 Angle : 0.582 10.837 12149 Z= 0.289 Chirality : 0.042 0.188 1390 Planarity : 0.004 0.057 1521 Dihedral : 5.239 53.322 1264 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.22 % Favored : 96.60 % Rotamer: Outliers : 4.04 % Allowed : 23.72 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.80 (0.25), residues: 1117 helix: 0.16 (0.28), residues: 383 sheet: -0.70 (0.29), residues: 256 loop : -0.87 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS A 244 PHE 0.013 0.001 PHE A 189 TYR 0.021 0.001 TYR B 59 ARG 0.007 0.000 ARG A 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3953.77 seconds wall clock time: 70 minutes 49.81 seconds (4249.81 seconds total)