Starting phenix.real_space_refine on Wed Feb 14 04:28:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdl_31922/02_2024/7vdl_31922_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdl_31922/02_2024/7vdl_31922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdl_31922/02_2024/7vdl_31922.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdl_31922/02_2024/7vdl_31922.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdl_31922/02_2024/7vdl_31922_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdl_31922/02_2024/7vdl_31922_updated.pdb" } resolution = 3.22 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= 0.006 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 5513 2.51 5 N 1440 2.21 5 O 1581 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 ARG 21": "NH1" <-> "NH2" 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 PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 231": "OD1" <-> "OD2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 272": "OD1" <-> "OD2" Residue "A PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 337": "OD1" <-> "OD2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B ASP 258": "OD1" <-> "OD2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "S PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 90": "OD1" <-> "OD2" Residue "S TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 148": "NH1" <-> "NH2" Residue "S TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 211": "OD1" <-> "OD2" Residue "S TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 58": "NH1" <-> "NH2" Residue "R ARG 60": "NH1" <-> "NH2" Residue "R PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 138": "NH1" <-> "NH2" Residue "R ARG 140": "NH1" <-> "NH2" Residue "R ARG 143": "NH1" <-> "NH2" Residue "R PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 184": "OD1" <-> "OD2" Residue "R ARG 208": "NH1" <-> "NH2" Residue "R ARG 214": "NH1" <-> "NH2" Residue "R ARG 220": "NH1" <-> "NH2" Residue "R TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 252": "OD1" <-> "OD2" Residue "R PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 8598 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1727 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 212} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: "C" 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: 2036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2036 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 8, 'TRANS': 247} Chain: "L" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 45 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.11, per 1000 atoms: 0.59 Number of scatterers: 8598 At special positions: 0 Unit cell: (117.52, 104, 106.08, 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 1581 8.00 N 1440 7.00 C 5513 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.07 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.32 Conformation dependent library (CDL) restraints added in 1.7 seconds 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2046 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 14 sheets defined 34.6% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 7 through 31 Processing helix chain 'A' and resid 46 through 53 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 227 through 230 removed outlier: 3.707A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 230' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 271 through 280 removed outlier: 5.520A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 298 through 310 removed outlier: 4.468A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 350 removed outlier: 4.283A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 30 through 43 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 helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing helix chain 'R' and resid 32 through 57 Processing helix chain 'R' and resid 63 through 94 removed outlier: 3.899A pdb=" N TYR R 67 " --> pdb=" O ALA R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 132 Processing helix chain 'R' and resid 134 through 139 Processing helix chain 'R' and resid 145 through 168 Processing helix chain 'R' and resid 177 through 212 removed outlier: 4.007A pdb=" N PHE R 183 " --> pdb=" O TRP R 179 " (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 248 No H-bonds generated for 'chain 'R' and resid 246 through 248' Processing helix chain 'R' and resid 255 through 279 removed outlier: 3.991A pdb=" N HIS R 259 " --> pdb=" O VAL R 255 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N HIS R 261 " --> pdb=" O PHE R 257 " (cutoff:3.500A) Proline residue: R 262 - end of helix removed outlier: 3.540A pdb=" N VAL R 265 " --> pdb=" O HIS R 261 " (cutoff:3.500A) 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 sheet with id= A, first strand: chain 'A' and resid 34 through 38 removed outlier: 3.651A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 223 through 226 Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.913A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.759A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.700A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.546A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.596A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.575A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.555A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.547A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 10 through 12 Processing sheet with id= L, first strand: chain 'S' and resid 95 through 99 removed outlier: 5.900A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.470A pdb=" N LYS S 232 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'S' and resid 143 through 147 387 hydrogen bonds defined for protein. 1116 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: 2.45 Time building geometry restraints manager: 3.51 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: 2693 1.34 - 1.47: 2328 1.47 - 1.60: 3678 1.60 - 1.74: 1 1.74 - 1.87: 88 Bond restraints: 8788 Sorted by residual: bond pdb=" C17 CLR R 401 " pdb=" C20 CLR R 401 " ideal model delta sigma weight residual 1.535 1.647 -0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" CA ARG R 61 " pdb=" C ARG R 61 " ideal model delta sigma weight residual 1.523 1.480 0.043 1.18e-02 7.18e+03 1.34e+01 bond pdb=" C HIS R 261 " pdb=" N PRO R 262 " ideal model delta sigma weight residual 1.336 1.369 -0.033 1.20e-02 6.94e+03 7.45e+00 bond pdb=" CA ARG B 52 " pdb=" CB ARG B 52 " ideal model delta sigma weight residual 1.527 1.589 -0.061 2.48e-02 1.63e+03 6.14e+00 bond pdb=" CA PHE R 281 " pdb=" C PHE R 281 " ideal model delta sigma weight residual 1.524 1.493 0.031 1.29e-02 6.01e+03 5.74e+00 ... (remaining 8783 not shown) Histogram of bond angle deviations from ideal: 95.80 - 103.48: 73 103.48 - 111.15: 3288 111.15 - 118.83: 3664 118.83 - 126.51: 4740 126.51 - 134.18: 148 Bond angle restraints: 11913 Sorted by residual: angle pdb=" N TYR R 279 " pdb=" CA TYR R 279 " pdb=" C TYR R 279 " ideal model delta sigma weight residual 111.36 119.24 -7.88 1.09e+00 8.42e-01 5.23e+01 angle pdb=" N ILE R 278 " pdb=" CA ILE R 278 " pdb=" C ILE R 278 " ideal model delta sigma weight residual 110.42 117.13 -6.71 9.60e-01 1.09e+00 4.88e+01 angle pdb=" N ARG R 61 " pdb=" CA ARG R 61 " pdb=" C ARG R 61 " ideal model delta sigma weight residual 109.95 119.88 -9.93 1.59e+00 3.96e-01 3.90e+01 angle pdb=" N PHE R 281 " pdb=" CA PHE R 281 " pdb=" C PHE R 281 " ideal model delta sigma weight residual 111.36 117.45 -6.09 1.09e+00 8.42e-01 3.12e+01 angle pdb=" CA CYS B 149 " pdb=" CB CYS B 149 " pdb=" SG CYS B 149 " ideal model delta sigma weight residual 114.40 127.06 -12.66 2.30e+00 1.89e-01 3.03e+01 ... (remaining 11908 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4717 17.97 - 35.93: 412 35.93 - 53.90: 66 53.90 - 71.86: 10 71.86 - 89.83: 5 Dihedral angle restraints: 5210 sinusoidal: 2038 harmonic: 3172 Sorted by residual: dihedral pdb=" CA THR A 295 " pdb=" C THR A 295 " pdb=" N TYR A 296 " pdb=" CA TYR A 296 " ideal model delta harmonic sigma weight residual 180.00 153.87 26.13 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" N ASN L 24 " pdb=" C ASN L 24 " pdb=" CA ASN L 24 " pdb=" CB ASN L 24 " ideal model delta harmonic sigma weight residual 122.80 135.03 -12.23 0 2.50e+00 1.60e-01 2.39e+01 dihedral pdb=" CA LEU B 261 " pdb=" C LEU B 261 " pdb=" N MET B 262 " pdb=" CA MET B 262 " ideal model delta harmonic sigma weight residual -180.00 -155.84 -24.16 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 5207 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1219 0.104 - 0.208: 121 0.208 - 0.311: 8 0.311 - 0.415: 5 0.415 - 0.519: 5 Chirality restraints: 1358 Sorted by residual: chirality pdb=" CA ASN L 24 " pdb=" N ASN L 24 " pdb=" C ASN L 24 " pdb=" CB ASN L 24 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.73e+00 chirality pdb=" CB ILE R 32 " pdb=" CA ILE R 32 " pdb=" CG1 ILE R 32 " pdb=" CG2 ILE R 32 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" CA ARG R 61 " pdb=" N ARG R 61 " pdb=" C ARG R 61 " pdb=" CB ARG R 61 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.27e+00 ... (remaining 1355 not shown) Planarity restraints: 1490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR S 103 " -0.006 2.00e-02 2.50e+03 2.31e-02 1.07e+01 pdb=" CG TYR S 103 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR S 103 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR S 103 " -0.036 2.00e-02 2.50e+03 pdb=" CE1 TYR S 103 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR S 103 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR S 103 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR S 103 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET S 180 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C MET S 180 " -0.055 2.00e-02 2.50e+03 pdb=" O MET S 180 " 0.021 2.00e-02 2.50e+03 pdb=" N SER S 181 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 52 " 0.050 5.00e-02 4.00e+02 7.59e-02 9.21e+00 pdb=" N PRO C 53 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO C 53 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 53 " 0.042 5.00e-02 4.00e+02 ... (remaining 1487 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 24 2.37 - 3.01: 4243 3.01 - 3.64: 13246 3.64 - 4.27: 20400 4.27 - 4.90: 34068 Nonbonded interactions: 71981 Sorted by model distance: nonbonded pdb=" O PHE R 50 " pdb=" CD1 LEU R 54 " model vdw 1.743 3.460 nonbonded pdb=" CD1 LEU R 120 " pdb=" OH TYR R 279 " model vdw 2.062 3.460 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.214 2.440 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.217 2.440 nonbonded pdb=" O SER S 30 " pdb=" OG SER S 53 " model vdw 2.237 2.440 ... (remaining 71976 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: 0.370 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: 1.710 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.760 Find NCS groups from input model: 0.250 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 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 : 0.008 0.112 8788 Z= 0.502 Angle : 1.158 14.967 11913 Z= 0.619 Chirality : 0.069 0.519 1358 Planarity : 0.007 0.076 1490 Dihedral : 13.815 89.831 3155 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.11 % Allowed : 1.18 % Favored : 98.72 % Cbeta Deviations : 0.10 % 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: -1.82 (0.24), residues: 1082 helix: -1.14 (0.23), residues: 380 sheet: -0.84 (0.31), residues: 277 loop : -1.29 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 297 HIS 0.004 0.002 HIS A 322 PHE 0.043 0.004 PHE R 257 TYR 0.049 0.004 TYR S 103 ARG 0.020 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 218 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ASP cc_start: 0.7046 (t0) cc_final: 0.6772 (t0) REVERT: A 277 LYS cc_start: 0.8203 (mtpt) cc_final: 0.7317 (tptt) REVERT: A 304 GLN cc_start: 0.8266 (tm130) cc_final: 0.8018 (tm-30) REVERT: B 211 TRP cc_start: 0.8839 (m100) cc_final: 0.8396 (m100) REVERT: S 218 MET cc_start: 0.9086 (ttp) cc_final: 0.8818 (ttp) REVERT: R 158 LEU cc_start: 0.7833 (tp) cc_final: 0.7311 (tt) REVERT: R 163 LEU cc_start: 0.7570 (tt) cc_final: 0.7256 (tp) REVERT: R 183 PHE cc_start: 0.4481 (m-80) cc_final: 0.4103 (m-80) REVERT: L 22 CYS cc_start: 0.4938 (p) cc_final: 0.4218 (t) outliers start: 1 outliers final: 0 residues processed: 218 average time/residue: 0.2228 time to fit residues: 64.5784 Evaluate side-chains 198 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.6980 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN B 220 GLN B 340 ASN S 3 GLN L 24 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8788 Z= 0.213 Angle : 0.649 13.455 11913 Z= 0.322 Chirality : 0.044 0.275 1358 Planarity : 0.004 0.051 1490 Dihedral : 6.579 59.142 1245 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.71 % Allowed : 9.52 % Favored : 88.77 % 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: -0.81 (0.25), residues: 1082 helix: 0.26 (0.26), residues: 380 sheet: -0.66 (0.31), residues: 279 loop : -1.05 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 82 HIS 0.002 0.001 HIS S 35 PHE 0.030 0.002 PHE R 50 TYR 0.026 0.002 TYR A 296 ARG 0.005 0.000 ARG R 208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 214 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 ASP cc_start: 0.7189 (t0) cc_final: 0.6845 (t0) REVERT: B 13 GLN cc_start: 0.7514 (tm-30) cc_final: 0.7206 (pt0) REVERT: R 158 LEU cc_start: 0.7854 (tp) cc_final: 0.7400 (tt) REVERT: R 193 PHE cc_start: 0.8064 (t80) cc_final: 0.7771 (t80) outliers start: 16 outliers final: 11 residues processed: 219 average time/residue: 0.2333 time to fit residues: 67.8836 Evaluate side-chains 203 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 192 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain L residue 24 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 33 optimal weight: 0.4980 chunk 78 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 3 GLN L 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8788 Z= 0.206 Angle : 0.614 14.232 11913 Z= 0.305 Chirality : 0.043 0.275 1358 Planarity : 0.004 0.042 1490 Dihedral : 6.284 59.081 1245 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.46 % Allowed : 12.94 % Favored : 84.60 % 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: -0.35 (0.26), residues: 1082 helix: 0.86 (0.27), residues: 380 sheet: -0.54 (0.31), residues: 280 loop : -0.90 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.020 0.001 PHE R 50 TYR 0.026 0.002 TYR R 279 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 204 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 193 ASP cc_start: 0.7073 (t0) cc_final: 0.6760 (t0) REVERT: A 312 LYS cc_start: 0.8137 (mmtp) cc_final: 0.7704 (mmmt) REVERT: B 13 GLN cc_start: 0.7533 (tm-30) cc_final: 0.7162 (pt0) REVERT: R 59 MET cc_start: 0.6612 (OUTLIER) cc_final: 0.6408 (mtm) REVERT: R 158 LEU cc_start: 0.7794 (tp) cc_final: 0.7431 (tt) REVERT: R 183 PHE cc_start: 0.5134 (m-80) cc_final: 0.4835 (m-80) REVERT: R 193 PHE cc_start: 0.8062 (t80) cc_final: 0.7732 (t80) outliers start: 23 outliers final: 15 residues processed: 214 average time/residue: 0.2272 time to fit residues: 64.8453 Evaluate side-chains 207 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 191 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 59 MET Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain L residue 22 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 50 optimal weight: 0.0050 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8788 Z= 0.193 Angle : 0.583 11.926 11913 Z= 0.291 Chirality : 0.042 0.269 1358 Planarity : 0.003 0.038 1490 Dihedral : 6.116 59.005 1245 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.99 % Allowed : 14.22 % Favored : 82.78 % 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: -0.13 (0.26), residues: 1082 helix: 1.11 (0.27), residues: 386 sheet: -0.48 (0.31), residues: 280 loop : -0.82 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 PHE 0.016 0.001 PHE R 50 TYR 0.020 0.002 TYR R 279 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 205 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 ASP cc_start: 0.7116 (t0) cc_final: 0.6781 (t0) REVERT: A 289 GLU cc_start: 0.7811 (pm20) cc_final: 0.7596 (pm20) REVERT: B 13 GLN cc_start: 0.7561 (tm-30) cc_final: 0.7153 (pt0) REVERT: B 23 LYS cc_start: 0.8389 (tppt) cc_final: 0.8189 (tppt) REVERT: S 206 ARG cc_start: 0.6929 (ptt-90) cc_final: 0.6616 (mmp80) REVERT: R 59 MET cc_start: 0.6713 (OUTLIER) cc_final: 0.6437 (mtm) REVERT: R 61 ARG cc_start: 0.5324 (mtm-85) cc_final: 0.4889 (mtm-85) REVERT: R 158 LEU cc_start: 0.7810 (tp) cc_final: 0.7498 (tt) REVERT: R 183 PHE cc_start: 0.5244 (m-80) cc_final: 0.4969 (m-80) REVERT: R 193 PHE cc_start: 0.8046 (t80) cc_final: 0.7789 (t80) outliers start: 28 outliers final: 19 residues processed: 219 average time/residue: 0.2330 time to fit residues: 67.9941 Evaluate side-chains 218 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 198 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 59 MET Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 8.9990 chunk 58 optimal weight: 0.0870 chunk 1 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN S 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8788 Z= 0.177 Angle : 0.582 14.010 11913 Z= 0.291 Chirality : 0.042 0.262 1358 Planarity : 0.003 0.035 1490 Dihedral : 5.977 59.205 1245 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.10 % Allowed : 16.79 % Favored : 80.11 % 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: -0.02 (0.26), residues: 1082 helix: 1.25 (0.27), residues: 386 sheet: -0.41 (0.31), residues: 283 loop : -0.83 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 PHE 0.013 0.001 PHE R 76 TYR 0.016 0.002 TYR R 279 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 201 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ASP cc_start: 0.7103 (t0) cc_final: 0.6761 (t0) REVERT: A 289 GLU cc_start: 0.7823 (pm20) cc_final: 0.7595 (pm20) REVERT: B 13 GLN cc_start: 0.7634 (tm-30) cc_final: 0.7212 (pt0) REVERT: B 23 LYS cc_start: 0.8364 (tppt) cc_final: 0.8156 (tppt) REVERT: S 19 LYS cc_start: 0.7603 (tttp) cc_final: 0.7075 (ttpt) REVERT: S 65 LYS cc_start: 0.8241 (tptt) cc_final: 0.7705 (mmtt) REVERT: S 206 ARG cc_start: 0.6869 (ptt-90) cc_final: 0.6612 (mmp80) REVERT: R 59 MET cc_start: 0.6669 (OUTLIER) cc_final: 0.6442 (mtm) REVERT: R 158 LEU cc_start: 0.7725 (tp) cc_final: 0.7454 (tt) REVERT: R 183 PHE cc_start: 0.5373 (m-80) cc_final: 0.4934 (m-80) REVERT: R 193 PHE cc_start: 0.8033 (t80) cc_final: 0.7764 (t80) outliers start: 29 outliers final: 22 residues processed: 219 average time/residue: 0.2402 time to fit residues: 70.1855 Evaluate side-chains 215 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 192 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain R residue 59 MET Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 chunk 85 optimal weight: 0.0570 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN S 182 ASN R 48 ASN R 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8788 Z= 0.153 Angle : 0.566 12.280 11913 Z= 0.281 Chirality : 0.042 0.250 1358 Planarity : 0.003 0.034 1490 Dihedral : 5.715 58.463 1245 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.10 % Allowed : 18.29 % Favored : 78.61 % 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: 0.15 (0.26), residues: 1082 helix: 1.44 (0.27), residues: 386 sheet: -0.29 (0.32), residues: 281 loop : -0.81 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.000 HIS S 35 PHE 0.011 0.001 PHE R 104 TYR 0.017 0.001 TYR S 95 ARG 0.002 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 204 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.7452 (ttt) REVERT: A 289 GLU cc_start: 0.7826 (pm20) cc_final: 0.7573 (pm20) REVERT: B 13 GLN cc_start: 0.7729 (tm-30) cc_final: 0.7350 (pt0) REVERT: B 23 LYS cc_start: 0.8349 (tppt) cc_final: 0.8129 (tppt) REVERT: S 19 LYS cc_start: 0.7547 (tttp) cc_final: 0.7144 (ttpt) REVERT: S 23 SER cc_start: 0.8290 (p) cc_final: 0.7852 (m) REVERT: S 65 LYS cc_start: 0.8207 (tptt) cc_final: 0.7666 (mmtt) REVERT: S 80 PHE cc_start: 0.7299 (OUTLIER) cc_final: 0.5736 (p90) REVERT: S 206 ARG cc_start: 0.6869 (ptt-90) cc_final: 0.6533 (mmp80) REVERT: R 59 MET cc_start: 0.6618 (OUTLIER) cc_final: 0.6382 (mtm) REVERT: R 120 LEU cc_start: 0.8244 (mt) cc_final: 0.8040 (mt) REVERT: R 183 PHE cc_start: 0.5255 (m-80) cc_final: 0.4798 (m-80) REVERT: R 193 PHE cc_start: 0.8028 (t80) cc_final: 0.7777 (t80) outliers start: 29 outliers final: 20 residues processed: 217 average time/residue: 0.2376 time to fit residues: 68.1084 Evaluate side-chains 220 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 197 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 59 MET Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 176 ASP Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 0.0070 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8788 Z= 0.163 Angle : 0.576 15.140 11913 Z= 0.284 Chirality : 0.042 0.238 1358 Planarity : 0.003 0.032 1490 Dihedral : 5.533 54.325 1245 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.74 % Allowed : 18.72 % Favored : 77.54 % 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: 1082 helix: 1.61 (0.27), residues: 382 sheet: -0.05 (0.32), residues: 266 loop : -0.80 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.000 HIS S 35 PHE 0.020 0.001 PHE A 334 TYR 0.016 0.001 TYR S 95 ARG 0.005 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 197 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 HIS cc_start: 0.6675 (OUTLIER) cc_final: 0.6126 (m-70) REVERT: B 13 GLN cc_start: 0.7729 (tm-30) cc_final: 0.7349 (pt0) REVERT: B 23 LYS cc_start: 0.8314 (tppt) cc_final: 0.8076 (tppt) REVERT: B 300 LEU cc_start: 0.6802 (mp) cc_final: 0.6585 (mt) REVERT: S 19 LYS cc_start: 0.7565 (tttp) cc_final: 0.7197 (ttpt) REVERT: S 23 SER cc_start: 0.8292 (p) cc_final: 0.7845 (m) REVERT: S 65 LYS cc_start: 0.8227 (tptt) cc_final: 0.7700 (mmtt) REVERT: S 80 PHE cc_start: 0.7306 (OUTLIER) cc_final: 0.5736 (p90) REVERT: S 206 ARG cc_start: 0.6790 (ptt-90) cc_final: 0.6532 (mmp80) REVERT: R 59 MET cc_start: 0.6634 (OUTLIER) cc_final: 0.6390 (mtm) REVERT: R 120 LEU cc_start: 0.8216 (mt) cc_final: 0.8015 (mt) REVERT: R 193 PHE cc_start: 0.8036 (t80) cc_final: 0.7784 (t80) REVERT: R 278 ILE cc_start: 0.8222 (mt) cc_final: 0.8015 (mt) outliers start: 35 outliers final: 26 residues processed: 215 average time/residue: 0.2316 time to fit residues: 66.3165 Evaluate side-chains 222 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 193 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 59 MET Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 176 ASP Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 268 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN ** R 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 242 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8788 Z= 0.206 Angle : 0.605 15.175 11913 Z= 0.298 Chirality : 0.042 0.232 1358 Planarity : 0.003 0.031 1490 Dihedral : 5.526 51.723 1245 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.64 % Allowed : 19.25 % Favored : 77.11 % 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: 1082 helix: 1.55 (0.27), residues: 382 sheet: -0.07 (0.32), residues: 268 loop : -0.72 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 PHE 0.021 0.001 PHE A 334 TYR 0.019 0.002 TYR S 95 ARG 0.005 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 197 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7515 (mt-10) REVERT: A 52 GLN cc_start: 0.6981 (pp30) cc_final: 0.6761 (pt0) REVERT: A 188 HIS cc_start: 0.6692 (OUTLIER) cc_final: 0.6174 (m-70) REVERT: B 13 GLN cc_start: 0.7729 (tm-30) cc_final: 0.7357 (pt0) REVERT: B 23 LYS cc_start: 0.8312 (tppt) cc_final: 0.8072 (tppt) REVERT: B 300 LEU cc_start: 0.6777 (mp) cc_final: 0.6474 (mt) REVERT: S 19 LYS cc_start: 0.7655 (tttp) cc_final: 0.7204 (ttpt) REVERT: S 65 LYS cc_start: 0.8240 (tptt) cc_final: 0.7689 (mmtt) REVERT: S 80 PHE cc_start: 0.7418 (OUTLIER) cc_final: 0.5802 (p90) REVERT: S 206 ARG cc_start: 0.6780 (ptt-90) cc_final: 0.6532 (mmp80) REVERT: R 59 MET cc_start: 0.6685 (OUTLIER) cc_final: 0.6429 (mtm) REVERT: R 193 PHE cc_start: 0.8085 (t80) cc_final: 0.7825 (t80) REVERT: R 278 ILE cc_start: 0.8267 (mt) cc_final: 0.8048 (mt) outliers start: 34 outliers final: 27 residues processed: 218 average time/residue: 0.2301 time to fit residues: 66.7146 Evaluate side-chains 221 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 191 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 59 MET Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 176 ASP Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 242 GLN Chi-restraints excluded: chain R residue 268 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 95 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN ** R 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8788 Z= 0.182 Angle : 0.613 15.533 11913 Z= 0.297 Chirality : 0.042 0.231 1358 Planarity : 0.003 0.032 1490 Dihedral : 5.348 47.779 1245 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.99 % Allowed : 19.68 % Favored : 77.33 % 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: 0.40 (0.26), residues: 1082 helix: 1.56 (0.27), residues: 382 sheet: 0.04 (0.33), residues: 266 loop : -0.70 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 PHE 0.019 0.001 PHE A 334 TYR 0.018 0.002 TYR S 95 ARG 0.003 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 195 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.6975 (pp30) cc_final: 0.6744 (pt0) REVERT: A 188 HIS cc_start: 0.6656 (OUTLIER) cc_final: 0.6122 (m-70) REVERT: B 13 GLN cc_start: 0.7728 (tm-30) cc_final: 0.7352 (pt0) REVERT: B 23 LYS cc_start: 0.8289 (tppt) cc_final: 0.8050 (tppt) REVERT: B 300 LEU cc_start: 0.6867 (mp) cc_final: 0.6534 (mt) REVERT: S 19 LYS cc_start: 0.7605 (tttp) cc_final: 0.7234 (ttpt) REVERT: S 65 LYS cc_start: 0.8230 (tptt) cc_final: 0.7699 (mmtt) REVERT: S 80 PHE cc_start: 0.7388 (OUTLIER) cc_final: 0.5830 (p90) REVERT: S 206 ARG cc_start: 0.6769 (ptt-90) cc_final: 0.6524 (mmp80) REVERT: R 59 MET cc_start: 0.6596 (OUTLIER) cc_final: 0.6394 (mtm) REVERT: R 193 PHE cc_start: 0.8104 (t80) cc_final: 0.7830 (t80) REVERT: R 246 ILE cc_start: 0.7155 (mm) cc_final: 0.6943 (mm) REVERT: R 278 ILE cc_start: 0.8254 (mt) cc_final: 0.8043 (mt) outliers start: 28 outliers final: 24 residues processed: 211 average time/residue: 0.2508 time to fit residues: 69.9528 Evaluate side-chains 217 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 190 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 59 MET Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 176 ASP Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 268 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 0.6980 chunk 48 optimal weight: 0.0670 chunk 70 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 84 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 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 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN S 3 GLN ** R 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8788 Z= 0.158 Angle : 0.601 15.155 11913 Z= 0.290 Chirality : 0.041 0.209 1358 Planarity : 0.003 0.033 1490 Dihedral : 4.929 50.258 1245 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.99 % Allowed : 20.11 % Favored : 76.90 % 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: 0.45 (0.26), residues: 1082 helix: 1.60 (0.27), residues: 382 sheet: -0.00 (0.33), residues: 262 loop : -0.61 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.000 HIS S 35 PHE 0.018 0.001 PHE R 76 TYR 0.017 0.002 TYR S 95 ARG 0.003 0.000 ARG B 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 198 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.6955 (pp30) cc_final: 0.6662 (pt0) REVERT: A 188 HIS cc_start: 0.6673 (OUTLIER) cc_final: 0.6146 (m-70) REVERT: B 13 GLN cc_start: 0.7780 (tm-30) cc_final: 0.7408 (pt0) REVERT: B 23 LYS cc_start: 0.8326 (tppt) cc_final: 0.8068 (tppt) REVERT: B 155 ASN cc_start: 0.7560 (OUTLIER) cc_final: 0.7117 (m-40) REVERT: B 300 LEU cc_start: 0.6789 (mp) cc_final: 0.6455 (mt) REVERT: S 19 LYS cc_start: 0.7600 (tttp) cc_final: 0.7201 (ttpt) REVERT: S 23 SER cc_start: 0.8250 (p) cc_final: 0.7802 (m) REVERT: S 65 LYS cc_start: 0.8229 (tptt) cc_final: 0.7701 (mmtt) REVERT: S 80 PHE cc_start: 0.7363 (OUTLIER) cc_final: 0.5790 (p90) REVERT: S 206 ARG cc_start: 0.6853 (ptt-90) cc_final: 0.6532 (mmp80) REVERT: R 193 PHE cc_start: 0.8050 (t80) cc_final: 0.7814 (t80) REVERT: R 278 ILE cc_start: 0.8217 (mt) cc_final: 0.8006 (mt) outliers start: 28 outliers final: 20 residues processed: 214 average time/residue: 0.2366 time to fit residues: 66.8779 Evaluate side-chains 213 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 190 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 176 ASP Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 85 optimal weight: 0.3980 chunk 35 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN ** R 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.183960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.147830 restraints weight = 9950.750| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.15 r_work: 0.3482 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8788 Z= 0.200 Angle : 0.626 14.849 11913 Z= 0.302 Chirality : 0.042 0.225 1358 Planarity : 0.003 0.032 1490 Dihedral : 4.909 54.059 1245 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.57 % Allowed : 20.43 % Favored : 77.01 % 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 (0.26), residues: 1082 helix: 1.59 (0.27), residues: 381 sheet: 0.11 (0.32), residues: 271 loop : -0.63 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 PHE 0.019 0.001 PHE R 76 TYR 0.019 0.002 TYR S 95 ARG 0.004 0.000 ARG A 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2378.37 seconds wall clock time: 43 minutes 56.69 seconds (2636.69 seconds total)