Starting phenix.real_space_refine on Mon Mar 11 17:31:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aue_11927/03_2024/7aue_11927_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aue_11927/03_2024/7aue_11927.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aue_11927/03_2024/7aue_11927.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aue_11927/03_2024/7aue_11927.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aue_11927/03_2024/7aue_11927_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aue_11927/03_2024/7aue_11927_updated.pdb" } resolution = 2.97 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: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 69 5.16 5 C 5580 2.51 5 N 1499 2.21 5 O 1606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 126": "OD1" <-> "OD2" Residue "R TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 165": "NH1" <-> "NH2" Residue "R ARG 220": "NH1" <-> "NH2" Residue "R PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 308": "OE1" <-> "OE2" Residue "R ARG 310": "NH1" <-> "NH2" Residue "A GLU 8": "OE1" <-> "OE2" Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 24": "NH1" <-> "NH2" Residue "A ARG 54": "NH1" <-> "NH2" Residue "A PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 202": "OD1" <-> "OD2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 259": "NH1" <-> "NH2" Residue "A ARG 262": "NH1" <-> "NH2" Residue "A TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 312": "NH1" <-> "NH2" Residue "A ARG 315": "NH1" <-> "NH2" Residue "A ASP 322": "OD1" <-> "OD2" Residue "A ARG 335": "NH1" <-> "NH2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 353": "NH1" <-> "NH2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A ARG 368": "NH1" <-> "NH2" Residue "B ARG 59": "NH1" <-> "NH2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B ARG 69": "NH1" <-> "NH2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B ARG 151": "NH1" <-> "NH2" Residue "B TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B ARG 268": "NH1" <-> "NH2" Residue "B ASP 284": "OD1" <-> "OD2" Residue "B ASP 329": "OD1" <-> "OD2" Residue "B ARG 331": "NH1" <-> "NH2" Residue "G ARG 13": "NH1" <-> "NH2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G ASP 48": "OD1" <-> "OD2" Residue "S PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 73": "OD1" <-> "OD2" Residue "S TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 98": "NH1" <-> "NH2" Residue "S PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 179": "NH1" <-> "NH2" Residue "S ARG 206": "NH1" <-> "NH2" Residue "S TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 7": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8755 Number of models: 1 Model: "" Number of chains: 8 Chain: "R" Number of atoms: 2050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2050 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 255} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1879 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2572 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "G" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 427 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1747 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Modifications used: {'PEPT-D': 2} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.07, per 1000 atoms: 0.58 Number of scatterers: 8755 At special positions: 0 Unit cell: (103.2, 121.26, 116.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 69 16.00 O 1606 8.00 N 1499 7.00 C 5580 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 40 " - pdb=" SG CYS R 279 " distance=2.03 Simple disulfide: pdb=" SG CYS R 271 " - pdb=" SG CYS R 277 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.00 Conformation dependent library (CDL) restraints added in 1.7 seconds 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAL C 4 " pdb=" CB DPN C 6 " Number of C-beta restraints generated: 2122 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 14 sheets defined 27.9% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'R' and resid 57 through 71 removed outlier: 3.804A pdb=" N LEU R 64 " --> pdb=" O LEU R 60 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE R 66 " --> pdb=" O ASN R 62 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 75 No H-bonds generated for 'chain 'R' and resid 73 through 75' Processing helix chain 'R' and resid 78 through 95 removed outlier: 3.636A pdb=" N PHE R 82 " --> pdb=" O PRO R 78 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE R 83 " --> pdb=" O MET R 79 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS R 84 " --> pdb=" O TYR R 80 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA R 89 " --> pdb=" O SER R 85 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL R 93 " --> pdb=" O ALA R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 107 removed outlier: 3.813A pdb=" N ILE R 102 " --> pdb=" O GLY R 98 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N VAL R 103 " --> pdb=" O SER R 99 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE R 104 " --> pdb=" O GLU R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 121 Processing helix chain 'R' and resid 125 through 152 removed outlier: 3.574A pdb=" N LEU R 134 " --> pdb=" O CYS R 130 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU R 140 " --> pdb=" O SER R 136 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA R 144 " --> pdb=" O LEU R 140 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR R 150 " --> pdb=" O ASP R 146 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE R 151 " --> pdb=" O ARG R 147 " (cutoff:3.500A) Processing helix chain 'R' and resid 163 through 183 removed outlier: 3.668A pdb=" N ILE R 168 " --> pdb=" O LYS R 164 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER R 171 " --> pdb=" O GLY R 167 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TRP R 174 " --> pdb=" O ILE R 170 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR R 178 " --> pdb=" O TRP R 174 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER R 180 " --> pdb=" O ALA R 176 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY R 181 " --> pdb=" O CYS R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 194 through 202 removed outlier: 3.615A pdb=" N THR R 199 " --> pdb=" O ILE R 195 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET R 200 " --> pdb=" O CYS R 196 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE R 201 " --> pdb=" O LEU R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 205 through 214 removed outlier: 4.378A pdb=" N SER R 210 " --> pdb=" O ALA R 206 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU R 211 " --> pdb=" O LEU R 207 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR R 212 " --> pdb=" O MET R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 224 No H-bonds generated for 'chain 'R' and resid 221 through 224' Processing helix chain 'R' and resid 243 through 250 removed outlier: 3.876A pdb=" N LEU R 247 " --> pdb=" O GLY R 243 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR R 248 " --> pdb=" O ALA R 244 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 270 removed outlier: 3.639A pdb=" N TRP R 258 " --> pdb=" O PHE R 254 " (cutoff:3.500A) Proline residue: R 260 - end of helix removed outlier: 3.568A pdb=" N HIS R 264 " --> pdb=" O PRO R 260 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU R 265 " --> pdb=" O PHE R 261 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE R 266 " --> pdb=" O PHE R 262 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE R 267 " --> pdb=" O LEU R 263 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE R 269 " --> pdb=" O LEU R 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 275 through 283 removed outlier: 3.750A pdb=" N CYS R 279 " --> pdb=" O PRO R 275 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N HIS R 283 " --> pdb=" O CYS R 279 " (cutoff:3.500A) Processing helix chain 'R' and resid 289 through 301 removed outlier: 3.721A pdb=" N SER R 295 " --> pdb=" O ILE R 291 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE R 296 " --> pdb=" O MET R 292 " (cutoff:3.500A) Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 307 through 314 removed outlier: 3.698A pdb=" N LYS R 311 " --> pdb=" O GLN R 307 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR R 312 " --> pdb=" O GLU R 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 27 removed outlier: 3.832A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 removed outlier: 3.524A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 246 through 256 removed outlier: 3.632A pdb=" N SER A 254 " --> pdb=" O ASN A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 273 through 280 removed outlier: 3.948A pdb=" N GLU A 278 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 290 No H-bonds generated for 'chain 'A' and resid 287 through 290' Processing helix chain 'A' and resid 311 through 330 removed outlier: 3.565A pdb=" N PHE A 319 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG A 321 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE A 324 " --> pdb=" O ILE A 320 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 325 " --> pdb=" O ARG A 321 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ILE A 327 " --> pdb=" O GLU A 323 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ALA A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 369 removed outlier: 3.855A pdb=" N ASP A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 362 " --> pdb=" O CYS A 358 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG A 368 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN A 369 " --> pdb=" O MET A 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 36 removed outlier: 3.510A pdb=" N ASN B 33 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLN B 34 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 50 No H-bonds generated for 'chain 'B' and resid 47 through 50' Processing helix chain 'G' and resid 11 through 19 removed outlier: 3.538A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 removed outlier: 3.627A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR G 40 " --> pdb=" O ASP G 36 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N CYS G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA G 43 " --> pdb=" O ALA G 39 " (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 sheet with id= A, first strand: chain 'A' and resid 265 through 271 removed outlier: 4.035A pdb=" N ALA A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ASN A 197 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N LEU A 36 " --> pdb=" O ASN A 197 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N HIS A 199 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LEU A 38 " --> pdb=" O HIS A 199 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE A 191 " --> pdb=" O PHE A 198 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 66 through 69 removed outlier: 4.295A pdb=" N PHE B 352 " --> pdb=" O SER B 348 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 348 " --> pdb=" O PHE B 352 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS B 334 " --> pdb=" O GLY B 347 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 75 through 80 removed outlier: 6.887A pdb=" N ALA B 90 " --> pdb=" O TYR B 76 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N MET B 78 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL B 88 " --> pdb=" O MET B 78 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N TRP B 80 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LEU B 86 " --> pdb=" O TRP B 80 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS B 95 " --> pdb=" O SER B 91 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HIS B 108 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ASP B 100 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LYS B 106 " --> pdb=" O ASP B 100 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 120 through 122 removed outlier: 3.777A pdb=" N ARG B 154 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ASN B 142 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N VAL B 152 " --> pdb=" O ASN B 142 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 163 through 168 removed outlier: 6.881A pdb=" N SER B 177 " --> pdb=" O SER B 164 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N CYS B 166 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL B 175 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N PHE B 168 " --> pdb=" O GLN B 173 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLN B 173 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 174 " --> pdb=" O TRP B 186 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR B 195 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASP B 187 " --> pdb=" O GLN B 193 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N GLN B 193 " --> pdb=" O ASP B 187 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 204 through 209 removed outlier: 7.153A pdb=" N GLY B 219 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU B 207 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL B 217 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LEU B 209 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU B 215 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN B 237 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASP B 229 " --> pdb=" O CYS B 235 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N CYS B 235 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 246 through 251 removed outlier: 6.678A pdb=" N GLY B 261 " --> pdb=" O ASN B 247 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE B 249 " --> pdb=" O ALA B 259 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA B 259 " --> pdb=" O ILE B 249 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N PHE B 251 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ALA B 257 " --> pdb=" O PHE B 251 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET B 279 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASP B 271 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLU B 277 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 311 through 315 removed outlier: 3.516A pdb=" N SER B 292 " --> pdb=" O GLY B 305 " (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 95 through 99 removed outlier: 3.511A pdb=" N TRP S 36 " --> pdb=" O ALA S 49 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR S 50 " --> pdb=" O TYR S 59 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 92 through 94 removed outlier: 3.591A pdb=" N ALA S 92 " --> pdb=" O LEU S 117 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.813A pdb=" N LYS S 232 " --> pdb=" O VAL S 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'S' and resid 143 through 148 removed outlier: 3.626A pdb=" N ALA S 199 " --> pdb=" O SER S 196 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'S' and resid 214 through 219 removed outlier: 3.756A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) 251 hydrogen bonds defined for protein. 714 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: 2.24 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1400 1.31 - 1.44: 2452 1.44 - 1.56: 4976 1.56 - 1.69: 1 1.69 - 1.82: 100 Bond restraints: 8929 Sorted by residual: bond pdb=" C ARG C 7 " pdb=" N TRP C 8 " ideal model delta sigma weight residual 1.329 1.470 -0.141 1.40e-02 5.10e+03 1.01e+02 bond pdb=" C DPN C 6 " pdb=" N ARG C 7 " ideal model delta sigma weight residual 1.329 1.461 -0.132 1.40e-02 5.10e+03 8.88e+01 bond pdb=" C CYS C 3 " pdb=" N DAL C 4 " ideal model delta sigma weight residual 1.329 1.460 -0.131 1.40e-02 5.10e+03 8.81e+01 bond pdb=" CZ ARG C 2 " pdb=" NH1 ARG C 2 " ideal model delta sigma weight residual 1.323 1.453 -0.130 1.40e-02 5.10e+03 8.64e+01 bond pdb=" CZ ARG C 7 " pdb=" NH2 ARG C 7 " ideal model delta sigma weight residual 1.330 1.450 -0.120 1.30e-02 5.92e+03 8.57e+01 ... (remaining 8924 not shown) Histogram of bond angle deviations from ideal: 100.39 - 107.11: 215 107.11 - 113.84: 4958 113.84 - 120.56: 3535 120.56 - 127.29: 3304 127.29 - 134.01: 91 Bond angle restraints: 12103 Sorted by residual: angle pdb=" C LYS B 297 " pdb=" N SER B 298 " pdb=" CA SER B 298 " ideal model delta sigma weight residual 121.54 132.92 -11.38 1.91e+00 2.74e-01 3.55e+01 angle pdb=" N GLY B 133 " pdb=" CA GLY B 133 " pdb=" C GLY B 133 " ideal model delta sigma weight residual 110.43 117.61 -7.18 1.35e+00 5.49e-01 2.83e+01 angle pdb=" C ARG A 296 " pdb=" N TYR A 297 " pdb=" CA TYR A 297 " ideal model delta sigma weight residual 121.54 130.52 -8.98 1.91e+00 2.74e-01 2.21e+01 angle pdb=" N VAL R 228 " pdb=" CA VAL R 228 " pdb=" C VAL R 228 " ideal model delta sigma weight residual 112.80 108.50 4.30 1.15e+00 7.56e-01 1.40e+01 angle pdb=" N TYR A 297 " pdb=" CA TYR A 297 " pdb=" C TYR A 297 " ideal model delta sigma weight residual 110.80 118.49 -7.69 2.13e+00 2.20e-01 1.30e+01 ... (remaining 12098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 5228 35.97 - 71.95: 63 71.95 - 107.92: 6 107.92 - 143.89: 0 143.89 - 179.87: 1 Dihedral angle restraints: 5298 sinusoidal: 2017 harmonic: 3281 Sorted by residual: dihedral pdb=" CH3 ACE C 1 " pdb=" C ACE C 1 " pdb=" N ARG C 2 " pdb=" CA ARG C 2 " ideal model delta sinusoidal sigma weight residual 180.00 0.13 179.87 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" CA LYS B 297 " pdb=" C LYS B 297 " pdb=" N SER B 298 " pdb=" CA SER B 298 " ideal model delta harmonic sigma weight residual -180.00 -157.94 -22.06 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CB CYS R 40 " pdb=" SG CYS R 40 " pdb=" SG CYS R 279 " pdb=" CB CYS R 279 " ideal model delta sinusoidal sigma weight residual -86.00 -121.09 35.09 1 1.00e+01 1.00e-02 1.75e+01 ... (remaining 5295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1049 0.054 - 0.109: 275 0.109 - 0.163: 67 0.163 - 0.218: 5 0.218 - 0.272: 1 Chirality restraints: 1397 Sorted by residual: chirality pdb=" CA TYR A 297 " pdb=" N TYR A 297 " pdb=" C TYR A 297 " pdb=" CB TYR A 297 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA ARG C 7 " pdb=" N ARG C 7 " pdb=" C ARG C 7 " pdb=" CB ARG C 7 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.18e-01 chirality pdb=" CG LEU B 86 " pdb=" CB LEU B 86 " pdb=" CD1 LEU B 86 " pdb=" CD2 LEU B 86 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.29e-01 ... (remaining 1394 not shown) Planarity restraints: 1525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP R 298 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.05e+00 pdb=" N PRO R 299 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO R 299 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO R 299 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA R 259 " 0.043 5.00e-02 4.00e+02 6.47e-02 6.70e+00 pdb=" N PRO R 260 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO R 260 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO R 260 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER R 77 " 0.041 5.00e-02 4.00e+02 6.20e-02 6.15e+00 pdb=" N PRO R 78 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO R 78 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 78 " 0.035 5.00e-02 4.00e+02 ... (remaining 1522 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 65 2.64 - 3.21: 6849 3.21 - 3.77: 12309 3.77 - 4.34: 17979 4.34 - 4.90: 29549 Nonbonded interactions: 66751 Sorted by model distance: nonbonded pdb=" OD1 ASP R 126 " pdb="CA CA R 501 " model vdw 2.077 2.510 nonbonded pdb=" OD2 ASP R 126 " pdb="CA CA R 501 " model vdw 2.142 2.510 nonbonded pdb=" OE2 GLU R 100 " pdb="CA CA R 501 " model vdw 2.297 2.510 nonbonded pdb=" OH TYR R 80 " pdb=" OG SER R 306 " model vdw 2.331 2.440 nonbonded pdb=" OG SER S 149 " pdb=" O LYS S 151 " model vdw 2.352 2.440 ... (remaining 66746 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: 2.300 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: 5.280 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.290 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 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 : 0.006 0.141 8929 Z= 0.445 Angle : 0.805 11.384 12103 Z= 0.450 Chirality : 0.052 0.272 1397 Planarity : 0.006 0.066 1525 Dihedral : 14.178 179.865 3164 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.11 % Allowed : 5.33 % Favored : 94.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -4.47 (0.20), residues: 1101 helix: -4.76 (0.10), residues: 381 sheet: -1.12 (0.30), residues: 264 loop : -2.23 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 228 HIS 0.011 0.002 HIS R 264 PHE 0.022 0.002 PHE B 216 TYR 0.028 0.002 TYR A 297 ARG 0.005 0.000 ARG B 268 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 172 time to evaluate : 0.965 Fit side-chains REVERT: R 215 MET cc_start: 0.8564 (mtp) cc_final: 0.8312 (mtp) REVERT: R 242 LYS cc_start: 0.7786 (tttp) cc_final: 0.7415 (tttm) REVERT: R 281 MET cc_start: 0.6996 (mtm) cc_final: 0.6730 (mtt) REVERT: R 310 ARG cc_start: 0.7942 (ttp-170) cc_final: 0.7644 (ttp80) REVERT: R 311 LYS cc_start: 0.8176 (mtpt) cc_final: 0.7388 (mttt) REVERT: A 199 HIS cc_start: 0.6932 (t-90) cc_final: 0.6516 (t-170) REVERT: A 301 GLU cc_start: 0.5476 (pm20) cc_final: 0.5197 (tm-30) REVERT: B 93 ASP cc_start: 0.7857 (p0) cc_final: 0.7541 (p0) REVERT: B 118 MET cc_start: 0.8630 (mtp) cc_final: 0.8207 (mtm) REVERT: B 284 ASP cc_start: 0.7222 (m-30) cc_final: 0.7020 (m-30) REVERT: G 47 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7138 (tt0) REVERT: S 128 MET cc_start: 0.8457 (mmm) cc_final: 0.8035 (mmt) outliers start: 1 outliers final: 1 residues processed: 173 average time/residue: 1.2938 time to fit residues: 237.1334 Evaluate side-chains 138 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 0.0170 chunk 64 optimal weight: 6.9990 chunk 99 optimal weight: 0.4980 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 62 ASN R 123 ASN R 294 ASN A 197 ASN A 250 ASN A 273 GLN B 33 ASN B 254 ASN S 13 GLN S 113 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8929 Z= 0.132 Angle : 0.534 9.820 12103 Z= 0.286 Chirality : 0.043 0.202 1397 Planarity : 0.004 0.044 1525 Dihedral : 7.321 179.905 1228 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.49 % Allowed : 13.86 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -3.10 (0.22), residues: 1101 helix: -3.33 (0.19), residues: 362 sheet: -0.58 (0.30), residues: 274 loop : -1.71 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 228 HIS 0.003 0.001 HIS R 264 PHE 0.014 0.001 PHE A 355 TYR 0.027 0.001 TYR A 297 ARG 0.002 0.000 ARG A 259 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 148 time to evaluate : 1.045 Fit side-chains REVERT: R 200 MET cc_start: 0.7093 (mtt) cc_final: 0.6705 (mtt) REVERT: R 204 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.6316 (mpp) REVERT: R 242 LYS cc_start: 0.7893 (tttp) cc_final: 0.7541 (tttm) REVERT: R 268 TYR cc_start: 0.8278 (t80) cc_final: 0.8075 (t80) REVERT: R 311 LYS cc_start: 0.8063 (mtpt) cc_final: 0.7327 (mttt) REVERT: A 199 HIS cc_start: 0.6846 (t-90) cc_final: 0.6394 (t-170) REVERT: A 259 ARG cc_start: 0.7606 (ptt-90) cc_final: 0.7359 (ptt90) REVERT: A 301 GLU cc_start: 0.5576 (pm20) cc_final: 0.5043 (tm-30) REVERT: A 351 ILE cc_start: 0.7463 (OUTLIER) cc_final: 0.7192 (mm) REVERT: B 37 ASP cc_start: 0.7520 (m-30) cc_final: 0.7216 (m-30) REVERT: B 93 ASP cc_start: 0.7818 (p0) cc_final: 0.7517 (p0) REVERT: B 118 MET cc_start: 0.8638 (mtp) cc_final: 0.8230 (mtm) REVERT: G 21 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7197 (tpp) REVERT: G 47 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7137 (tt0) REVERT: S 93 MET cc_start: 0.7732 (ttm) cc_final: 0.7504 (ttt) REVERT: S 128 MET cc_start: 0.8424 (mmm) cc_final: 0.8070 (mmt) outliers start: 14 outliers final: 2 residues processed: 153 average time/residue: 1.4301 time to fit residues: 230.9739 Evaluate side-chains 147 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 142 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 264 HIS A 273 GLN B 254 ASN S 113 GLN S 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 8929 Z= 0.392 Angle : 0.720 10.266 12103 Z= 0.382 Chirality : 0.051 0.245 1397 Planarity : 0.005 0.043 1525 Dihedral : 7.524 176.856 1224 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.09 % Allowed : 14.61 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.54 (0.23), residues: 1101 helix: -2.68 (0.22), residues: 368 sheet: -0.10 (0.31), residues: 272 loop : -1.67 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 99 HIS 0.006 0.002 HIS R 214 PHE 0.021 0.003 PHE A 355 TYR 0.033 0.002 TYR A 297 ARG 0.004 0.001 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 140 time to evaluate : 0.962 Fit side-chains REVERT: R 122 ASP cc_start: 0.7517 (t0) cc_final: 0.7273 (t0) REVERT: R 204 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.6583 (mpp) REVERT: R 242 LYS cc_start: 0.7951 (tttp) cc_final: 0.7507 (tttm) REVERT: R 311 LYS cc_start: 0.8120 (mtpt) cc_final: 0.7335 (mttt) REVERT: A 301 GLU cc_start: 0.5679 (pm20) cc_final: 0.4868 (pp20) REVERT: B 37 ASP cc_start: 0.7322 (m-30) cc_final: 0.7076 (m-30) REVERT: B 93 ASP cc_start: 0.7856 (p0) cc_final: 0.7536 (p0) REVERT: B 118 MET cc_start: 0.8654 (mtp) cc_final: 0.8213 (mtm) REVERT: G 47 GLU cc_start: 0.7480 (mt-10) cc_final: 0.7160 (tt0) REVERT: S 93 MET cc_start: 0.7754 (ttm) cc_final: 0.7549 (ttt) outliers start: 29 outliers final: 9 residues processed: 155 average time/residue: 1.3942 time to fit residues: 228.4745 Evaluate side-chains 145 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 135 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain G residue 46 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 0.0270 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 52 optimal weight: 0.0270 chunk 95 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN B 254 ASN S 13 GLN S 113 GLN S 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 8929 Z= 0.141 Angle : 0.525 10.337 12103 Z= 0.278 Chirality : 0.043 0.175 1397 Planarity : 0.003 0.036 1525 Dihedral : 6.966 179.263 1224 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.13 % Allowed : 16.95 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.92 (0.24), residues: 1101 helix: -1.96 (0.25), residues: 369 sheet: 0.09 (0.31), residues: 273 loop : -1.39 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 228 HIS 0.003 0.001 HIS R 264 PHE 0.016 0.001 PHE B 216 TYR 0.020 0.001 TYR A 297 ARG 0.005 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 141 time to evaluate : 1.013 Fit side-chains REVERT: R 46 VAL cc_start: 0.8514 (p) cc_final: 0.8310 (t) REVERT: R 204 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.6363 (mpp) REVERT: R 242 LYS cc_start: 0.7924 (tttp) cc_final: 0.7619 (tttm) REVERT: R 310 ARG cc_start: 0.7813 (ttp-170) cc_final: 0.7563 (ttp80) REVERT: R 311 LYS cc_start: 0.8029 (mtpt) cc_final: 0.7231 (mttt) REVERT: A 259 ARG cc_start: 0.7603 (ptt-90) cc_final: 0.7311 (ptt90) REVERT: A 301 GLU cc_start: 0.5615 (pm20) cc_final: 0.4743 (pp20) REVERT: B 93 ASP cc_start: 0.7811 (p0) cc_final: 0.7483 (p0) REVERT: B 118 MET cc_start: 0.8661 (mtp) cc_final: 0.8232 (mtm) REVERT: B 147 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7214 (mm-30) REVERT: B 290 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8458 (mp) REVERT: G 22 GLU cc_start: 0.7277 (tt0) cc_final: 0.6594 (mt-10) REVERT: G 47 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7154 (tt0) REVERT: S 93 MET cc_start: 0.7720 (ttm) cc_final: 0.7466 (ttt) outliers start: 20 outliers final: 5 residues processed: 150 average time/residue: 1.5105 time to fit residues: 239.3400 Evaluate side-chains 147 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 140 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 290 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 1 optimal weight: 0.0370 chunk 79 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 overall best weight: 2.6062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 307 GLN A 52 GLN A 273 GLN B 254 ASN S 113 GLN S 171 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 8929 Z= 0.278 Angle : 0.630 10.253 12103 Z= 0.333 Chirality : 0.047 0.181 1397 Planarity : 0.004 0.035 1525 Dihedral : 7.218 177.780 1224 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.35 % Allowed : 18.23 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.77 (0.24), residues: 1101 helix: -1.82 (0.25), residues: 362 sheet: 0.20 (0.31), residues: 272 loop : -1.34 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 99 HIS 0.008 0.001 HIS R 264 PHE 0.018 0.002 PHE B 216 TYR 0.017 0.002 TYR A 297 ARG 0.006 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 139 time to evaluate : 0.964 Fit side-chains REVERT: R 204 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.6538 (mpp) REVERT: R 242 LYS cc_start: 0.7891 (tttp) cc_final: 0.7459 (tttm) REVERT: R 311 LYS cc_start: 0.8090 (mtpt) cc_final: 0.7318 (mttt) REVERT: A 259 ARG cc_start: 0.7678 (ptt-90) cc_final: 0.7377 (ptt90) REVERT: A 301 GLU cc_start: 0.5545 (pm20) cc_final: 0.4754 (pp20) REVERT: A 351 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7465 (mm) REVERT: B 118 MET cc_start: 0.8655 (mtp) cc_final: 0.8215 (mtm) REVERT: B 147 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7302 (mm-30) REVERT: B 192 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7300 (mp10) REVERT: G 22 GLU cc_start: 0.7305 (tt0) cc_final: 0.6670 (mt-10) REVERT: G 47 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7109 (tt0) REVERT: S 93 MET cc_start: 0.7746 (ttm) cc_final: 0.7513 (ttt) outliers start: 22 outliers final: 12 residues processed: 148 average time/residue: 1.3934 time to fit residues: 218.1933 Evaluate side-chains 154 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 139 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain S residue 150 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 21 optimal weight: 0.1980 chunk 62 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 307 GLN A 52 GLN A 273 GLN B 254 ASN G 24 ASN S 13 GLN S 113 GLN S 171 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 8929 Z= 0.353 Angle : 0.696 10.153 12103 Z= 0.367 Chirality : 0.049 0.183 1397 Planarity : 0.004 0.042 1525 Dihedral : 7.415 177.151 1224 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.84 % Allowed : 17.38 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.80 (0.24), residues: 1101 helix: -1.89 (0.25), residues: 362 sheet: 0.23 (0.31), residues: 272 loop : -1.36 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 99 HIS 0.009 0.002 HIS R 264 PHE 0.020 0.002 PHE B 216 TYR 0.017 0.002 TYR A 297 ARG 0.011 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 136 time to evaluate : 1.042 Fit side-chains REVERT: R 204 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.6560 (mpp) REVERT: R 242 LYS cc_start: 0.7876 (tttp) cc_final: 0.7487 (tttm) REVERT: R 281 MET cc_start: 0.6456 (OUTLIER) cc_final: 0.6238 (mmt) REVERT: R 311 LYS cc_start: 0.8107 (mtpt) cc_final: 0.7330 (mttt) REVERT: A 288 GLU cc_start: 0.5920 (OUTLIER) cc_final: 0.5419 (tp30) REVERT: A 301 GLU cc_start: 0.5677 (pm20) cc_final: 0.4847 (pp20) REVERT: A 351 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7647 (pt) REVERT: B 118 MET cc_start: 0.8649 (mtp) cc_final: 0.8284 (mtm) REVERT: B 290 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8457 (mp) REVERT: G 47 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7164 (tt0) REVERT: S 93 MET cc_start: 0.7797 (ttm) cc_final: 0.7564 (ttt) outliers start: 36 outliers final: 18 residues processed: 158 average time/residue: 1.3340 time to fit residues: 223.3848 Evaluate side-chains 159 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 136 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 84 CYS Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 281 MET Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain S residue 150 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 273 GLN B 254 ASN G 24 ASN S 13 GLN S 113 GLN S 171 GLN C 5 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 8929 Z= 0.204 Angle : 0.583 10.513 12103 Z= 0.307 Chirality : 0.045 0.150 1397 Planarity : 0.004 0.045 1525 Dihedral : 7.108 178.939 1224 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.30 % Allowed : 18.23 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.53 (0.25), residues: 1101 helix: -1.54 (0.26), residues: 362 sheet: 0.25 (0.31), residues: 276 loop : -1.22 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 228 HIS 0.005 0.001 HIS R 264 PHE 0.017 0.002 PHE B 216 TYR 0.015 0.001 TYR A 297 ARG 0.012 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 142 time to evaluate : 0.961 Fit side-chains REVERT: R 46 VAL cc_start: 0.8519 (p) cc_final: 0.8235 (t) REVERT: R 204 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.6533 (mpp) REVERT: R 215 MET cc_start: 0.8564 (mtp) cc_final: 0.8333 (mtp) REVERT: R 242 LYS cc_start: 0.7870 (tttp) cc_final: 0.7455 (tttm) REVERT: R 281 MET cc_start: 0.6321 (OUTLIER) cc_final: 0.6059 (mmt) REVERT: R 311 LYS cc_start: 0.8080 (mtpt) cc_final: 0.7310 (mttt) REVERT: A 259 ARG cc_start: 0.7655 (ptt-90) cc_final: 0.7342 (ptt90) REVERT: A 301 GLU cc_start: 0.5426 (pm20) cc_final: 0.4633 (pp20) REVERT: A 351 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7404 (mm) REVERT: B 118 MET cc_start: 0.8636 (mtp) cc_final: 0.8206 (mtm) REVERT: B 290 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8413 (mp) REVERT: B 320 ASP cc_start: 0.7226 (t70) cc_final: 0.7013 (t0) REVERT: G 21 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.7235 (tpp) REVERT: G 47 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7078 (tt0) REVERT: S 65 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7256 (ttmp) REVERT: S 93 MET cc_start: 0.7740 (ttm) cc_final: 0.7489 (ttt) REVERT: S 207 LEU cc_start: 0.7148 (mp) cc_final: 0.6888 (pt) outliers start: 31 outliers final: 18 residues processed: 158 average time/residue: 1.2884 time to fit residues: 216.0384 Evaluate side-chains 164 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 140 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 84 CYS Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 281 MET Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain S residue 65 LYS Chi-restraints excluded: chain S residue 150 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 83 optimal weight: 0.0270 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN B 254 ASN G 24 ASN S 13 GLN S 113 GLN S 171 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.099 8929 Z= 0.151 Angle : 0.528 10.480 12103 Z= 0.277 Chirality : 0.043 0.142 1397 Planarity : 0.003 0.051 1525 Dihedral : 6.820 179.552 1224 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.56 % Allowed : 19.51 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.22 (0.25), residues: 1101 helix: -1.24 (0.27), residues: 373 sheet: 0.41 (0.32), residues: 271 loop : -1.04 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 228 HIS 0.003 0.001 HIS R 264 PHE 0.015 0.001 PHE B 216 TYR 0.013 0.001 TYR A 297 ARG 0.013 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 140 time to evaluate : 1.096 Fit side-chains REVERT: R 204 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.6463 (mpp) REVERT: R 215 MET cc_start: 0.8535 (mtp) cc_final: 0.8319 (mtp) REVERT: R 242 LYS cc_start: 0.7903 (tttp) cc_final: 0.7590 (tttm) REVERT: R 281 MET cc_start: 0.6288 (mtt) cc_final: 0.6048 (mmt) REVERT: R 311 LYS cc_start: 0.8012 (mtpt) cc_final: 0.7257 (mttt) REVERT: A 232 TYR cc_start: 0.7593 (p90) cc_final: 0.7283 (p90) REVERT: A 259 ARG cc_start: 0.7577 (ptt-90) cc_final: 0.7274 (ptt90) REVERT: A 301 GLU cc_start: 0.5312 (pm20) cc_final: 0.4525 (pp20) REVERT: A 351 ILE cc_start: 0.7649 (OUTLIER) cc_final: 0.7417 (mm) REVERT: B 118 MET cc_start: 0.8623 (mtp) cc_final: 0.8188 (mtm) REVERT: G 47 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7093 (tt0) REVERT: S 65 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7187 (ttmp) REVERT: S 93 MET cc_start: 0.7711 (ttm) cc_final: 0.7441 (ttt) outliers start: 24 outliers final: 11 residues processed: 154 average time/residue: 1.4450 time to fit residues: 235.5071 Evaluate side-chains 149 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 135 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 84 CYS Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain S residue 65 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 43 optimal weight: 0.4980 chunk 77 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 89 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 ASN S 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.102 8929 Z= 0.139 Angle : 0.511 10.504 12103 Z= 0.267 Chirality : 0.042 0.138 1397 Planarity : 0.003 0.049 1525 Dihedral : 6.689 179.699 1224 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.92 % Allowed : 20.26 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.99 (0.26), residues: 1101 helix: -0.96 (0.27), residues: 374 sheet: 0.39 (0.32), residues: 273 loop : -0.90 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 228 HIS 0.003 0.001 HIS R 264 PHE 0.014 0.001 PHE B 216 TYR 0.013 0.001 TYR A 290 ARG 0.012 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 0.907 Fit side-chains REVERT: R 204 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.6484 (mpp) REVERT: R 215 MET cc_start: 0.8539 (mtp) cc_final: 0.8332 (mtp) REVERT: R 242 LYS cc_start: 0.7883 (tttp) cc_final: 0.7550 (tttm) REVERT: R 311 LYS cc_start: 0.8020 (mtpt) cc_final: 0.7258 (mttt) REVERT: A 259 ARG cc_start: 0.7567 (ptt-90) cc_final: 0.7266 (ptt90) REVERT: A 293 GLU cc_start: 0.7767 (tp30) cc_final: 0.7551 (mm-30) REVERT: A 301 GLU cc_start: 0.5443 (pm20) cc_final: 0.4657 (pp20) REVERT: B 118 MET cc_start: 0.8622 (mtp) cc_final: 0.8181 (mtm) REVERT: G 47 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7068 (tt0) REVERT: S 93 MET cc_start: 0.7693 (ttm) cc_final: 0.7414 (ttt) REVERT: S 207 LEU cc_start: 0.6528 (OUTLIER) cc_final: 0.6202 (pp) REVERT: C 2 ARG cc_start: 0.4731 (OUTLIER) cc_final: 0.3263 (tpm170) outliers start: 18 outliers final: 11 residues processed: 140 average time/residue: 1.4072 time to fit residues: 208.4226 Evaluate side-chains 144 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 130 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 84 CYS Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain C residue 2 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 0.0270 chunk 69 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 overall best weight: 1.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 8929 Z= 0.232 Angle : 0.591 10.439 12103 Z= 0.310 Chirality : 0.046 0.157 1397 Planarity : 0.004 0.046 1525 Dihedral : 6.938 178.256 1224 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.81 % Allowed : 20.58 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.04 (0.25), residues: 1101 helix: -1.00 (0.27), residues: 364 sheet: 0.48 (0.32), residues: 271 loop : -1.02 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.006 0.001 HIS R 264 PHE 0.016 0.002 PHE B 216 TYR 0.014 0.002 TYR R 153 ARG 0.012 0.001 ARG B 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 138 time to evaluate : 1.073 Fit side-chains REVERT: R 204 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.6559 (mpp) REVERT: R 215 MET cc_start: 0.8587 (mtp) cc_final: 0.8335 (mtp) REVERT: R 242 LYS cc_start: 0.7970 (tttp) cc_final: 0.7657 (tttm) REVERT: R 281 MET cc_start: 0.6419 (mmt) cc_final: 0.5960 (mmt) REVERT: R 311 LYS cc_start: 0.8104 (mtpt) cc_final: 0.7320 (mttt) REVERT: A 24 ARG cc_start: 0.7405 (ttm110) cc_final: 0.6700 (ttm110) REVERT: A 259 ARG cc_start: 0.7642 (ptt-90) cc_final: 0.7345 (ptt90) REVERT: A 301 GLU cc_start: 0.5284 (pm20) cc_final: 0.4497 (pp20) REVERT: B 118 MET cc_start: 0.8635 (mtp) cc_final: 0.8204 (mtm) REVERT: B 192 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7255 (mp10) REVERT: G 47 GLU cc_start: 0.7480 (mt-10) cc_final: 0.7140 (tt0) REVERT: S 65 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7173 (ttmp) REVERT: S 93 MET cc_start: 0.7735 (ttm) cc_final: 0.7470 (ttt) REVERT: S 207 LEU cc_start: 0.6795 (OUTLIER) cc_final: 0.6464 (pp) outliers start: 17 outliers final: 11 residues processed: 149 average time/residue: 1.4276 time to fit residues: 224.7788 Evaluate side-chains 151 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 136 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 84 CYS Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 65 LYS Chi-restraints excluded: chain S residue 207 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 ASN S 13 GLN S 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.137895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.107589 restraints weight = 10812.429| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.83 r_work: 0.3070 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.103 8929 Z= 0.142 Angle : 0.513 10.635 12103 Z= 0.267 Chirality : 0.042 0.134 1397 Planarity : 0.003 0.052 1525 Dihedral : 6.678 179.855 1224 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.60 % Allowed : 20.58 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.78 (0.26), residues: 1101 helix: -0.66 (0.28), residues: 368 sheet: 0.50 (0.32), residues: 272 loop : -0.89 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 228 HIS 0.003 0.001 HIS R 264 PHE 0.014 0.001 PHE B 216 TYR 0.010 0.001 TYR A 297 ARG 0.013 0.000 ARG B 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3959.82 seconds wall clock time: 70 minutes 35.72 seconds (4235.72 seconds total)