Starting phenix.real_space_refine on Thu Jan 18 12:52:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aue_11927/01_2024/7aue_11927_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aue_11927/01_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_11927/01_2024/7aue_11927.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aue_11927/01_2024/7aue_11927.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aue_11927/01_2024/7aue_11927_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aue_11927/01_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-1.21-5211/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: 4.80, per 1000 atoms: 0.55 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: 3.15 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: 1.72 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: 2.23 Time building geometry restraints manager: 3.41 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 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: 5.110 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.010 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.570 ------------------------------------------------------------------------------- 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= 0.447 Angle : 0.804 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 : 1.098 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: 1.2483 time to fit residues: 229.4709 Evaluate side-chains 138 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 C 5 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8929 Z= 0.133 Angle : 0.532 9.579 12103 Z= 0.285 Chirality : 0.043 0.201 1397 Planarity : 0.004 0.045 1525 Dihedral : 7.312 179.982 1228 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.60 % Allowed : 13.75 % 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: -3.12 (0.22), residues: 1101 helix: -3.37 (0.19), residues: 362 sheet: -0.59 (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 B 216 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: 15 poor density : 147 time to evaluate : 1.003 Fit side-chains REVERT: R 200 MET cc_start: 0.7098 (mtt) cc_final: 0.6710 (mtt) REVERT: R 204 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.6318 (mpp) REVERT: R 242 LYS cc_start: 0.7893 (tttp) cc_final: 0.7542 (tttm) REVERT: R 311 LYS cc_start: 0.8058 (mtpt) cc_final: 0.7329 (mttt) REVERT: A 199 HIS cc_start: 0.6842 (t-90) cc_final: 0.6390 (t-170) REVERT: A 259 ARG cc_start: 0.7605 (ptt-90) cc_final: 0.7358 (ptt90) REVERT: A 301 GLU cc_start: 0.5580 (pm20) cc_final: 0.5044 (tm-30) REVERT: A 351 ILE cc_start: 0.7456 (OUTLIER) cc_final: 0.7185 (mm) REVERT: B 37 ASP cc_start: 0.7519 (m-30) cc_final: 0.7216 (m-30) REVERT: B 93 ASP cc_start: 0.7816 (p0) cc_final: 0.7517 (p0) REVERT: B 118 MET cc_start: 0.8637 (mtp) cc_final: 0.8229 (mtm) REVERT: G 21 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7197 (tpp) REVERT: G 47 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7138 (tt0) REVERT: S 93 MET cc_start: 0.7730 (ttm) cc_final: 0.7505 (ttt) REVERT: S 128 MET cc_start: 0.8424 (mmm) cc_final: 0.8072 (mmt) outliers start: 15 outliers final: 2 residues processed: 152 average time/residue: 1.4130 time to fit residues: 226.9102 Evaluate side-chains 147 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 142 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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: 0.2980 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: 4.9990 chunk 108 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 0.4980 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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: 0.8156 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8929 Z= 0.275 Angle : 0.631 10.108 12103 Z= 0.335 Chirality : 0.047 0.228 1397 Planarity : 0.004 0.038 1525 Dihedral : 7.242 177.035 1224 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.45 % Allowed : 14.93 % Favored : 82.62 % 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: -2.39 (0.23), residues: 1101 helix: -2.53 (0.23), residues: 367 sheet: -0.04 (0.31), residues: 272 loop : -1.58 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 99 HIS 0.005 0.001 HIS B 71 PHE 0.017 0.002 PHE A 355 TYR 0.029 0.002 TYR A 297 ARG 0.003 0.000 ARG A 326 *********************** 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 164 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 141 time to evaluate : 1.027 Fit side-chains REVERT: R 204 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.6437 (mpp) REVERT: R 242 LYS cc_start: 0.7959 (tttp) cc_final: 0.7527 (tttm) REVERT: R 281 MET cc_start: 0.6807 (mtm) cc_final: 0.6532 (mtm) REVERT: R 311 LYS cc_start: 0.8091 (mtpt) cc_final: 0.7327 (mttt) REVERT: A 199 HIS cc_start: 0.6957 (t-90) cc_final: 0.6422 (t-170) REVERT: A 301 GLU cc_start: 0.5668 (pm20) cc_final: 0.4731 (pp20) REVERT: B 37 ASP cc_start: 0.7348 (m-30) cc_final: 0.7073 (m-30) REVERT: B 93 ASP cc_start: 0.7855 (p0) cc_final: 0.7550 (p0) REVERT: B 118 MET cc_start: 0.8646 (mtp) cc_final: 0.8207 (mtm) REVERT: B 192 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7387 (mp10) REVERT: G 47 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7108 (tt0) REVERT: S 93 MET cc_start: 0.7772 (ttm) cc_final: 0.7544 (ttt) outliers start: 23 outliers final: 5 residues processed: 153 average time/residue: 1.4590 time to fit residues: 235.6594 Evaluate side-chains 141 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 134 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 245 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 7.9990 chunk 75 optimal weight: 0.5980 chunk 51 optimal weight: 0.0070 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.1000 ------------------------------------------------------------------------------- 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: 0.8103 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 8929 Z= 0.146 Angle : 0.527 10.331 12103 Z= 0.278 Chirality : 0.043 0.188 1397 Planarity : 0.003 0.035 1525 Dihedral : 6.911 178.994 1224 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.45 % Allowed : 16.31 % Favored : 81.24 % 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: -1.83 (0.24), residues: 1101 helix: -1.85 (0.26), residues: 364 sheet: 0.05 (0.31), residues: 273 loop : -1.31 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 228 HIS 0.004 0.001 HIS R 264 PHE 0.015 0.001 PHE B 216 TYR 0.024 0.001 TYR A 297 ARG 0.005 0.000 ARG S 87 *********************** 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 164 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 141 time to evaluate : 0.956 Fit side-chains REVERT: R 46 VAL cc_start: 0.8511 (p) cc_final: 0.8308 (t) REVERT: R 204 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.6403 (mpp) REVERT: R 242 LYS cc_start: 0.7914 (tttp) cc_final: 0.7604 (tttm) REVERT: R 310 ARG cc_start: 0.7803 (ttp-170) cc_final: 0.7551 (ttp80) REVERT: R 311 LYS cc_start: 0.8053 (mtpt) cc_final: 0.7232 (mttt) REVERT: A 259 ARG cc_start: 0.7617 (ptt-90) cc_final: 0.7333 (ptt90) REVERT: A 301 GLU cc_start: 0.5610 (pm20) cc_final: 0.4725 (pp20) REVERT: A 351 ILE cc_start: 0.7684 (OUTLIER) cc_final: 0.7376 (mm) REVERT: B 93 ASP cc_start: 0.7794 (p0) cc_final: 0.7462 (p0) REVERT: B 118 MET cc_start: 0.8639 (mtp) cc_final: 0.8211 (mtm) REVERT: B 192 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7356 (mp10) REVERT: B 290 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8463 (mp) REVERT: G 21 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.7049 (tpp) REVERT: G 47 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7151 (tt0) REVERT: S 65 LYS cc_start: 0.7580 (tptt) cc_final: 0.7361 (tttp) REVERT: S 93 MET cc_start: 0.7712 (ttm) cc_final: 0.7458 (ttt) outliers start: 23 outliers final: 8 residues processed: 149 average time/residue: 1.4296 time to fit residues: 224.8316 Evaluate side-chains 153 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 140 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 234 MET Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 351 ILE 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 B residue 290 ILE Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 46 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 0.1980 chunk 95 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- 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 S 113 GLN S 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 8929 Z= 0.354 Angle : 0.681 10.141 12103 Z= 0.360 Chirality : 0.049 0.190 1397 Planarity : 0.004 0.038 1525 Dihedral : 7.334 176.773 1224 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.77 % Allowed : 17.06 % Favored : 80.17 % 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: -1.86 (0.24), residues: 1101 helix: -1.96 (0.25), residues: 363 sheet: 0.19 (0.31), residues: 272 loop : -1.34 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 99 HIS 0.009 0.002 HIS R 264 PHE 0.020 0.002 PHE B 216 TYR 0.020 0.002 TYR A 297 ARG 0.005 0.001 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 167 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 141 time to evaluate : 0.953 Fit side-chains REVERT: R 204 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.6568 (mpp) REVERT: R 242 LYS cc_start: 0.7871 (tttp) cc_final: 0.7478 (tttm) REVERT: R 311 LYS cc_start: 0.8118 (mtpt) cc_final: 0.7329 (mttt) REVERT: A 297 TYR cc_start: 0.5872 (t80) cc_final: 0.5604 (t80) REVERT: A 301 GLU cc_start: 0.5578 (pm20) cc_final: 0.4774 (pp20) REVERT: A 351 ILE cc_start: 0.7849 (OUTLIER) cc_final: 0.7490 (mt) REVERT: A 353 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7009 (mtm180) REVERT: B 118 MET cc_start: 0.8654 (mtp) cc_final: 0.8228 (mtm) REVERT: B 290 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8450 (mp) REVERT: G 47 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7105 (tt0) REVERT: S 93 MET cc_start: 0.7777 (ttm) cc_final: 0.7546 (ttt) outliers start: 26 outliers final: 13 residues processed: 154 average time/residue: 1.3326 time to fit residues: 217.2611 Evaluate side-chains 154 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 234 MET Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 353 ARG 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 285 ASN Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 290 ILE 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: 3.9990 chunk 95 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 102 optimal weight: 0.0770 overall best weight: 2.6146 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 8929 Z= 0.275 Angle : 0.629 10.100 12103 Z= 0.333 Chirality : 0.047 0.184 1397 Planarity : 0.004 0.036 1525 Dihedral : 7.253 177.530 1224 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.73 % Allowed : 16.95 % Favored : 79.32 % 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: -1.72 (0.24), residues: 1101 helix: -1.79 (0.25), residues: 362 sheet: 0.18 (0.31), residues: 277 loop : -1.27 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 228 HIS 0.007 0.001 HIS R 264 PHE 0.019 0.002 PHE B 216 TYR 0.018 0.002 TYR A 297 ARG 0.006 0.000 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: 35 poor density : 137 time to evaluate : 0.991 Fit side-chains REVERT: R 204 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.6592 (mpp) REVERT: R 215 MET cc_start: 0.8566 (mtp) cc_final: 0.8340 (mtp) REVERT: R 242 LYS cc_start: 0.7867 (tttp) cc_final: 0.7468 (tttm) REVERT: R 311 LYS cc_start: 0.8116 (mtpt) cc_final: 0.7325 (mttt) REVERT: A 288 GLU cc_start: 0.5781 (OUTLIER) cc_final: 0.5295 (tp30) REVERT: A 301 GLU cc_start: 0.5598 (pm20) cc_final: 0.4763 (pp20) REVERT: A 351 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7512 (mt) REVERT: B 118 MET cc_start: 0.8649 (mtp) cc_final: 0.8289 (mtm) REVERT: B 192 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7282 (mp10) REVERT: B 290 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8450 (mp) REVERT: G 47 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7088 (tt0) REVERT: S 93 MET cc_start: 0.7756 (ttm) cc_final: 0.7522 (ttt) outliers start: 35 outliers final: 16 residues processed: 157 average time/residue: 1.3261 time to fit residues: 220.6628 Evaluate side-chains 158 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 137 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 228 VAL Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 231 SER 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 351 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 192 GLN 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 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: 4.9990 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2268 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= 0.142 Angle : 0.516 10.434 12103 Z= 0.271 Chirality : 0.043 0.152 1397 Planarity : 0.003 0.050 1525 Dihedral : 6.826 179.871 1224 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.13 % Allowed : 18.44 % 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: -1.30 (0.25), residues: 1101 helix: -1.30 (0.27), residues: 363 sheet: 0.35 (0.32), residues: 273 loop : -1.12 (0.28), residues: 465 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 0.011 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 161 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 141 time to evaluate : 0.974 Fit side-chains REVERT: R 46 VAL cc_start: 0.8505 (p) cc_final: 0.8295 (t) REVERT: R 204 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.6396 (mpp) REVERT: R 242 LYS cc_start: 0.7907 (tttp) cc_final: 0.7592 (tttm) REVERT: R 310 ARG cc_start: 0.7739 (ttp-170) cc_final: 0.7456 (ttp80) REVERT: R 311 LYS cc_start: 0.8001 (mtpt) cc_final: 0.7247 (mttt) REVERT: A 259 ARG cc_start: 0.7613 (ptt-90) cc_final: 0.7314 (ptt90) REVERT: A 301 GLU cc_start: 0.5356 (pm20) cc_final: 0.4566 (pp20) REVERT: A 351 ILE cc_start: 0.7698 (OUTLIER) cc_final: 0.7467 (mm) REVERT: B 118 MET cc_start: 0.8626 (mtp) cc_final: 0.8191 (mtm) REVERT: G 47 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7096 (tt0) REVERT: S 93 MET cc_start: 0.7711 (ttm) cc_final: 0.7436 (ttt) outliers start: 20 outliers final: 9 residues processed: 150 average time/residue: 1.3033 time to fit residues: 207.5560 Evaluate side-chains 148 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 137 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 204 MET Chi-restraints excluded: chain R residue 228 VAL 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 A residue 351 ILE Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 286 ILE 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: 3.9990 chunk 20 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 72 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 101 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 307 GLN B 254 ASN G 24 ASN S 113 GLN ** S 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 8929 Z= 0.292 Angle : 0.639 10.389 12103 Z= 0.336 Chirality : 0.048 0.161 1397 Planarity : 0.004 0.043 1525 Dihedral : 7.147 176.989 1224 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.99 % Allowed : 18.98 % Favored : 78.04 % 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: -1.44 (0.25), residues: 1101 helix: -1.52 (0.26), residues: 366 sheet: 0.40 (0.32), residues: 272 loop : -1.18 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 99 HIS 0.009 0.001 HIS R 264 PHE 0.018 0.002 PHE B 216 TYR 0.016 0.002 TYR R 153 ARG 0.012 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 161 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 133 time to evaluate : 0.912 Fit side-chains REVERT: R 204 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.6572 (mpp) REVERT: R 242 LYS cc_start: 0.7869 (tttp) cc_final: 0.7426 (tttm) REVERT: R 281 MET cc_start: 0.6953 (mtm) cc_final: 0.6554 (mtm) REVERT: R 311 LYS cc_start: 0.8118 (mtpt) cc_final: 0.7325 (mttt) REVERT: A 232 TYR cc_start: 0.7708 (p90) cc_final: 0.7450 (p90) REVERT: A 259 ARG cc_start: 0.7689 (ptt-90) cc_final: 0.7371 (ptt90) REVERT: A 301 GLU cc_start: 0.5438 (pm20) cc_final: 0.4621 (pp20) REVERT: A 351 ILE cc_start: 0.7834 (OUTLIER) cc_final: 0.7476 (mm) REVERT: A 353 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7118 (mtp180) REVERT: B 118 MET cc_start: 0.8651 (mtp) cc_final: 0.8286 (mtm) REVERT: G 47 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7103 (tt0) REVERT: S 93 MET cc_start: 0.7763 (ttm) cc_final: 0.7513 (ttt) REVERT: S 207 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6629 (pp) outliers start: 28 outliers final: 15 residues processed: 150 average time/residue: 1.3376 time to fit residues: 212.8217 Evaluate side-chains 152 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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 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 231 SER Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 353 ARG 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 46 LYS Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 207 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 307 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: 0.8188 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 8929 Z= 0.368 Angle : 0.701 10.178 12103 Z= 0.370 Chirality : 0.050 0.173 1397 Planarity : 0.004 0.045 1525 Dihedral : 7.374 176.800 1224 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.77 % Allowed : 19.40 % 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: -1.60 (0.25), residues: 1101 helix: -1.67 (0.25), residues: 363 sheet: 0.39 (0.32), residues: 272 loop : -1.31 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 99 HIS 0.010 0.002 HIS R 264 PHE 0.020 0.002 PHE B 216 TYR 0.016 0.002 TYR A 297 ARG 0.013 0.001 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 157 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 131 time to evaluate : 0.991 Fit side-chains REVERT: R 204 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.6514 (mpp) REVERT: R 242 LYS cc_start: 0.7853 (tttp) cc_final: 0.7462 (tttm) REVERT: R 311 LYS cc_start: 0.8124 (mtpt) cc_final: 0.7333 (mttt) REVERT: A 232 TYR cc_start: 0.7836 (p90) cc_final: 0.7518 (p90) REVERT: A 301 GLU cc_start: 0.5512 (pm20) cc_final: 0.4654 (pp20) REVERT: A 328 SER cc_start: 0.8584 (t) cc_final: 0.8357 (t) REVERT: A 351 ILE cc_start: 0.7865 (OUTLIER) cc_final: 0.7517 (mt) REVERT: A 353 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7120 (mtp180) REVERT: B 118 MET cc_start: 0.8654 (mtp) cc_final: 0.8289 (mtm) REVERT: G 47 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7169 (tt0) REVERT: S 93 MET cc_start: 0.7805 (ttm) cc_final: 0.7568 (ttt) outliers start: 26 outliers final: 19 residues processed: 150 average time/residue: 1.3030 time to fit residues: 207.6173 Evaluate side-chains 152 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 130 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 197 LEU 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 231 SER 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 A residue 353 ARG 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 285 ASN Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 150 SER 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: 0.9980 chunk 109 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 307 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: 0.8136 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 8929 Z= 0.192 Angle : 0.570 10.231 12103 Z= 0.300 Chirality : 0.045 0.144 1397 Planarity : 0.004 0.057 1525 Dihedral : 7.032 178.685 1224 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.24 % Allowed : 20.47 % Favored : 77.29 % 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: -1.30 (0.25), residues: 1101 helix: -1.31 (0.26), residues: 366 sheet: 0.46 (0.32), residues: 271 loop : -1.18 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 228 HIS 0.004 0.001 HIS R 264 PHE 0.017 0.001 PHE B 216 TYR 0.012 0.001 TYR A 297 ARG 0.014 0.000 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 152 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 1.040 Fit side-chains REVERT: R 46 VAL cc_start: 0.8505 (p) cc_final: 0.8263 (t) REVERT: R 204 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.6553 (mpp) REVERT: R 242 LYS cc_start: 0.7874 (tttp) cc_final: 0.7492 (tttm) REVERT: R 311 LYS cc_start: 0.8066 (mtpt) cc_final: 0.7302 (mttt) REVERT: A 259 ARG cc_start: 0.7654 (ptt-90) cc_final: 0.7331 (ptt90) REVERT: A 301 GLU cc_start: 0.5391 (pm20) cc_final: 0.4566 (pp20) REVERT: A 351 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7464 (mm) REVERT: B 118 MET cc_start: 0.8639 (mtp) cc_final: 0.8267 (mtm) REVERT: G 47 GLU cc_start: 0.7469 (mt-10) cc_final: 0.7082 (tt0) REVERT: S 93 MET cc_start: 0.7734 (ttm) cc_final: 0.7481 (ttt) outliers start: 21 outliers final: 15 residues processed: 143 average time/residue: 1.3721 time to fit residues: 207.8550 Evaluate side-chains 146 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 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 231 SER Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 351 ILE 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 46 LYS Chi-restraints excluded: chain S residue 143 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.0570 chunk 87 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 307 GLN B 254 ASN G 24 ASN S 13 GLN S 113 GLN S 171 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.138250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.107893 restraints weight = 10716.135| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.84 r_work: 0.3046 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2422 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= 0.154 Angle : 0.529 10.498 12103 Z= 0.276 Chirality : 0.043 0.137 1397 Planarity : 0.003 0.052 1525 Dihedral : 6.776 179.489 1224 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.71 % Allowed : 20.90 % Favored : 77.40 % 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: -1.03 (0.25), residues: 1101 helix: -0.96 (0.27), residues: 368 sheet: 0.44 (0.32), residues: 273 loop : -1.00 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 228 HIS 0.004 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3829.53 seconds wall clock time: 68 minutes 29.69 seconds (4109.69 seconds total)