Starting phenix.real_space_refine on Sat Apr 6 12:19:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smv_40603/04_2024/8smv_40603_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smv_40603/04_2024/8smv_40603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smv_40603/04_2024/8smv_40603.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smv_40603/04_2024/8smv_40603.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smv_40603/04_2024/8smv_40603_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smv_40603/04_2024/8smv_40603_updated.pdb" } resolution = 2.74 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= -0.008 sd= 0.817 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 5217 2.51 5 N 1404 2.21 5 O 1493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 92": "OE1" <-> "OE2" Residue "R GLU 306": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 50": "OD1" <-> "OD2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A ASP 33": "OD1" <-> "OD2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A ASP 223": "OD1" <-> "OD2" Residue "A ASP 240": "OD1" <-> "OD2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A ASP 295": "OD1" <-> "OD2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A ASP 331": "OD1" <-> "OD2" Residue "A TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 368": "OD1" <-> "OD2" Residue "A ASP 378": "OD1" <-> "OD2" Residue "A TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B ASP 76": "OD1" <-> "OD2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 186": "OD1" <-> "OD2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 312": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8169 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2152 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 10, 'TRANS': 257} Chain breaks: 1 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 438 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 970 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1989 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 1 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2592 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.39, per 1000 atoms: 0.54 Number of scatterers: 8169 At special positions: 0 Unit cell: (76.54, 104.06, 131.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 1493 8.00 N 1404 7.00 C 5217 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 178 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 1.5 seconds 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1940 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 11 sheets defined 38.5% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'R' and resid 31 through 54 removed outlier: 3.876A pdb=" N ILE R 35 " --> pdb=" O PHE R 31 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN R 45 " --> pdb=" O VAL R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 58 No H-bonds generated for 'chain 'R' and resid 56 through 58' Processing helix chain 'R' and resid 63 through 79 removed outlier: 3.747A pdb=" N VAL R 78 " --> pdb=" O PHE R 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 90 Processing helix chain 'R' and resid 97 through 130 removed outlier: 3.855A pdb=" N ASN R 101 " --> pdb=" O VAL R 97 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE R 102 " --> pdb=" O VAL R 98 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU R 118 " --> pdb=" O SER R 114 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY R 119 " --> pdb=" O MET R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 135 through 138 No H-bonds generated for 'chain 'R' and resid 135 through 138' Processing helix chain 'R' and resid 141 through 163 removed outlier: 3.654A pdb=" N TRP R 152 " --> pdb=" O LEU R 148 " (cutoff:3.500A) Proline residue: R 161 - end of helix Processing helix chain 'R' and resid 182 through 184 No H-bonds generated for 'chain 'R' and resid 182 through 184' Processing helix chain 'R' and resid 188 through 196 removed outlier: 3.666A pdb=" N GLN R 193 " --> pdb=" O THR R 189 " (cutoff:3.500A) Processing helix chain 'R' and resid 198 through 219 removed outlier: 3.669A pdb=" N ARG R 213 " --> pdb=" O GLY R 209 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL R 214 " --> pdb=" O PHE R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 296 removed outlier: 3.940A pdb=" N PHE R 279 " --> pdb=" O VAL R 275 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET R 280 " --> pdb=" O LEU R 276 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR R 282 " --> pdb=" O ALA R 278 " (cutoff:3.500A) Proline residue: R 285 - end of helix Processing helix chain 'R' and resid 298 through 300 No H-bonds generated for 'chain 'R' and resid 298 through 300' Processing helix chain 'R' and resid 303 through 324 removed outlier: 3.635A pdb=" N SER R 313 " --> pdb=" O ALA R 309 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE R 314 " --> pdb=" O THR R 310 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA R 315 " --> pdb=" O TRP R 311 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER R 316 " --> pdb=" O LEU R 312 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA R 317 " --> pdb=" O SER R 313 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL R 318 " --> pdb=" O PHE R 314 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N CYS R 319 " --> pdb=" O ALA R 315 " (cutoff:3.500A) Proline residue: R 321 - end of helix Processing helix chain 'R' and resid 329 through 339 Processing helix chain 'G' and resid 6 through 24 removed outlier: 3.764A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'A' and resid 10 through 38 removed outlier: 3.970A pdb=" N ASN A 23 " --> pdb=" O GLN A 19 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 63 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.716A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.596A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.711A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 2 through 25 removed outlier: 3.986A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing sheet with id= A, first strand: chain 'R' and resid 169 through 172 removed outlier: 3.983A pdb=" N MET R 177 " --> pdb=" O ASP R 172 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'N' and resid 3 through 8 removed outlier: 3.548A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.574A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.026A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 44 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.992A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.215A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.799A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.951A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.758A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.168A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.699A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) 358 hydrogen bonds defined for protein. 1023 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: 2.19 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2634 1.34 - 1.46: 2053 1.46 - 1.58: 3586 1.58 - 1.70: 0 1.70 - 1.82: 78 Bond restraints: 8351 Sorted by residual: bond pdb=" C6 CLR R 601 " pdb=" C7 CLR R 601 " ideal model delta sigma weight residual 1.492 1.399 0.093 2.00e-02 2.50e+03 2.14e+01 bond pdb=" C10 CLR R 601 " pdb=" C5 CLR R 601 " ideal model delta sigma weight residual 1.519 1.428 0.091 2.00e-02 2.50e+03 2.09e+01 bond pdb=" C4 CLR R 601 " pdb=" C5 CLR R 601 " ideal model delta sigma weight residual 1.506 1.416 0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C5 CLR R 601 " pdb=" C6 CLR R 601 " ideal model delta sigma weight residual 1.332 1.412 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" N THR A 9 " pdb=" CA THR A 9 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.22e+00 ... (remaining 8346 not shown) Histogram of bond angle deviations from ideal: 96.39 - 103.92: 87 103.92 - 111.45: 3669 111.45 - 118.98: 3071 118.98 - 126.51: 4354 126.51 - 134.04: 150 Bond angle restraints: 11331 Sorted by residual: angle pdb=" N THR B 181 " pdb=" CA THR B 181 " pdb=" C THR B 181 " ideal model delta sigma weight residual 110.44 113.70 -3.26 1.20e+00 6.94e-01 7.39e+00 angle pdb=" CA LYS A 338 " pdb=" CB LYS A 338 " pdb=" CG LYS A 338 " ideal model delta sigma weight residual 114.10 118.98 -4.88 2.00e+00 2.50e-01 5.95e+00 angle pdb=" C ASN B 313 " pdb=" N ARG B 314 " pdb=" CA ARG B 314 " ideal model delta sigma weight residual 121.56 125.17 -3.61 1.56e+00 4.11e-01 5.36e+00 angle pdb=" N MET R 137 " pdb=" CA MET R 137 " pdb=" C MET R 137 " ideal model delta sigma weight residual 113.88 111.12 2.76 1.23e+00 6.61e-01 5.04e+00 angle pdb=" CA THR B 181 " pdb=" C THR B 181 " pdb=" O THR B 181 " ideal model delta sigma weight residual 121.89 119.03 2.86 1.29e+00 6.01e-01 4.90e+00 ... (remaining 11326 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4638 17.73 - 35.47: 284 35.47 - 53.20: 44 53.20 - 70.93: 13 70.93 - 88.67: 9 Dihedral angle restraints: 4988 sinusoidal: 1985 harmonic: 3003 Sorted by residual: dihedral pdb=" CA LEU A 291 " pdb=" C LEU A 291 " pdb=" N ASN A 292 " pdb=" CA ASN A 292 " ideal model delta harmonic sigma weight residual -180.00 -149.30 -30.70 0 5.00e+00 4.00e-02 3.77e+01 dihedral pdb=" CA ARG A 231 " pdb=" C ARG A 231 " pdb=" N ARG A 232 " pdb=" CA ARG A 232 " ideal model delta harmonic sigma weight residual -180.00 -156.64 -23.36 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual -180.00 -157.23 -22.77 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 4985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1121 0.064 - 0.128: 139 0.128 - 0.192: 15 0.192 - 0.256: 2 0.256 - 0.320: 1 Chirality restraints: 1278 Sorted by residual: chirality pdb=" C14 CLR R 601 " pdb=" C13 CLR R 601 " pdb=" C15 CLR R 601 " pdb=" C8 CLR R 601 " both_signs ideal model delta sigma weight residual False -2.32 -2.64 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" C10 CLR R 601 " pdb=" C1 CLR R 601 " pdb=" C5 CLR R 601 " pdb=" C9 CLR R 601 " both_signs ideal model delta sigma weight residual False -2.85 -2.61 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C20 CLR R 601 " pdb=" C17 CLR R 601 " pdb=" C21 CLR R 601 " pdb=" C22 CLR R 601 " both_signs ideal model delta sigma weight residual False 2.59 2.80 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1275 not shown) Planarity restraints: 1426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG G 13 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.98e+00 pdb=" C ARG G 13 " 0.035 2.00e-02 2.50e+03 pdb=" O ARG G 13 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS G 14 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.031 5.00e-02 4.00e+02 4.64e-02 3.44e+00 pdb=" N PRO B 236 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 311 " -0.014 2.00e-02 2.50e+03 1.17e-02 3.41e+00 pdb=" CG TRP R 311 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP R 311 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP R 311 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP R 311 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 311 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 311 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 311 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 311 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP R 311 " -0.002 2.00e-02 2.50e+03 ... (remaining 1423 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 207 2.71 - 3.26: 7936 3.26 - 3.80: 11851 3.80 - 4.35: 15663 4.35 - 4.90: 27230 Nonbonded interactions: 62887 Sorted by model distance: nonbonded pdb=" O ASN B 313 " pdb=" OG SER B 331 " model vdw 2.162 2.440 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.171 2.440 nonbonded pdb=" OD1 ASN B 16 " pdb=" NH2 ARG B 19 " model vdw 2.199 2.520 nonbonded pdb=" OD1 ASN B 110 " pdb=" NZ LYS B 127 " model vdw 2.203 2.520 nonbonded pdb=" OE1 GLU R 170 " pdb=" NH2 ARG R 184 " model vdw 2.252 2.520 ... (remaining 62882 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=0.00 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.480 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 24.940 Find NCS groups from input model: 0.220 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:13.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 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 : 0.004 0.093 8351 Z= 0.245 Angle : 0.648 5.932 11331 Z= 0.359 Chirality : 0.045 0.320 1278 Planarity : 0.004 0.046 1426 Dihedral : 12.716 88.667 3039 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.53 (0.27), residues: 1020 helix: 1.64 (0.28), residues: 374 sheet: 0.68 (0.35), residues: 214 loop : -0.99 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP R 311 HIS 0.006 0.001 HIS R 154 PHE 0.009 0.001 PHE B 151 TYR 0.009 0.001 TYR R 324 ARG 0.004 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.040 Fit side-chains REVERT: A 214 VAL cc_start: 0.8988 (p) cc_final: 0.8734 (t) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 1.4260 time to fit residues: 232.4184 Evaluate side-chains 115 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 51 optimal weight: 0.0670 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 0.3980 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 ASN N 3 GLN N 120 GLN A 220 HIS B 75 GLN B 175 GLN B 176 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8351 Z= 0.173 Angle : 0.548 5.725 11331 Z= 0.295 Chirality : 0.044 0.169 1278 Planarity : 0.004 0.045 1426 Dihedral : 4.757 28.401 1189 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.51 % Allowed : 9.68 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.59 (0.26), residues: 1020 helix: 1.69 (0.27), residues: 389 sheet: 0.77 (0.35), residues: 216 loop : -1.09 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 311 HIS 0.004 0.001 HIS R 154 PHE 0.014 0.001 PHE A 212 TYR 0.014 0.001 TYR B 59 ARG 0.005 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 1.185 Fit side-chains REVERT: R 185 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8008 (mt-10) REVERT: A 19 GLN cc_start: 0.7548 (tt0) cc_final: 0.7300 (pt0) REVERT: A 295 ASP cc_start: 0.8111 (p0) cc_final: 0.7857 (p0) outliers start: 22 outliers final: 8 residues processed: 146 average time/residue: 1.4049 time to fit residues: 216.1810 Evaluate side-chains 125 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 116 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain R residue 185 GLU Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 99 optimal weight: 0.1980 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 ASN N 120 GLN A 220 HIS B 156 GLN B 175 GLN B 259 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8351 Z= 0.296 Angle : 0.639 8.469 11331 Z= 0.341 Chirality : 0.048 0.180 1278 Planarity : 0.005 0.047 1426 Dihedral : 5.143 31.037 1189 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.99 % Allowed : 11.39 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.26), residues: 1020 helix: 1.52 (0.27), residues: 388 sheet: 0.82 (0.34), residues: 208 loop : -1.24 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 311 HIS 0.005 0.001 HIS R 154 PHE 0.013 0.002 PHE B 234 TYR 0.012 0.002 TYR R 135 ARG 0.003 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 117 time to evaluate : 0.978 Fit side-chains REVERT: R 35 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8515 (mm) REVERT: R 39 ILE cc_start: 0.8972 (mm) cc_final: 0.8741 (mp) REVERT: N 19 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7572 (ptm160) REVERT: A 19 GLN cc_start: 0.7567 (tt0) cc_final: 0.7331 (pt0) REVERT: B 23 LYS cc_start: 0.8382 (tptt) cc_final: 0.8026 (tppt) REVERT: B 292 PHE cc_start: 0.7774 (OUTLIER) cc_final: 0.7281 (p90) outliers start: 35 outliers final: 14 residues processed: 136 average time/residue: 1.3835 time to fit residues: 198.5257 Evaluate side-chains 130 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain R residue 87 SER Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 292 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 48 optimal weight: 0.1980 chunk 87 optimal weight: 0.8980 chunk 26 optimal weight: 0.0870 chunk 81 optimal weight: 10.0000 overall best weight: 0.5160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 ASN N 120 GLN A 220 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8351 Z= 0.121 Angle : 0.468 5.600 11331 Z= 0.256 Chirality : 0.042 0.163 1278 Planarity : 0.004 0.046 1426 Dihedral : 4.282 26.864 1189 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.16 % Allowed : 14.01 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.62 (0.26), residues: 1020 helix: 1.80 (0.27), residues: 390 sheet: 0.91 (0.33), residues: 214 loop : -1.24 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 311 HIS 0.003 0.001 HIS R 154 PHE 0.012 0.001 PHE A 212 TYR 0.023 0.001 TYR R 150 ARG 0.003 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 0.974 Fit side-chains REVERT: A 19 GLN cc_start: 0.7522 (tt0) cc_final: 0.7315 (pt0) REVERT: B 14 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7978 (mm) REVERT: B 23 LYS cc_start: 0.8479 (tptt) cc_final: 0.8076 (tppt) REVERT: B 217 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7491 (ppp) REVERT: B 292 PHE cc_start: 0.7588 (OUTLIER) cc_final: 0.7217 (p90) outliers start: 19 outliers final: 8 residues processed: 138 average time/residue: 1.4203 time to fit residues: 206.9876 Evaluate side-chains 129 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 292 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 72 optimal weight: 0.4980 chunk 40 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 0.0770 overall best weight: 1.3144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 ASN N 120 GLN A 220 HIS B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8351 Z= 0.195 Angle : 0.540 6.250 11331 Z= 0.292 Chirality : 0.044 0.157 1278 Planarity : 0.004 0.046 1426 Dihedral : 4.504 28.644 1189 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.19 % Allowed : 14.35 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.60 (0.26), residues: 1020 helix: 1.78 (0.27), residues: 391 sheet: 0.93 (0.33), residues: 209 loop : -1.27 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 311 HIS 0.004 0.001 HIS R 154 PHE 0.012 0.001 PHE A 212 TYR 0.015 0.001 TYR R 150 ARG 0.005 0.000 ARG R 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 116 time to evaluate : 1.067 Fit side-chains REVERT: R 287 MET cc_start: 0.9041 (mmp) cc_final: 0.8609 (mmt) REVERT: N 19 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7485 (ptm160) REVERT: B 14 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8040 (mm) REVERT: B 19 ARG cc_start: 0.8009 (ttp80) cc_final: 0.7510 (ttp80) REVERT: B 23 LYS cc_start: 0.8466 (tptt) cc_final: 0.8065 (tppt) REVERT: B 59 TYR cc_start: 0.8548 (OUTLIER) cc_final: 0.8107 (t80) REVERT: B 292 PHE cc_start: 0.7656 (OUTLIER) cc_final: 0.7173 (p90) outliers start: 28 outliers final: 9 residues processed: 131 average time/residue: 1.4173 time to fit residues: 195.6767 Evaluate side-chains 124 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 292 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 57 optimal weight: 0.2980 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 0.1980 chunk 94 optimal weight: 5.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 ASN N 120 GLN A 220 HIS B 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8351 Z= 0.125 Angle : 0.472 6.805 11331 Z= 0.256 Chirality : 0.041 0.161 1278 Planarity : 0.004 0.045 1426 Dihedral : 4.115 25.966 1189 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.85 % Allowed : 15.60 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.76 (0.26), residues: 1020 helix: 1.92 (0.27), residues: 390 sheet: 0.90 (0.32), residues: 228 loop : -1.20 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 311 HIS 0.003 0.001 HIS R 154 PHE 0.012 0.001 PHE A 212 TYR 0.007 0.001 TYR R 324 ARG 0.004 0.000 ARG R 91 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 121 time to evaluate : 0.976 Fit side-chains REVERT: R 61 LEU cc_start: 0.8935 (tt) cc_final: 0.8731 (tt) REVERT: R 287 MET cc_start: 0.8981 (mmp) cc_final: 0.8540 (mmt) REVERT: N 19 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7269 (ptm160) REVERT: B 14 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7985 (mm) REVERT: B 17 GLN cc_start: 0.7560 (tm-30) cc_final: 0.7284 (tm-30) REVERT: B 292 PHE cc_start: 0.7430 (OUTLIER) cc_final: 0.6901 (p90) outliers start: 25 outliers final: 8 residues processed: 138 average time/residue: 1.3885 time to fit residues: 201.9556 Evaluate side-chains 126 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 115 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 292 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 ASN N 39 GLN N 120 GLN A 220 HIS B 175 GLN B 259 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8351 Z= 0.200 Angle : 0.546 6.406 11331 Z= 0.292 Chirality : 0.044 0.172 1278 Planarity : 0.004 0.045 1426 Dihedral : 4.456 28.375 1189 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.19 % Allowed : 15.15 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.64 (0.26), residues: 1020 helix: 1.75 (0.27), residues: 397 sheet: 0.94 (0.33), residues: 211 loop : -1.22 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 311 HIS 0.004 0.001 HIS R 154 PHE 0.012 0.001 PHE A 212 TYR 0.010 0.001 TYR R 324 ARG 0.006 0.000 ARG R 91 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 112 time to evaluate : 0.895 Fit side-chains REVERT: R 61 LEU cc_start: 0.8959 (tt) cc_final: 0.8711 (tt) REVERT: G 17 GLU cc_start: 0.7409 (mp0) cc_final: 0.7155 (pm20) REVERT: N 19 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7485 (ptm160) REVERT: B 14 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.8016 (mm) REVERT: B 19 ARG cc_start: 0.8018 (ttp80) cc_final: 0.7516 (ttp80) REVERT: B 23 LYS cc_start: 0.8408 (tptt) cc_final: 0.8076 (tppt) REVERT: B 292 PHE cc_start: 0.7623 (OUTLIER) cc_final: 0.7039 (p90) outliers start: 28 outliers final: 14 residues processed: 129 average time/residue: 1.3666 time to fit residues: 186.2824 Evaluate side-chains 126 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 109 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 87 SER Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 292 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 ASN N 120 GLN A 220 HIS B 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8351 Z= 0.197 Angle : 0.543 7.049 11331 Z= 0.292 Chirality : 0.044 0.160 1278 Planarity : 0.004 0.045 1426 Dihedral : 4.468 28.961 1189 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.96 % Allowed : 16.17 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.63 (0.26), residues: 1020 helix: 1.71 (0.27), residues: 397 sheet: 0.98 (0.34), residues: 210 loop : -1.22 (0.27), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 311 HIS 0.005 0.001 HIS R 154 PHE 0.012 0.001 PHE A 212 TYR 0.009 0.001 TYR R 324 ARG 0.006 0.000 ARG R 91 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 112 time to evaluate : 0.917 Fit side-chains REVERT: R 61 LEU cc_start: 0.8927 (tt) cc_final: 0.8657 (tt) REVERT: R 195 TRP cc_start: 0.8541 (OUTLIER) cc_final: 0.6894 (t60) REVERT: N 19 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7483 (ptm160) REVERT: B 14 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.8008 (mm) REVERT: B 17 GLN cc_start: 0.7509 (tm-30) cc_final: 0.7091 (tm-30) REVERT: B 19 ARG cc_start: 0.7976 (ttp80) cc_final: 0.7489 (ttp80) REVERT: B 23 LYS cc_start: 0.8358 (tptt) cc_final: 0.7965 (tppt) REVERT: B 217 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7512 (ppp) REVERT: B 292 PHE cc_start: 0.7643 (OUTLIER) cc_final: 0.7155 (p90) outliers start: 26 outliers final: 14 residues processed: 129 average time/residue: 1.3545 time to fit residues: 184.2580 Evaluate side-chains 126 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 87 SER Chi-restraints excluded: chain R residue 195 TRP Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 292 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 27 optimal weight: 0.1980 chunk 81 optimal weight: 0.0870 chunk 85 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 ASN N 120 GLN A 220 HIS B 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8351 Z= 0.132 Angle : 0.484 6.536 11331 Z= 0.262 Chirality : 0.042 0.158 1278 Planarity : 0.004 0.045 1426 Dihedral : 4.112 25.948 1189 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.39 % Allowed : 16.40 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1020 helix: 1.79 (0.27), residues: 397 sheet: 1.01 (0.32), residues: 229 loop : -1.16 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 311 HIS 0.004 0.001 HIS R 154 PHE 0.012 0.001 PHE A 212 TYR 0.007 0.001 TYR R 324 ARG 0.006 0.000 ARG R 91 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 117 time to evaluate : 1.003 Fit side-chains REVERT: R 61 LEU cc_start: 0.8907 (tt) cc_final: 0.8628 (tt) REVERT: R 195 TRP cc_start: 0.8472 (OUTLIER) cc_final: 0.7254 (t60) REVERT: R 287 MET cc_start: 0.8963 (mmp) cc_final: 0.8577 (mmt) REVERT: N 19 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7324 (ptm160) REVERT: B 14 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7970 (mm) REVERT: B 17 GLN cc_start: 0.7562 (tm-30) cc_final: 0.7202 (tm-30) REVERT: B 19 ARG cc_start: 0.7993 (ttp80) cc_final: 0.7524 (ttp80) REVERT: B 23 LYS cc_start: 0.8413 (tptt) cc_final: 0.7964 (tppt) REVERT: B 292 PHE cc_start: 0.7425 (OUTLIER) cc_final: 0.6885 (p90) outliers start: 21 outliers final: 10 residues processed: 129 average time/residue: 1.4015 time to fit residues: 190.7222 Evaluate side-chains 125 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 87 SER Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain R residue 195 TRP Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 292 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 100 optimal weight: 0.0980 chunk 92 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 24 optimal weight: 0.0770 overall best weight: 0.8344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 ASN N 120 GLN A 220 HIS B 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8351 Z= 0.152 Angle : 0.504 7.487 11331 Z= 0.273 Chirality : 0.042 0.171 1278 Planarity : 0.004 0.046 1426 Dihedral : 4.182 26.285 1189 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.16 % Allowed : 16.51 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.80 (0.26), residues: 1020 helix: 1.80 (0.27), residues: 396 sheet: 1.12 (0.33), residues: 222 loop : -1.14 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP R 311 HIS 0.004 0.001 HIS R 154 PHE 0.012 0.001 PHE A 212 TYR 0.009 0.001 TYR R 324 ARG 0.007 0.000 ARG R 91 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 1.024 Fit side-chains REVERT: R 61 LEU cc_start: 0.8911 (tt) cc_final: 0.8602 (tt) REVERT: R 195 TRP cc_start: 0.8485 (OUTLIER) cc_final: 0.6953 (t60) REVERT: N 19 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7348 (ptm160) REVERT: B 14 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7941 (mm) REVERT: B 17 GLN cc_start: 0.7554 (tm-30) cc_final: 0.7222 (tm-30) REVERT: B 19 ARG cc_start: 0.7999 (ttp80) cc_final: 0.7518 (ttp80) REVERT: B 23 LYS cc_start: 0.8440 (tptt) cc_final: 0.7959 (tppt) REVERT: B 292 PHE cc_start: 0.7444 (OUTLIER) cc_final: 0.6894 (p90) outliers start: 19 outliers final: 13 residues processed: 124 average time/residue: 1.5168 time to fit residues: 198.3771 Evaluate side-chains 127 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 110 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 87 SER Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 195 TRP Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 292 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.0980 chunk 11 optimal weight: 5.9990 chunk 22 optimal weight: 0.0370 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 0.2980 chunk 70 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 0.0970 overall best weight: 0.2256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 ASN N 120 GLN A 220 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.145230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.120060 restraints weight = 10762.067| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.81 r_work: 0.3405 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8351 Z= 0.105 Angle : 0.445 7.253 11331 Z= 0.242 Chirality : 0.040 0.191 1278 Planarity : 0.004 0.045 1426 Dihedral : 3.774 24.735 1189 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.48 % Allowed : 16.97 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.00 (0.26), residues: 1020 helix: 1.89 (0.27), residues: 397 sheet: 1.19 (0.32), residues: 235 loop : -1.00 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 311 HIS 0.003 0.000 HIS R 154 PHE 0.011 0.001 PHE A 212 TYR 0.008 0.001 TYR B 124 ARG 0.006 0.000 ARG R 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3663.59 seconds wall clock time: 66 minutes 7.43 seconds (3967.43 seconds total)