Starting phenix.real_space_refine on Mon Feb 19 10:41:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n38_9341/02_2024/6n38_9341.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n38_9341/02_2024/6n38_9341.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n38_9341/02_2024/6n38_9341.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n38_9341/02_2024/6n38_9341.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n38_9341/02_2024/6n38_9341.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n38_9341/02_2024/6n38_9341.pdb" } resolution = 3.7 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= 0.003 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 110 5.16 5 C 15545 2.51 5 N 4442 2.21 5 O 4359 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I ARG 59": "NH1" <-> "NH2" Residue "I ASP 66": "OD1" <-> "OD2" Residue "I ASP 151": "OD1" <-> "OD2" Residue "I PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 228": "NH1" <-> "NH2" Residue "I PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 262": "OE1" <-> "OE2" Residue "I PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 291": "OD1" <-> "OD2" Residue "I PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 330": "OD1" <-> "OD2" Residue "I TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 152": "OD1" <-> "OD2" Residue "G PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 351": "OE1" <-> "OE2" Residue "G ARG 365": "NH1" <-> "NH2" Residue "H TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 228": "NH1" <-> "NH2" Residue "H PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 359": "NH1" <-> "NH2" Residue "H TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 579": "OE1" <-> "OE2" Residue "A TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 93": "OD1" <-> "OD2" Residue "B TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 80": "OD1" <-> "OD2" Residue "E TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 87": "OD1" <-> "OD2" Residue "C PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24456 Number of models: 1 Model: "" Number of chains: 11 Chain: "I" Number of atoms: 4047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4047 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 32, 'TRANS': 495} Chain breaks: 1 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 16, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 114 Chain: "G" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1903 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 14, 'TRANS': 225} Chain breaks: 1 Chain: "H" Number of atoms: 4085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4085 Classifications: {'peptide': 532} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 32, 'TRANS': 499} Chain breaks: 1 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 18, 'ARG:plan': 6, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 132 Chain: "K" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 105 Classifications: {'peptide': 21} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'TRANS': 20} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'UNK:plan-1': 21} Unresolved non-hydrogen planarities: 21 Chain: "L" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 90 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'TRANS': 17} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2375 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2376 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2378 Classifications: {'peptide': 300} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2374 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 279} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 2356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2356 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 21, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "F" Number of atoms: 2367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2367 Classifications: {'peptide': 300} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 12.44, per 1000 atoms: 0.51 Number of scatterers: 24456 At special positions: 0 Unit cell: (134.26, 143.85, 183.58, 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 110 16.00 O 4359 8.00 N 4442 7.00 C 15545 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 8.81 Conformation dependent library (CDL) restraints added in 4.3 seconds 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5960 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 41 sheets defined 37.7% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain 'I' and resid 47 through 67 removed outlier: 3.780A pdb=" N ASP I 67 " --> pdb=" O LYS I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 77 removed outlier: 4.656A pdb=" N SER I 74 " --> pdb=" O GLU I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 196 removed outlier: 5.036A pdb=" N THR I 189 " --> pdb=" O PRO I 185 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU I 192 " --> pdb=" O SER I 188 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 248 removed outlier: 4.935A pdb=" N LEU I 243 " --> pdb=" O GLY I 239 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU I 244 " --> pdb=" O TYR I 240 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 253 Processing helix chain 'I' and resid 261 through 264 Processing helix chain 'I' and resid 290 through 292 No H-bonds generated for 'chain 'I' and resid 290 through 292' Processing helix chain 'I' and resid 327 through 331 Processing helix chain 'I' and resid 355 through 360 Processing helix chain 'I' and resid 364 through 369 Processing helix chain 'I' and resid 420 through 426 Processing helix chain 'I' and resid 459 through 469 removed outlier: 3.719A pdb=" N LEU I 468 " --> pdb=" O VAL I 464 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY I 469 " --> pdb=" O MET I 465 " (cutoff:3.500A) Processing helix chain 'I' and resid 470 through 476 Processing helix chain 'I' and resid 478 through 487 Processing helix chain 'I' and resid 488 through 490 No H-bonds generated for 'chain 'I' and resid 488 through 490' Processing helix chain 'I' and resid 494 through 502 Processing helix chain 'I' and resid 532 through 535 Processing helix chain 'I' and resid 536 through 553 removed outlier: 3.596A pdb=" N ASP I 540 " --> pdb=" O ALA I 536 " (cutoff:3.500A) Processing helix chain 'I' and resid 554 through 556 No H-bonds generated for 'chain 'I' and resid 554 through 556' Processing helix chain 'G' and resid 123 through 140 removed outlier: 3.793A pdb=" N TYR G 140 " --> pdb=" O ILE G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 146 Processing helix chain 'G' and resid 152 through 162 Processing helix chain 'G' and resid 169 through 173 Processing helix chain 'G' and resid 176 through 187 Proline residue: G 185 - end of helix Processing helix chain 'G' and resid 193 through 205 removed outlier: 3.550A pdb=" N LEU G 197 " --> pdb=" O THR G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 235 through 239 Processing helix chain 'G' and resid 261 through 269 Processing helix chain 'G' and resid 272 through 286 removed outlier: 4.225A pdb=" N VAL G 284 " --> pdb=" O ALA G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 303 No H-bonds generated for 'chain 'G' and resid 301 through 303' Processing helix chain 'H' and resid 46 through 65 Processing helix chain 'H' and resid 67 through 80 removed outlier: 3.597A pdb=" N LEU H 71 " --> pdb=" O ASP H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 120 through 124 removed outlier: 4.094A pdb=" N THR H 124 " --> pdb=" O PRO H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 197 removed outlier: 4.849A pdb=" N THR H 189 " --> pdb=" O PRO H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 237 through 249 Processing helix chain 'H' and resid 250 through 253 Processing helix chain 'H' and resid 261 through 264 Processing helix chain 'H' and resid 290 through 292 No H-bonds generated for 'chain 'H' and resid 290 through 292' Processing helix chain 'H' and resid 359 through 364 Processing helix chain 'H' and resid 420 through 425 removed outlier: 3.948A pdb=" N GLN H 425 " --> pdb=" O ARG H 421 " (cutoff:3.500A) Processing helix chain 'H' and resid 460 through 471 Processing helix chain 'H' and resid 478 through 488 removed outlier: 3.618A pdb=" N LEU H 488 " --> pdb=" O GLY H 484 " (cutoff:3.500A) Processing helix chain 'H' and resid 494 through 502 Processing helix chain 'H' and resid 532 through 535 Processing helix chain 'H' and resid 536 through 554 removed outlier: 3.917A pdb=" N ASP H 540 " --> pdb=" O ALA H 536 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 20 Processing helix chain 'L' and resid 2 through 18 Processing helix chain 'A' and resid 15 through 35 removed outlier: 3.888A pdb=" N PHE A 19 " --> pdb=" O MET A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 56 Proline residue: A 55 - end of helix Processing helix chain 'A' and resid 89 through 92 Processing helix chain 'A' and resid 190 through 193 Processing helix chain 'A' and resid 194 through 219 Processing helix chain 'A' and resid 233 through 256 removed outlier: 3.886A pdb=" N ALA A 242 " --> pdb=" O TRP A 238 " (cutoff:3.500A) Proline residue: A 248 - end of helix removed outlier: 4.137A pdb=" N GLU A 252 " --> pdb=" O PRO A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 276 removed outlier: 4.225A pdb=" N LEU A 264 " --> pdb=" O HIS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 removed outlier: 3.507A pdb=" N VAL A 287 " --> pdb=" O VAL A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 297 Processing helix chain 'A' and resid 298 through 312 Processing helix chain 'D' and resid 15 through 35 removed outlier: 3.653A pdb=" N PHE D 19 " --> pdb=" O MET D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 56 Proline residue: D 55 - end of helix Processing helix chain 'D' and resid 89 through 92 removed outlier: 3.795A pdb=" N SER D 92 " --> pdb=" O SER D 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 89 through 92' Processing helix chain 'D' and resid 190 through 193 Processing helix chain 'D' and resid 194 through 217 Processing helix chain 'D' and resid 233 through 256 Proline residue: D 248 - end of helix removed outlier: 4.055A pdb=" N GLU D 252 " --> pdb=" O PRO D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 276 Processing helix chain 'D' and resid 294 through 297 Processing helix chain 'D' and resid 298 through 312 Processing helix chain 'B' and resid 15 through 35 removed outlier: 3.524A pdb=" N PHE B 19 " --> pdb=" O MET B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 56 Proline residue: B 55 - end of helix Processing helix chain 'B' and resid 89 through 92 removed outlier: 3.767A pdb=" N SER B 92 " --> pdb=" O SER B 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 89 through 92' Processing helix chain 'B' and resid 190 through 193 Processing helix chain 'B' and resid 194 through 218 Processing helix chain 'B' and resid 234 through 256 Proline residue: B 248 - end of helix removed outlier: 4.091A pdb=" N GLU B 252 " --> pdb=" O PRO B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 276 removed outlier: 4.222A pdb=" N LEU B 264 " --> pdb=" O HIS B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 297 Processing helix chain 'B' and resid 298 through 312 Processing helix chain 'E' and resid 15 through 35 removed outlier: 3.931A pdb=" N PHE E 19 " --> pdb=" O MET E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 56 Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 190 through 193 Processing helix chain 'E' and resid 194 through 218 Processing helix chain 'E' and resid 233 through 256 Proline residue: E 248 - end of helix removed outlier: 4.281A pdb=" N GLU E 252 " --> pdb=" O PRO E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 276 removed outlier: 4.211A pdb=" N LEU E 264 " --> pdb=" O HIS E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 287 removed outlier: 4.253A pdb=" N VAL E 287 " --> pdb=" O VAL E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 297 Processing helix chain 'E' and resid 298 through 311 Processing helix chain 'C' and resid 15 through 35 removed outlier: 3.896A pdb=" N PHE C 19 " --> pdb=" O MET C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 56 Proline residue: C 55 - end of helix Processing helix chain 'C' and resid 89 through 92 Processing helix chain 'C' and resid 190 through 193 Processing helix chain 'C' and resid 194 through 218 Processing helix chain 'C' and resid 233 through 256 Proline residue: C 248 - end of helix removed outlier: 4.085A pdb=" N GLU C 252 " --> pdb=" O PRO C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 276 removed outlier: 4.073A pdb=" N LEU C 264 " --> pdb=" O HIS C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 287 Processing helix chain 'C' and resid 294 through 297 Processing helix chain 'C' and resid 298 through 312 Processing helix chain 'F' and resid 15 through 35 removed outlier: 4.025A pdb=" N PHE F 19 " --> pdb=" O MET F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 56 removed outlier: 3.566A pdb=" N LEU F 54 " --> pdb=" O ASP F 51 " (cutoff:3.500A) Proline residue: F 55 - end of helix No H-bonds generated for 'chain 'F' and resid 51 through 56' Processing helix chain 'F' and resid 89 through 92 Processing helix chain 'F' and resid 190 through 193 Processing helix chain 'F' and resid 194 through 219 Processing helix chain 'F' and resid 233 through 256 Proline residue: F 248 - end of helix Processing helix chain 'F' and resid 260 through 276 removed outlier: 4.180A pdb=" N LEU F 264 " --> pdb=" O HIS F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 297 Processing helix chain 'F' and resid 298 through 313 Processing sheet with id=AA1, first strand: chain 'I' and resid 429 through 432 removed outlier: 4.793A pdb=" N THR I 115 " --> pdb=" O ASP I 430 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N CYS I 432 " --> pdb=" O GLU I 113 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N GLU I 113 " --> pdb=" O CYS I 432 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 106 through 108 Processing sheet with id=AA3, first strand: chain 'I' and resid 139 through 148 removed outlier: 5.801A pdb=" N VAL I 141 " --> pdb=" O ALA I 161 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA I 161 " --> pdb=" O VAL I 141 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER I 154 " --> pdb=" O LEU I 279 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 217 through 220 Processing sheet with id=AA5, first strand: chain 'I' and resid 305 through 307 removed outlier: 4.688A pdb=" N ILE I 412 " --> pdb=" O LEU I 307 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 305 through 307 removed outlier: 4.688A pdb=" N ILE I 412 " --> pdb=" O LEU I 307 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR I 407 " --> pdb=" O GLY I 343 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY I 343 " --> pdb=" O THR I 407 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N SER I 409 " --> pdb=" O VAL I 341 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VAL I 341 " --> pdb=" O SER I 409 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ARG I 411 " --> pdb=" O ASP I 339 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N THR I 415 " --> pdb=" O ILE I 335 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ILE I 335 " --> pdb=" O THR I 415 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 321 through 323 removed outlier: 4.110A pdb=" N THR I 388 " --> pdb=" O LEU I 323 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL I 353 " --> pdb=" O TYR I 374 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N THR I 376 " --> pdb=" O VAL I 353 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 504 through 516 removed outlier: 3.526A pdb=" N ALA I 506 " --> pdb=" O THR I 529 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 209 through 221 removed outlier: 4.277A pdb=" N ALA G 210 " --> pdb=" O GLN G 256 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLN G 256 " --> pdb=" O ALA G 210 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL G 212 " --> pdb=" O LEU G 254 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU G 254 " --> pdb=" O VAL G 212 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N HIS G 214 " --> pdb=" O GLN G 252 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N GLN G 252 " --> pdb=" O HIS G 214 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ASP G 216 " --> pdb=" O ASN G 250 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ASN G 250 " --> pdb=" O ASP G 216 " (cutoff:3.500A) removed outlier: 10.412A pdb=" N ASP G 291 " --> pdb=" O VAL G 249 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLY G 251 " --> pdb=" O ASP G 291 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ARG G 293 " --> pdb=" O GLY G 251 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL G 253 " --> pdb=" O ARG G 293 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N GLN G 295 " --> pdb=" O VAL G 253 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU G 255 " --> pdb=" O GLN G 295 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N CYS G 297 " --> pdb=" O LEU G 255 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU G 257 " --> pdb=" O CYS G 297 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N GLU G 299 " --> pdb=" O LEU G 257 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL G 292 " --> pdb=" O ARG G 345 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ARG G 345 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU G 294 " --> pdb=" O LEU G 343 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 429 through 432 removed outlier: 4.917A pdb=" N THR H 115 " --> pdb=" O ASP H 430 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N CYS H 432 " --> pdb=" O GLU H 113 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N GLU H 113 " --> pdb=" O CYS H 432 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 106 through 108 Processing sheet with id=AB3, first strand: chain 'H' and resid 139 through 148 removed outlier: 5.789A pdb=" N VAL H 141 " --> pdb=" O ALA H 161 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ALA H 161 " --> pdb=" O VAL H 141 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER H 154 " --> pdb=" O LEU H 279 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LEU H 201 " --> pdb=" O ILE H 214 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 217 through 220 Processing sheet with id=AB5, first strand: chain 'H' and resid 305 through 306 Processing sheet with id=AB6, first strand: chain 'H' and resid 305 through 306 removed outlier: 7.446A pdb=" N THR H 407 " --> pdb=" O THR H 342 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR H 342 " --> pdb=" O THR H 407 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N SER H 409 " --> pdb=" O ALA H 340 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA H 340 " --> pdb=" O SER H 409 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ARG H 411 " --> pdb=" O VAL H 338 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N VAL H 338 " --> pdb=" O ARG H 411 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR H 413 " --> pdb=" O TYR H 336 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 320 through 322 removed outlier: 6.146A pdb=" N VAL H 353 " --> pdb=" O TYR H 374 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N THR H 376 " --> pdb=" O VAL H 353 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 504 through 516 Processing sheet with id=AB9, first strand: chain 'A' and resid 43 through 49 removed outlier: 6.874A pdb=" N VAL A 44 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL A 66 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ALA A 46 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LEU A 64 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLU A 48 " --> pdb=" O THR A 62 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 58 through 59 Processing sheet with id=AC2, first strand: chain 'A' and resid 151 through 154 removed outlier: 6.716A pdb=" N VAL A 97 " --> pdb=" O ARG A 169 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ARG A 169 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE A 99 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 125 through 133 Processing sheet with id=AC4, first strand: chain 'D' and resid 43 through 50 removed outlier: 6.846A pdb=" N VAL D 44 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL D 66 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA D 46 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU D 64 " --> pdb=" O ALA D 46 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLU D 48 " --> pdb=" O THR D 62 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN D 60 " --> pdb=" O ASP D 50 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 43 through 50 removed outlier: 6.846A pdb=" N VAL D 44 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL D 66 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA D 46 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU D 64 " --> pdb=" O ALA D 46 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLU D 48 " --> pdb=" O THR D 62 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN D 60 " --> pdb=" O ASP D 50 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 151 through 154 removed outlier: 6.595A pdb=" N VAL D 97 " --> pdb=" O ARG D 169 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ARG D 169 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ILE D 99 " --> pdb=" O VAL D 167 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 125 through 133 Processing sheet with id=AC8, first strand: chain 'B' and resid 43 through 50 removed outlier: 6.802A pdb=" N VAL B 44 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL B 66 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA B 46 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LEU B 64 " --> pdb=" O ALA B 46 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLU B 48 " --> pdb=" O THR B 62 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN B 60 " --> pdb=" O ASP B 50 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 43 through 50 removed outlier: 6.802A pdb=" N VAL B 44 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL B 66 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA B 46 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LEU B 64 " --> pdb=" O ALA B 46 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLU B 48 " --> pdb=" O THR B 62 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN B 60 " --> pdb=" O ASP B 50 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 151 through 154 removed outlier: 6.861A pdb=" N VAL B 97 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ARG B 169 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ILE B 99 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 125 through 133 Processing sheet with id=AD3, first strand: chain 'E' and resid 43 through 50 removed outlier: 6.908A pdb=" N VAL E 44 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL E 66 " --> pdb=" O VAL E 44 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALA E 46 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LEU E 64 " --> pdb=" O ALA E 46 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLU E 48 " --> pdb=" O THR E 62 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN E 60 " --> pdb=" O ASP E 50 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 43 through 50 removed outlier: 6.908A pdb=" N VAL E 44 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL E 66 " --> pdb=" O VAL E 44 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALA E 46 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LEU E 64 " --> pdb=" O ALA E 46 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLU E 48 " --> pdb=" O THR E 62 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN E 60 " --> pdb=" O ASP E 50 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 151 through 154 removed outlier: 6.758A pdb=" N VAL E 97 " --> pdb=" O ARG E 169 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ARG E 169 " --> pdb=" O VAL E 97 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ILE E 99 " --> pdb=" O VAL E 167 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 125 through 133 Processing sheet with id=AD7, first strand: chain 'C' and resid 43 through 50 removed outlier: 6.540A pdb=" N ILE C 65 " --> pdb=" O VAL C 45 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA C 47 " --> pdb=" O ARG C 63 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG C 63 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE C 49 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ALA C 61 " --> pdb=" O PHE C 49 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 43 through 50 removed outlier: 6.540A pdb=" N ILE C 65 " --> pdb=" O VAL C 45 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA C 47 " --> pdb=" O ARG C 63 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG C 63 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE C 49 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ALA C 61 " --> pdb=" O PHE C 49 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 151 through 154 removed outlier: 6.843A pdb=" N VAL C 97 " --> pdb=" O ARG C 169 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ARG C 169 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ILE C 99 " --> pdb=" O VAL C 167 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 125 through 133 Processing sheet with id=AE2, first strand: chain 'F' and resid 43 through 50 removed outlier: 6.976A pdb=" N VAL F 44 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL F 66 " --> pdb=" O VAL F 44 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA F 46 " --> pdb=" O LEU F 64 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU F 64 " --> pdb=" O ALA F 46 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLU F 48 " --> pdb=" O THR F 62 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASN F 60 " --> pdb=" O ASP F 50 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 43 through 50 removed outlier: 6.976A pdb=" N VAL F 44 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL F 66 " --> pdb=" O VAL F 44 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA F 46 " --> pdb=" O LEU F 64 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU F 64 " --> pdb=" O ALA F 46 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLU F 48 " --> pdb=" O THR F 62 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASN F 60 " --> pdb=" O ASP F 50 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 151 through 154 removed outlier: 6.525A pdb=" N VAL F 97 " --> pdb=" O ARG F 169 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ARG F 169 " --> pdb=" O VAL F 97 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ILE F 99 " --> pdb=" O VAL F 167 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 125 through 133 1086 hydrogen bonds defined for protein. 2994 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: 8.62 Time building geometry restraints manager: 9.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4767 1.32 - 1.45: 6139 1.45 - 1.57: 13932 1.57 - 1.70: 11 1.70 - 1.83: 185 Bond restraints: 25034 Sorted by residual: bond pdb=" CA PRO F 300 " pdb=" C PRO F 300 " ideal model delta sigma weight residual 1.517 1.559 -0.042 9.30e-03 1.16e+04 2.08e+01 bond pdb=" CB LEU I 287 " pdb=" CG LEU I 287 " ideal model delta sigma weight residual 1.530 1.620 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" NE ARG H 359 " pdb=" CZ ARG H 359 " ideal model delta sigma weight residual 1.326 1.375 -0.049 1.10e-02 8.26e+03 2.02e+01 bond pdb=" CB HIS I 467 " pdb=" CG HIS I 467 " ideal model delta sigma weight residual 1.497 1.435 0.062 1.40e-02 5.10e+03 1.98e+01 bond pdb=" CA PRO C 300 " pdb=" C PRO C 300 " ideal model delta sigma weight residual 1.517 1.557 -0.040 9.30e-03 1.16e+04 1.88e+01 ... (remaining 25029 not shown) Histogram of bond angle deviations from ideal: 98.82 - 105.89: 908 105.89 - 112.96: 13322 112.96 - 120.03: 8244 120.03 - 127.10: 11358 127.10 - 134.17: 305 Bond angle restraints: 34137 Sorted by residual: angle pdb=" CD1 LEU I 365 " pdb=" CG LEU I 365 " pdb=" CD2 LEU I 365 " ideal model delta sigma weight residual 110.80 132.96 -22.16 2.20e+00 2.07e-01 1.01e+02 angle pdb=" CA VAL I 101 " pdb=" CB VAL I 101 " pdb=" CG2 VAL I 101 " ideal model delta sigma weight residual 110.40 127.50 -17.10 1.70e+00 3.46e-01 1.01e+02 angle pdb=" CD1 LEU I 165 " pdb=" CG LEU I 165 " pdb=" CD2 LEU I 165 " ideal model delta sigma weight residual 110.80 132.48 -21.68 2.20e+00 2.07e-01 9.72e+01 angle pdb=" CA VAL D 234 " pdb=" CB VAL D 234 " pdb=" CG2 VAL D 234 " ideal model delta sigma weight residual 110.40 126.68 -16.28 1.70e+00 3.46e-01 9.17e+01 angle pdb=" CD1 LEU I 287 " pdb=" CG LEU I 287 " pdb=" CD2 LEU I 287 " ideal model delta sigma weight residual 110.80 131.81 -21.01 2.20e+00 2.07e-01 9.12e+01 ... (remaining 34132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.51: 14384 15.51 - 31.02: 537 31.02 - 46.53: 116 46.53 - 62.04: 50 62.04 - 77.55: 17 Dihedral angle restraints: 15104 sinusoidal: 5961 harmonic: 9143 Sorted by residual: dihedral pdb=" CA SER I 271 " pdb=" C SER I 271 " pdb=" N GLY I 272 " pdb=" CA GLY I 272 " ideal model delta harmonic sigma weight residual 180.00 -159.24 -20.76 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA GLN I 281 " pdb=" C GLN I 281 " pdb=" N PRO I 282 " pdb=" CA PRO I 282 " ideal model delta harmonic sigma weight residual 180.00 160.24 19.76 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA TRP F 162 " pdb=" C TRP F 162 " pdb=" N LEU F 163 " pdb=" CA LEU F 163 " ideal model delta harmonic sigma weight residual 180.00 162.53 17.47 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 15101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 3654 0.139 - 0.278: 235 0.278 - 0.417: 3 0.417 - 0.555: 0 0.555 - 0.694: 9 Chirality restraints: 3901 Sorted by residual: chirality pdb=" CB VAL I 101 " pdb=" CA VAL I 101 " pdb=" CG1 VAL I 101 " pdb=" CG2 VAL I 101 " both_signs ideal model delta sigma weight residual False -2.63 -1.93 -0.69 2.00e-01 2.50e+01 1.20e+01 chirality pdb=" CB VAL D 234 " pdb=" CA VAL D 234 " pdb=" CG1 VAL D 234 " pdb=" CG2 VAL D 234 " both_signs ideal model delta sigma weight residual False -2.63 -1.96 -0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" CG LEU H 287 " pdb=" CB LEU H 287 " pdb=" CD1 LEU H 287 " pdb=" CD2 LEU H 287 " both_signs ideal model delta sigma weight residual False -2.59 -1.95 -0.64 2.00e-01 2.50e+01 1.02e+01 ... (remaining 3898 not shown) Planarity restraints: 4430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY H 587 " -0.021 2.00e-02 2.50e+03 4.22e-02 1.78e+01 pdb=" C GLY H 587 " 0.073 2.00e-02 2.50e+03 pdb=" O GLY H 587 " -0.026 2.00e-02 2.50e+03 pdb=" OXT GLY H 587 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 238 " 0.043 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" CG TRP F 238 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP F 238 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP F 238 " -0.021 2.00e-02 2.50e+03 pdb=" NE1 TRP F 238 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP F 238 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP F 238 " -0.020 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 238 " 0.025 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 238 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP F 238 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER I 271 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.12e+00 pdb=" C SER I 271 " -0.043 2.00e-02 2.50e+03 pdb=" O SER I 271 " 0.016 2.00e-02 2.50e+03 pdb=" N GLY I 272 " 0.014 2.00e-02 2.50e+03 ... (remaining 4427 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3154 2.75 - 3.29: 23284 3.29 - 3.83: 39478 3.83 - 4.36: 47357 4.36 - 4.90: 80635 Nonbonded interactions: 193908 Sorted by model distance: nonbonded pdb=" OG1 THR H 96 " pdb=" OG SER H 441 " model vdw 2.216 2.440 nonbonded pdb=" OH TYR F 265 " pdb=" O PRO F 288 " model vdw 2.379 2.440 nonbonded pdb=" O PRO I 586 " pdb=" OXT GLY I 587 " model vdw 2.386 3.040 nonbonded pdb=" O SER B 313 " pdb=" OG SER B 313 " model vdw 2.495 2.440 nonbonded pdb=" N ASP I 493 " pdb=" OD1 ASP I 493 " model vdw 2.496 2.520 ... (remaining 193903 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 9 or (resid 10 and (name N or name CA or name C \ or name O or name CB )) or resid 11 through 117 or (resid 118 and (name N or nam \ e CA or name C or name O or name CB )) or resid 119 or (resid 120 and (name N or \ name CA or name C or name O or name CB )) or resid 121 through 174 or (resid 17 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 176 or (resi \ d 177 and (name N or name CA or name C or name O or name CB )) or resid 178 thro \ ugh 199 or (resid 200 and (name N or name CA or name C or name O or name CB )) o \ r resid 201 through 219 or (resid 233 and (name N or name CA or name C or name O \ or name CB )) or resid 234 through 292 or (resid 293 and (name N or name CA or \ name C or name O or name CB )) or resid 294 through 310 or (resid 311 through 31 \ 2 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'B' and (resid 2 through 117 or (resid 118 and (name N or name CA or name \ C or name O or name CB )) or resid 119 through 138 or (resid 139 and (name N or \ name CA or name C or name O or name CB )) or resid 140 through 174 or (resid 17 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 176 or (resi \ d 177 and (name N or name CA or name C or name O or name CB )) or resid 178 thro \ ugh 199 or (resid 200 and (name N or name CA or name C or name O or name CB )) o \ r resid 201 through 280 or (resid 281 and (name N or name CA or name C or name O \ or name CB )) or resid 282 through 310 or (resid 311 through 312 and (name N or \ name CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 2 through 9 or (resid 10 and (name N or name CA or name C \ or name O or name CB )) or resid 11 through 199 or (resid 200 and (name N or nam \ e CA or name C or name O or name CB )) or resid 201 through 219 or resid 233 thr \ ough 280 or (resid 281 and (name N or name CA or name C or name O or name CB )) \ or resid 282 through 292 or (resid 293 and (name N or name CA or name C or name \ O or name CB )) or resid 294 through 312)) selection = (chain 'D' and (resid 2 through 9 or (resid 10 and (name N or name CA or name C \ or name O or name CB )) or resid 11 through 117 or (resid 118 and (name N or nam \ e CA or name C or name O or name CB )) or resid 119 through 138 or (resid 139 an \ d (name N or name CA or name C or name O or name CB )) or resid 140 through 174 \ or (resid 175 and (name N or name CA or name C or name O or name CB )) or resid \ 176 or (resid 177 and (name N or name CA or name C or name O or name CB )) or re \ sid 178 through 199 or (resid 200 and (name N or name CA or name C or name O or \ name CB )) or resid 201 through 219 or resid 233 through 280 or (resid 281 and ( \ name N or name CA or name C or name O or name CB )) or resid 282 through 292 or \ (resid 293 and (name N or name CA or name C or name O or name CB )) or resid 294 \ through 310 or (resid 311 through 312 and (name N or name CA or name C or name \ O or name CB )))) selection = (chain 'E' and (resid 2 through 9 or (resid 10 and (name N or name CA or name C \ or name O or name CB )) or resid 11 through 174 or (resid 175 and (name N or nam \ e CA or name C or name O or name CB )) or resid 176 or (resid 177 and (name N or \ name CA or name C or name O or name CB )) or resid 178 through 199 or (resid 20 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 201 through \ 219 or resid 233 through 292 or (resid 293 and (name N or name CA or name C or n \ ame O or name CB )) or resid 294 through 312)) selection = (chain 'F' and (resid 2 through 174 or (resid 175 and (name N or name CA or name \ C or name O or name CB )) or resid 176 or (resid 177 and (name N or name CA or \ name C or name O or name CB )) or resid 178 through 219 or resid 233 through 280 \ or (resid 281 and (name N or name CA or name C or name O or name CB )) or resid \ 282 through 292 or (resid 293 and (name N or name CA or name C or name O or nam \ e CB )) or resid 294 through 310 or (resid 311 through 312 and (name N or name C \ A or name C or name O or name CB )))) } ncs_group { reference = (chain 'H' and (resid 47 through 69 or (resid 70 and (name N or name CA or name \ C or name O or name CB )) or resid 71 through 311 or (resid 312 through 315 and \ (name N or name CA or name C or name O or name CB )) or resid 316 or (resid 317 \ and (name N or name CA or name C or name O or name CB )) or resid 318 through 32 \ 8 or (resid 329 and (name N or name CA or name C or name O or name CB )) or resi \ d 330 through 365 or (resid 366 and (name N or name CA or name C or name O or na \ me CB )) or resid 367 through 378 or (resid 379 through 380 and (name N or name \ CA or name C or name O or name CB )) or resid 381 through 404 or (resid 407 thro \ ugh 408 and (name N or name CA or name C or name O or name CB )) or resid 409 th \ rough 423 or (resid 424 and (name N or name CA or name C or name O or name CB )) \ or resid 425 through 446 or (resid 447 and (name N or name CA or name C or name \ O or name CB )) or resid 448 through 479 or (resid 480 and (name N or name CA o \ r name C or name O or name CB )) or resid 481 through 515 or (resid 516 and (nam \ e N or name CA or name C or name O or name CB )) or resid 517 through 530 or (re \ sid 531 and (name N or name CA or name C or name O or name CB )) or resid 532 th \ rough 587)) selection = (chain 'I' and (resid 47 through 203 or (resid 204 and (name N or name CA or nam \ e C or name O or name CB )) or resid 205 through 261 or (resid 262 and (name N o \ r name CA or name C or name O or name CB )) or resid 263 through 275 or (resid 2 \ 76 and (name N or name CA or name C or name O or name CB )) or resid 277 through \ 285 or (resid 286 and (name N or name CA or name C or name O or name CB )) or r \ esid 287 through 309 or (resid 310 and (name N or name CA or name C or name O or \ name CB )) or resid 311 through 326 or (resid 327 and (name N or name CA or nam \ e C or name O or name CB )) or resid 328 through 348 or (resid 349 through 351 a \ nd (name N or name CA or name C or name O or name CB )) or resid 352 through 367 \ or (resid 368 through 369 and (name N or name CA or name C or name O or name CB \ )) or resid 370 through 456 or (resid 457 through 458 and (name N or name CA or \ name C or name O or name CB )) or resid 459 through 492 or (resid 493 and (name \ N or name CA or name C or name O or name CB )) or resid 494 through 587)) } ncs_group { reference = (chain 'K' and resid 4 through 21) selection = chain 'L' } 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 group one per residue 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: 1.210 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: 0.030 Extract box with map and model: 6.210 Check model and map are aligned: 0.390 Set scattering table: 0.270 Process input model: 62.720 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 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 : 0.013 0.090 25034 Z= 0.874 Angle : 1.294 22.161 34137 Z= 0.876 Chirality : 0.076 0.694 3901 Planarity : 0.006 0.042 4430 Dihedral : 9.997 77.550 9144 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.71 % Favored : 97.16 % Rotamer: Outliers : 0.31 % Allowed : 1.24 % Favored : 98.45 % 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: 0.10 (0.15), residues: 3062 helix: 0.60 (0.16), residues: 948 sheet: -0.52 (0.19), residues: 626 loop : 0.15 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.005 TRP F 238 HIS 0.005 0.001 HIS A 156 PHE 0.028 0.003 PHE H 460 TYR 0.034 0.005 TYR I 373 ARG 0.007 0.001 ARG E 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 700 time to evaluate : 2.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 102 MET cc_start: 0.5442 (ttt) cc_final: 0.4678 (ptm) REVERT: I 279 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7261 (pp) REVERT: I 374 TYR cc_start: 0.6187 (p90) cc_final: 0.5930 (p90) REVERT: G 137 TRP cc_start: 0.6526 (t60) cc_final: 0.6191 (t60) REVERT: G 138 ARG cc_start: 0.7227 (ttt90) cc_final: 0.6018 (ttm170) REVERT: G 140 TYR cc_start: 0.7445 (m-80) cc_final: 0.6218 (m-10) REVERT: H 151 ASP cc_start: 0.5681 (m-30) cc_final: 0.4948 (p0) REVERT: H 372 ARG cc_start: 0.6331 (mmm160) cc_final: 0.5866 (mmt-90) REVERT: H 388 THR cc_start: 0.8229 (m) cc_final: 0.7681 (p) REVERT: H 407 THR cc_start: 0.5000 (m) cc_final: 0.4344 (p) REVERT: H 447 LYS cc_start: 0.7711 (ptpt) cc_final: 0.7508 (mmtt) REVERT: H 465 MET cc_start: 0.8559 (tpp) cc_final: 0.8318 (tpp) REVERT: A 184 PHE cc_start: 0.8761 (t80) cc_final: 0.8440 (t80) REVERT: A 294 THR cc_start: 0.8675 (m) cc_final: 0.8326 (p) REVERT: D 258 TYR cc_start: 0.8132 (m-80) cc_final: 0.7746 (m-10) REVERT: D 305 LEU cc_start: 0.9210 (tp) cc_final: 0.8955 (tp) REVERT: B 14 LEU cc_start: 0.9065 (mt) cc_final: 0.8804 (mt) REVERT: C 8 TRP cc_start: 0.8736 (m100) cc_final: 0.8521 (m100) REVERT: C 15 MET cc_start: 0.8837 (mtm) cc_final: 0.8499 (mtm) REVERT: C 215 LEU cc_start: 0.9053 (mt) cc_final: 0.8849 (mt) REVERT: F 194 SER cc_start: 0.7730 (t) cc_final: 0.7313 (p) outliers start: 8 outliers final: 3 residues processed: 704 average time/residue: 0.4279 time to fit residues: 441.6269 Evaluate side-chains 318 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 314 time to evaluate : 2.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 279 LEU Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain H residue 287 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 0.6980 chunk 234 optimal weight: 0.8980 chunk 129 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 242 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 147 optimal weight: 0.8980 chunk 180 optimal weight: 0.6980 chunk 280 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 367 HIS I 461 HIS G 132 GLN G 328 GLN ** G 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 263 ASN H 498 HIS H 542 HIS A 109 ASN A 140 GLN A 175 GLN A 282 HIS D 297 ASN B 109 ASN E 40 HIS C 17 GLN C 207 HIS F 17 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25034 Z= 0.242 Angle : 0.684 12.904 34137 Z= 0.341 Chirality : 0.043 0.302 3901 Planarity : 0.005 0.051 4430 Dihedral : 4.557 58.083 3442 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.93 % Favored : 98.04 % Rotamer: Outliers : 2.68 % Allowed : 8.72 % Favored : 88.60 % 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: 0.82 (0.15), residues: 3062 helix: 1.91 (0.17), residues: 956 sheet: -0.42 (0.18), residues: 692 loop : 0.23 (0.17), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 238 HIS 0.006 0.001 HIS I 510 PHE 0.024 0.002 PHE B 278 TYR 0.021 0.002 TYR I 489 ARG 0.008 0.001 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 357 time to evaluate : 2.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 57 MET cc_start: 0.4717 (mmm) cc_final: 0.4399 (mmt) REVERT: I 102 MET cc_start: 0.5285 (ttt) cc_final: 0.5052 (ptm) REVERT: I 178 LEU cc_start: 0.8272 (tp) cc_final: 0.8036 (mm) REVERT: I 279 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7457 (pp) REVERT: I 356 THR cc_start: 0.7343 (p) cc_final: 0.7068 (t) REVERT: I 359 ARG cc_start: 0.7500 (tpp-160) cc_final: 0.6960 (tpp80) REVERT: I 519 PHE cc_start: 0.7756 (t80) cc_final: 0.7489 (t80) REVERT: G 138 ARG cc_start: 0.7448 (ttt90) cc_final: 0.6222 (ttm170) REVERT: G 140 TYR cc_start: 0.7699 (m-80) cc_final: 0.6591 (m-10) REVERT: G 147 GLU cc_start: 0.6885 (tm-30) cc_final: 0.6410 (pt0) REVERT: H 67 ASP cc_start: 0.7545 (t0) cc_final: 0.7330 (t0) REVERT: H 151 ASP cc_start: 0.5732 (m-30) cc_final: 0.5014 (p0) REVERT: H 172 ASP cc_start: 0.5978 (p0) cc_final: 0.5702 (p0) REVERT: H 263 ASN cc_start: 0.5238 (OUTLIER) cc_final: 0.4990 (t0) REVERT: H 388 THR cc_start: 0.8258 (m) cc_final: 0.8056 (t) REVERT: H 407 THR cc_start: 0.4552 (m) cc_final: 0.4035 (p) REVERT: H 424 LEU cc_start: 0.6623 (mm) cc_final: 0.6282 (mm) REVERT: H 446 CYS cc_start: 0.7209 (m) cc_final: 0.6746 (p) REVERT: H 465 MET cc_start: 0.8759 (tpp) cc_final: 0.8491 (tpp) REVERT: H 499 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7674 (ttm170) REVERT: H 547 MET cc_start: 0.7804 (tmm) cc_final: 0.7381 (tmm) REVERT: A 294 THR cc_start: 0.8580 (m) cc_final: 0.8339 (p) REVERT: D 194 SER cc_start: 0.8972 (t) cc_final: 0.8459 (p) REVERT: B 31 ASP cc_start: 0.8390 (t70) cc_final: 0.8078 (t0) REVERT: B 309 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9110 (mm) REVERT: E 103 LEU cc_start: 0.9249 (tp) cc_final: 0.9002 (tt) REVERT: E 198 MET cc_start: 0.8245 (tpp) cc_final: 0.7784 (mmm) REVERT: F 80 ASP cc_start: 0.8442 (m-30) cc_final: 0.8179 (m-30) REVERT: F 133 GLN cc_start: 0.8695 (tp-100) cc_final: 0.8377 (tm-30) REVERT: F 247 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8088 (tm-30) outliers start: 69 outliers final: 40 residues processed: 407 average time/residue: 0.3462 time to fit residues: 222.7749 Evaluate side-chains 320 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 276 time to evaluate : 3.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 262 GLU Chi-restraints excluded: chain I residue 279 LEU Chi-restraints excluded: chain I residue 283 TRP Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 263 ASN Chi-restraints excluded: chain H residue 287 LEU Chi-restraints excluded: chain H residue 387 ASP Chi-restraints excluded: chain H residue 416 ASN Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 462 TRP Chi-restraints excluded: chain H residue 499 ARG Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 279 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 233 optimal weight: 2.9990 chunk 191 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 281 optimal weight: 1.9990 chunk 303 optimal weight: 4.9990 chunk 250 optimal weight: 1.9990 chunk 278 optimal weight: 0.0050 chunk 95 optimal weight: 2.9990 chunk 225 optimal weight: 0.8980 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 283 HIS G 354 GLN H 560 GLN H 581 HIS F 17 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25034 Z= 0.242 Angle : 0.626 13.392 34137 Z= 0.308 Chirality : 0.042 0.254 3901 Planarity : 0.005 0.049 4430 Dihedral : 4.414 49.638 3442 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.68 % Favored : 97.29 % Rotamer: Outliers : 2.48 % Allowed : 9.62 % Favored : 87.90 % 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: 0.82 (0.15), residues: 3062 helix: 2.04 (0.17), residues: 957 sheet: -0.37 (0.19), residues: 681 loop : 0.08 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 238 HIS 0.007 0.001 HIS I 360 PHE 0.032 0.002 PHE D 278 TYR 0.019 0.001 TYR G 346 ARG 0.008 0.000 ARG C 212 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 302 time to evaluate : 2.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 102 MET cc_start: 0.5420 (ttt) cc_final: 0.4776 (tpp) REVERT: I 178 LEU cc_start: 0.8204 (tp) cc_final: 0.7986 (mm) REVERT: I 266 LEU cc_start: 0.5598 (pt) cc_final: 0.5383 (mp) REVERT: I 279 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.6827 (pp) REVERT: I 307 LEU cc_start: 0.7471 (mm) cc_final: 0.7122 (mp) REVERT: I 326 LYS cc_start: 0.4556 (mmtt) cc_final: 0.3607 (pttp) REVERT: I 359 ARG cc_start: 0.7567 (tpp-160) cc_final: 0.6414 (mmt90) REVERT: I 374 TYR cc_start: 0.6601 (p90) cc_final: 0.6382 (p90) REVERT: I 519 PHE cc_start: 0.7824 (t80) cc_final: 0.7597 (t80) REVERT: I 547 MET cc_start: 0.7830 (tmm) cc_final: 0.7569 (tmm) REVERT: G 140 TYR cc_start: 0.7424 (m-80) cc_final: 0.6646 (m-10) REVERT: G 291 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.8053 (m-30) REVERT: H 67 ASP cc_start: 0.7683 (t0) cc_final: 0.7332 (t0) REVERT: H 364 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.6637 (mtm) REVERT: H 388 THR cc_start: 0.8313 (m) cc_final: 0.8019 (t) REVERT: H 407 THR cc_start: 0.4597 (m) cc_final: 0.4100 (p) REVERT: H 424 LEU cc_start: 0.6801 (mm) cc_final: 0.6458 (mm) REVERT: H 465 MET cc_start: 0.8908 (tpp) cc_final: 0.8675 (tpp) REVERT: H 547 MET cc_start: 0.7774 (tmm) cc_final: 0.7345 (tmm) REVERT: A 294 THR cc_start: 0.8643 (m) cc_final: 0.8380 (p) REVERT: D 194 SER cc_start: 0.8893 (t) cc_final: 0.8345 (p) REVERT: B 31 ASP cc_start: 0.8491 (t70) cc_final: 0.8124 (t0) REVERT: B 309 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9100 (mm) REVERT: E 14 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8384 (mp) REVERT: E 256 MET cc_start: 0.7969 (mmm) cc_final: 0.7734 (mmt) REVERT: C 8 TRP cc_start: 0.8927 (m100) cc_final: 0.8480 (m100) REVERT: F 133 GLN cc_start: 0.8773 (tp-100) cc_final: 0.8408 (tm-30) REVERT: F 247 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8123 (tm-30) outliers start: 64 outliers final: 40 residues processed: 352 average time/residue: 0.3377 time to fit residues: 192.0805 Evaluate side-chains 308 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 263 time to evaluate : 2.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 279 LEU Chi-restraints excluded: chain I residue 283 TRP Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 305 ASP Chi-restraints excluded: chain G residue 354 GLN Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 235 SER Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain H residue 287 LEU Chi-restraints excluded: chain H residue 364 MET Chi-restraints excluded: chain H residue 387 ASP Chi-restraints excluded: chain H residue 427 THR Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 267 GLU Chi-restraints excluded: chain F residue 279 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 277 optimal weight: 0.7980 chunk 211 optimal weight: 3.9990 chunk 145 optimal weight: 0.1980 chunk 31 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 188 optimal weight: 0.8980 chunk 282 optimal weight: 1.9990 chunk 298 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 chunk 267 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 360 HIS I 580 ASN G 361 ASN H 263 ASN H 542 HIS A 148 HIS B 282 HIS C 213 GLN C 297 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25034 Z= 0.196 Angle : 0.592 13.583 34137 Z= 0.288 Chirality : 0.041 0.225 3901 Planarity : 0.005 0.052 4430 Dihedral : 4.290 42.594 3442 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.55 % Favored : 97.42 % Rotamer: Outliers : 2.60 % Allowed : 10.35 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.83 (0.15), residues: 3062 helix: 2.05 (0.17), residues: 958 sheet: -0.29 (0.19), residues: 685 loop : 0.05 (0.17), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP D 238 HIS 0.011 0.001 HIS H 581 PHE 0.023 0.001 PHE D 278 TYR 0.013 0.001 TYR I 332 ARG 0.006 0.000 ARG C 212 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 300 time to evaluate : 2.797 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 78 MET cc_start: 0.7637 (mmm) cc_final: 0.7157 (mmt) REVERT: I 102 MET cc_start: 0.5456 (ttt) cc_final: 0.4728 (tpp) REVERT: I 266 LEU cc_start: 0.5796 (pt) cc_final: 0.5584 (mp) REVERT: I 279 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.6963 (pp) REVERT: I 307 LEU cc_start: 0.7458 (mm) cc_final: 0.7109 (mp) REVERT: I 326 LYS cc_start: 0.4557 (mmtt) cc_final: 0.3810 (pttp) REVERT: I 359 ARG cc_start: 0.7743 (tpp-160) cc_final: 0.6475 (tpp80) REVERT: I 374 TYR cc_start: 0.6455 (p90) cc_final: 0.6148 (p90) REVERT: I 519 PHE cc_start: 0.7853 (t80) cc_final: 0.7594 (t80) REVERT: I 547 MET cc_start: 0.7912 (tmm) cc_final: 0.7569 (tmm) REVERT: G 138 ARG cc_start: 0.7003 (ttt90) cc_final: 0.6285 (ttm170) REVERT: G 140 TYR cc_start: 0.7425 (m-80) cc_final: 0.6835 (m-10) REVERT: G 277 ASP cc_start: 0.8051 (m-30) cc_final: 0.7829 (m-30) REVERT: G 291 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.8041 (m-30) REVERT: G 354 GLN cc_start: 0.5883 (OUTLIER) cc_final: 0.4619 (pp30) REVERT: H 67 ASP cc_start: 0.7768 (t0) cc_final: 0.7326 (t0) REVERT: H 364 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.6992 (mtm) REVERT: H 407 THR cc_start: 0.4889 (m) cc_final: 0.4466 (p) REVERT: H 424 LEU cc_start: 0.6858 (OUTLIER) cc_final: 0.6470 (mm) REVERT: H 501 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8522 (pp) REVERT: A 294 THR cc_start: 0.8592 (m) cc_final: 0.8378 (p) REVERT: D 194 SER cc_start: 0.8843 (t) cc_final: 0.8325 (p) REVERT: B 31 ASP cc_start: 0.8483 (t70) cc_final: 0.8116 (t0) REVERT: B 239 LEU cc_start: 0.8755 (tt) cc_final: 0.8543 (tt) REVERT: B 309 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9080 (mm) REVERT: E 14 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8447 (mp) REVERT: E 198 MET cc_start: 0.8412 (tpp) cc_final: 0.7995 (mmm) REVERT: C 126 LYS cc_start: 0.7766 (mttm) cc_final: 0.7378 (mtmt) REVERT: F 15 MET cc_start: 0.8816 (mtp) cc_final: 0.8573 (mtp) REVERT: F 133 GLN cc_start: 0.8813 (tp-100) cc_final: 0.8528 (tm-30) REVERT: F 151 THR cc_start: 0.9116 (t) cc_final: 0.8599 (m) REVERT: F 215 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8451 (mm) REVERT: F 251 LYS cc_start: 0.8481 (ttmt) cc_final: 0.8178 (tmmt) outliers start: 67 outliers final: 39 residues processed: 353 average time/residue: 0.3328 time to fit residues: 190.2429 Evaluate side-chains 302 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 254 time to evaluate : 2.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 279 LEU Chi-restraints excluded: chain I residue 280 SER Chi-restraints excluded: chain I residue 283 TRP Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 360 HIS Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 354 GLN Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 235 SER Chi-restraints excluded: chain H residue 263 ASN Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain H residue 287 LEU Chi-restraints excluded: chain H residue 364 MET Chi-restraints excluded: chain H residue 387 ASP Chi-restraints excluded: chain H residue 424 LEU Chi-restraints excluded: chain H residue 427 THR Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 501 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 267 GLU Chi-restraints excluded: chain F residue 279 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 222 optimal weight: 2.9990 chunk 123 optimal weight: 0.3980 chunk 254 optimal weight: 1.9990 chunk 206 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 152 optimal weight: 0.6980 chunk 268 optimal weight: 0.0020 chunk 75 optimal weight: 7.9990 overall best weight: 0.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 360 HIS D 241 ASN ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25034 Z= 0.207 Angle : 0.594 14.711 34137 Z= 0.284 Chirality : 0.041 0.262 3901 Planarity : 0.005 0.053 4430 Dihedral : 4.203 41.098 3442 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.87 % Favored : 97.09 % Rotamer: Outliers : 2.48 % Allowed : 11.90 % Favored : 85.61 % 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: 0.75 (0.15), residues: 3062 helix: 2.04 (0.17), residues: 962 sheet: -0.29 (0.19), residues: 697 loop : -0.08 (0.17), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.001 TRP C 238 HIS 0.020 0.001 HIS I 360 PHE 0.024 0.002 PHE B 237 TYR 0.019 0.001 TYR I 489 ARG 0.004 0.000 ARG H 463 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 277 time to evaluate : 2.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 102 MET cc_start: 0.5493 (ttt) cc_final: 0.4769 (tpp) REVERT: I 266 LEU cc_start: 0.5829 (pt) cc_final: 0.5624 (mp) REVERT: I 307 LEU cc_start: 0.7417 (mm) cc_final: 0.7096 (mp) REVERT: I 326 LYS cc_start: 0.4585 (mmtt) cc_final: 0.3844 (pttp) REVERT: I 359 ARG cc_start: 0.7880 (tpp-160) cc_final: 0.7232 (tpp80) REVERT: I 498 HIS cc_start: 0.7863 (OUTLIER) cc_final: 0.7389 (m90) REVERT: I 519 PHE cc_start: 0.7758 (t80) cc_final: 0.7491 (t80) REVERT: I 547 MET cc_start: 0.8024 (tmm) cc_final: 0.7760 (tmm) REVERT: G 138 ARG cc_start: 0.7051 (ttt90) cc_final: 0.6413 (ttm170) REVERT: G 140 TYR cc_start: 0.7445 (m-80) cc_final: 0.6917 (m-10) REVERT: G 277 ASP cc_start: 0.8081 (m-30) cc_final: 0.7853 (m-30) REVERT: G 291 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.8024 (m-30) REVERT: H 67 ASP cc_start: 0.7685 (t0) cc_final: 0.7195 (t0) REVERT: H 364 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.6999 (mtm) REVERT: H 407 THR cc_start: 0.4910 (m) cc_final: 0.4463 (p) REVERT: H 424 LEU cc_start: 0.6914 (OUTLIER) cc_final: 0.6590 (mm) REVERT: H 465 MET cc_start: 0.8906 (tpp) cc_final: 0.8548 (tpp) REVERT: H 501 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8555 (pp) REVERT: H 540 ASP cc_start: 0.7318 (t0) cc_final: 0.6942 (t70) REVERT: A 294 THR cc_start: 0.8588 (m) cc_final: 0.8378 (p) REVERT: D 194 SER cc_start: 0.8881 (t) cc_final: 0.8408 (p) REVERT: D 278 PHE cc_start: 0.6592 (m-80) cc_final: 0.6220 (m-10) REVERT: B 31 ASP cc_start: 0.8501 (t70) cc_final: 0.8133 (t0) REVERT: B 239 LEU cc_start: 0.8735 (tt) cc_final: 0.8498 (tt) REVERT: B 309 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9097 (mm) REVERT: E 14 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8479 (mp) REVERT: C 126 LYS cc_start: 0.7778 (mttm) cc_final: 0.7483 (mtmt) REVERT: F 133 GLN cc_start: 0.8793 (tp-100) cc_final: 0.8496 (tm-30) REVERT: F 151 THR cc_start: 0.9100 (t) cc_final: 0.8609 (m) REVERT: F 215 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8467 (mm) REVERT: F 247 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8134 (tm-30) REVERT: F 251 LYS cc_start: 0.8517 (ttmt) cc_final: 0.8219 (ttmt) outliers start: 64 outliers final: 42 residues processed: 328 average time/residue: 0.3193 time to fit residues: 171.9423 Evaluate side-chains 309 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 259 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 162 CYS Chi-restraints excluded: chain I residue 283 TRP Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 365 LEU Chi-restraints excluded: chain I residue 498 HIS Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 305 ASP Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 235 SER Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain H residue 287 LEU Chi-restraints excluded: chain H residue 364 MET Chi-restraints excluded: chain H residue 387 ASP Chi-restraints excluded: chain H residue 424 LEU Chi-restraints excluded: chain H residue 427 THR Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 501 LEU Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 237 PHE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 267 GLU Chi-restraints excluded: chain F residue 279 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 100 optimal weight: 0.5980 chunk 268 optimal weight: 0.0870 chunk 59 optimal weight: 0.0060 chunk 175 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 156 optimal weight: 4.9990 overall best weight: 0.5174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25034 Z= 0.162 Angle : 0.573 13.744 34137 Z= 0.272 Chirality : 0.040 0.249 3901 Planarity : 0.005 0.053 4430 Dihedral : 4.022 26.333 3440 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.35 % Favored : 97.62 % Rotamer: Outliers : 2.21 % Allowed : 12.76 % Favored : 85.03 % 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: 0.82 (0.15), residues: 3062 helix: 2.07 (0.17), residues: 977 sheet: -0.24 (0.19), residues: 655 loop : -0.06 (0.17), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.001 TRP C 238 HIS 0.007 0.001 HIS H 581 PHE 0.022 0.001 PHE D 278 TYR 0.013 0.001 TYR I 489 ARG 0.005 0.000 ARG C 212 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 271 time to evaluate : 2.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 102 MET cc_start: 0.5266 (ttt) cc_final: 0.4886 (tpp) REVERT: I 279 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.6931 (pp) REVERT: I 307 LEU cc_start: 0.7377 (mm) cc_final: 0.7068 (mp) REVERT: I 326 LYS cc_start: 0.4514 (mmtt) cc_final: 0.3795 (pttp) REVERT: I 359 ARG cc_start: 0.7858 (tpp-160) cc_final: 0.7374 (tpp80) REVERT: I 498 HIS cc_start: 0.7734 (OUTLIER) cc_final: 0.7346 (m90) REVERT: I 519 PHE cc_start: 0.7722 (t80) cc_final: 0.7436 (t80) REVERT: I 547 MET cc_start: 0.8107 (tmm) cc_final: 0.7815 (tmm) REVERT: G 138 ARG cc_start: 0.6977 (ttt90) cc_final: 0.6366 (ttm170) REVERT: G 140 TYR cc_start: 0.7412 (m-80) cc_final: 0.6916 (m-10) REVERT: G 277 ASP cc_start: 0.7956 (m-30) cc_final: 0.7730 (m-30) REVERT: H 67 ASP cc_start: 0.7709 (t0) cc_final: 0.7157 (t0) REVERT: H 364 MET cc_start: 0.7324 (OUTLIER) cc_final: 0.6956 (mtm) REVERT: H 407 THR cc_start: 0.4930 (m) cc_final: 0.4492 (p) REVERT: H 424 LEU cc_start: 0.6904 (OUTLIER) cc_final: 0.6575 (mm) REVERT: H 465 MET cc_start: 0.8908 (tpp) cc_final: 0.8515 (tpp) REVERT: H 501 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8542 (pp) REVERT: A 80 ASP cc_start: 0.7645 (t0) cc_final: 0.7208 (t0) REVERT: D 194 SER cc_start: 0.8800 (t) cc_final: 0.8311 (p) REVERT: D 219 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7571 (ttm110) REVERT: B 31 ASP cc_start: 0.8448 (t70) cc_final: 0.8117 (t0) REVERT: B 309 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9099 (mm) REVERT: E 14 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8500 (mp) REVERT: E 198 MET cc_start: 0.8259 (mmm) cc_final: 0.7744 (mmm) REVERT: C 126 LYS cc_start: 0.7941 (mttm) cc_final: 0.7557 (mtmt) REVERT: C 238 TRP cc_start: 0.5723 (m-10) cc_final: 0.5175 (m-10) REVERT: F 133 GLN cc_start: 0.8725 (tp-100) cc_final: 0.8449 (tm-30) REVERT: F 151 THR cc_start: 0.9054 (t) cc_final: 0.8609 (m) REVERT: F 251 LYS cc_start: 0.8482 (ttmt) cc_final: 0.8214 (ttmt) outliers start: 57 outliers final: 40 residues processed: 316 average time/residue: 0.3243 time to fit residues: 165.8166 Evaluate side-chains 301 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 253 time to evaluate : 2.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 162 CYS Chi-restraints excluded: chain I residue 279 LEU Chi-restraints excluded: chain I residue 283 TRP Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 365 LEU Chi-restraints excluded: chain I residue 498 HIS Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 305 ASP Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain H residue 364 MET Chi-restraints excluded: chain H residue 387 ASP Chi-restraints excluded: chain H residue 424 LEU Chi-restraints excluded: chain H residue 427 THR Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 501 LEU Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 219 ARG Chi-restraints excluded: chain D residue 237 PHE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 267 GLU Chi-restraints excluded: chain F residue 279 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 288 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 170 optimal weight: 2.9990 chunk 218 optimal weight: 0.9980 chunk 169 optimal weight: 5.9990 chunk 251 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 297 optimal weight: 0.0040 chunk 186 optimal weight: 0.0670 chunk 181 optimal weight: 0.6980 chunk 137 optimal weight: 0.1980 overall best weight: 0.3530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 360 HIS B 148 HIS B 297 ASN F 156 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25034 Z= 0.146 Angle : 0.569 14.273 34137 Z= 0.267 Chirality : 0.039 0.178 3901 Planarity : 0.004 0.053 4430 Dihedral : 3.923 21.725 3438 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.55 % Favored : 97.42 % Rotamer: Outliers : 2.02 % Allowed : 13.34 % Favored : 84.65 % 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: 0.91 (0.15), residues: 3062 helix: 2.16 (0.17), residues: 981 sheet: -0.27 (0.19), residues: 660 loop : 0.02 (0.17), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP C 238 HIS 0.006 0.000 HIS H 581 PHE 0.030 0.001 PHE F 237 TYR 0.009 0.001 TYR G 346 ARG 0.005 0.000 ARG C 212 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 280 time to evaluate : 2.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 66 ASP cc_start: 0.5749 (m-30) cc_final: 0.5391 (m-30) REVERT: I 102 MET cc_start: 0.5252 (ttt) cc_final: 0.4877 (tpp) REVERT: I 279 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.6942 (pp) REVERT: I 307 LEU cc_start: 0.7329 (mm) cc_final: 0.7014 (mp) REVERT: I 326 LYS cc_start: 0.4483 (mmtt) cc_final: 0.3764 (pttp) REVERT: I 498 HIS cc_start: 0.7538 (OUTLIER) cc_final: 0.7157 (m90) REVERT: I 519 PHE cc_start: 0.7690 (t80) cc_final: 0.7406 (t80) REVERT: I 547 MET cc_start: 0.8161 (tmm) cc_final: 0.7932 (tmm) REVERT: G 140 TYR cc_start: 0.7340 (m-80) cc_final: 0.6861 (m-10) REVERT: G 277 ASP cc_start: 0.7965 (m-30) cc_final: 0.7761 (m-30) REVERT: H 67 ASP cc_start: 0.7680 (t0) cc_final: 0.7122 (t0) REVERT: H 333 THR cc_start: 0.7832 (m) cc_final: 0.7451 (p) REVERT: H 364 MET cc_start: 0.7324 (OUTLIER) cc_final: 0.6964 (mtm) REVERT: H 407 THR cc_start: 0.4948 (m) cc_final: 0.4504 (p) REVERT: H 424 LEU cc_start: 0.6899 (OUTLIER) cc_final: 0.6572 (mm) REVERT: H 465 MET cc_start: 0.8882 (tpp) cc_final: 0.8471 (tpp) REVERT: H 501 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8444 (pp) REVERT: A 80 ASP cc_start: 0.7762 (t0) cc_final: 0.7397 (t0) REVERT: D 194 SER cc_start: 0.8706 (t) cc_final: 0.8194 (p) REVERT: D 274 SER cc_start: 0.8677 (t) cc_final: 0.8204 (p) REVERT: B 31 ASP cc_start: 0.8446 (t70) cc_final: 0.8096 (t0) REVERT: B 309 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9043 (mp) REVERT: E 198 MET cc_start: 0.8178 (mmm) cc_final: 0.7822 (mmm) REVERT: C 126 LYS cc_start: 0.7949 (mttm) cc_final: 0.7628 (mtmt) REVERT: F 151 THR cc_start: 0.8997 (t) cc_final: 0.8598 (m) REVERT: F 198 MET cc_start: 0.8858 (mmt) cc_final: 0.8563 (mmm) REVERT: F 247 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8264 (tm-30) outliers start: 52 outliers final: 33 residues processed: 320 average time/residue: 0.3387 time to fit residues: 176.0577 Evaluate side-chains 298 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 259 time to evaluate : 2.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 279 LEU Chi-restraints excluded: chain I residue 283 TRP Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 360 HIS Chi-restraints excluded: chain I residue 365 LEU Chi-restraints excluded: chain I residue 498 HIS Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 126 CYS Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain H residue 364 MET Chi-restraints excluded: chain H residue 387 ASP Chi-restraints excluded: chain H residue 424 LEU Chi-restraints excluded: chain H residue 427 THR Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 501 LEU Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 237 PHE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 267 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 177 optimal weight: 0.7980 chunk 89 optimal weight: 0.0010 chunk 58 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 189 optimal weight: 0.0050 chunk 202 optimal weight: 0.0570 chunk 147 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 234 optimal weight: 2.9990 overall best weight: 0.3118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 498 HIS G 359 GLN D 40 HIS B 148 HIS C 17 GLN F 17 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25034 Z= 0.144 Angle : 0.569 14.805 34137 Z= 0.265 Chirality : 0.039 0.186 3901 Planarity : 0.004 0.054 4430 Dihedral : 3.865 20.638 3438 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.19 % Favored : 97.78 % Rotamer: Outliers : 1.78 % Allowed : 13.77 % Favored : 84.45 % 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: 0.96 (0.15), residues: 3062 helix: 2.19 (0.17), residues: 981 sheet: -0.16 (0.19), residues: 660 loop : 0.02 (0.17), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 238 HIS 0.014 0.001 HIS I 360 PHE 0.022 0.001 PHE F 237 TYR 0.011 0.001 TYR I 489 ARG 0.004 0.000 ARG A 308 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 269 time to evaluate : 3.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 61 ARG cc_start: 0.7737 (ttp80) cc_final: 0.7331 (ttp80) REVERT: I 66 ASP cc_start: 0.6062 (m-30) cc_final: 0.5648 (m-30) REVERT: I 102 MET cc_start: 0.5247 (ttt) cc_final: 0.4878 (tpp) REVERT: I 279 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.6944 (pp) REVERT: I 307 LEU cc_start: 0.7212 (mm) cc_final: 0.6893 (mp) REVERT: I 326 LYS cc_start: 0.4487 (mmtt) cc_final: 0.3756 (pttp) REVERT: I 498 HIS cc_start: 0.7460 (OUTLIER) cc_final: 0.7181 (m-70) REVERT: I 519 PHE cc_start: 0.7685 (t80) cc_final: 0.7414 (t80) REVERT: I 547 MET cc_start: 0.8154 (tmm) cc_final: 0.7929 (tmm) REVERT: G 140 TYR cc_start: 0.7255 (m-80) cc_final: 0.6786 (m-10) REVERT: G 286 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8841 (mp) REVERT: H 67 ASP cc_start: 0.7783 (t0) cc_final: 0.7169 (t0) REVERT: H 333 THR cc_start: 0.7836 (m) cc_final: 0.7455 (p) REVERT: H 364 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.6958 (mtm) REVERT: H 407 THR cc_start: 0.5000 (m) cc_final: 0.4592 (p) REVERT: H 424 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6452 (mm) REVERT: H 465 MET cc_start: 0.8929 (tpp) cc_final: 0.8522 (tpp) REVERT: H 501 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8430 (pp) REVERT: H 540 ASP cc_start: 0.6775 (t0) cc_final: 0.6550 (t70) REVERT: H 558 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8223 (mmm) REVERT: A 80 ASP cc_start: 0.7759 (t0) cc_final: 0.7426 (t0) REVERT: D 194 SER cc_start: 0.8677 (t) cc_final: 0.8131 (p) REVERT: B 31 ASP cc_start: 0.8453 (t70) cc_final: 0.8074 (t0) REVERT: B 309 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9065 (mp) REVERT: E 198 MET cc_start: 0.8160 (mmm) cc_final: 0.7775 (mmm) REVERT: C 126 LYS cc_start: 0.7985 (mttm) cc_final: 0.7623 (mtmt) REVERT: F 198 MET cc_start: 0.8776 (mmt) cc_final: 0.8518 (mmm) outliers start: 46 outliers final: 32 residues processed: 305 average time/residue: 0.3754 time to fit residues: 187.0352 Evaluate side-chains 297 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 257 time to evaluate : 2.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 162 CYS Chi-restraints excluded: chain I residue 279 LEU Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 360 HIS Chi-restraints excluded: chain I residue 498 HIS Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 126 CYS Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 235 SER Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain H residue 364 MET Chi-restraints excluded: chain H residue 387 ASP Chi-restraints excluded: chain H residue 424 LEU Chi-restraints excluded: chain H residue 427 THR Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 501 LEU Chi-restraints excluded: chain H residue 558 MET Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 237 PHE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 267 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 0.9980 chunk 285 optimal weight: 0.9980 chunk 260 optimal weight: 3.9990 chunk 277 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 217 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 250 optimal weight: 1.9990 chunk 262 optimal weight: 3.9990 chunk 276 optimal weight: 0.3980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 191 HIS I 360 HIS C 17 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25034 Z= 0.200 Angle : 0.585 14.037 34137 Z= 0.274 Chirality : 0.040 0.236 3901 Planarity : 0.005 0.054 4430 Dihedral : 3.891 20.518 3438 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.65 % Favored : 97.32 % Rotamer: Outliers : 1.98 % Allowed : 13.53 % Favored : 84.49 % 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: 0.94 (0.15), residues: 3062 helix: 2.15 (0.17), residues: 982 sheet: -0.14 (0.19), residues: 670 loop : 0.01 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.001 TRP A 238 HIS 0.022 0.001 HIS I 498 PHE 0.023 0.001 PHE F 237 TYR 0.011 0.001 TYR I 489 ARG 0.005 0.000 ARG I 359 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 263 time to evaluate : 3.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 61 ARG cc_start: 0.7864 (ttp80) cc_final: 0.7454 (ttp80) REVERT: I 66 ASP cc_start: 0.6175 (m-30) cc_final: 0.5779 (m-30) REVERT: I 102 MET cc_start: 0.5322 (ttt) cc_final: 0.5043 (tpp) REVERT: I 279 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.6671 (pp) REVERT: I 307 LEU cc_start: 0.7229 (mm) cc_final: 0.6899 (mp) REVERT: I 326 LYS cc_start: 0.4222 (mmtt) cc_final: 0.3609 (pttp) REVERT: I 519 PHE cc_start: 0.7754 (t80) cc_final: 0.7479 (t80) REVERT: I 547 MET cc_start: 0.8155 (tmm) cc_final: 0.7890 (tmm) REVERT: G 140 TYR cc_start: 0.7114 (m-80) cc_final: 0.6641 (m-10) REVERT: G 286 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8835 (mp) REVERT: H 67 ASP cc_start: 0.7800 (t0) cc_final: 0.7198 (t0) REVERT: H 333 THR cc_start: 0.8056 (m) cc_final: 0.7622 (p) REVERT: H 364 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6978 (mtm) REVERT: H 407 THR cc_start: 0.5044 (m) cc_final: 0.4640 (p) REVERT: H 424 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6564 (mm) REVERT: H 465 MET cc_start: 0.8905 (tpp) cc_final: 0.8349 (tpp) REVERT: H 558 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.7915 (mmm) REVERT: A 80 ASP cc_start: 0.7692 (t0) cc_final: 0.7331 (t0) REVERT: D 194 SER cc_start: 0.8739 (t) cc_final: 0.8216 (p) REVERT: D 256 MET cc_start: 0.8058 (mmt) cc_final: 0.7846 (mmt) REVERT: B 31 ASP cc_start: 0.8459 (t70) cc_final: 0.8110 (t0) REVERT: B 309 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9076 (mp) REVERT: E 14 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8490 (mp) REVERT: E 198 MET cc_start: 0.8217 (mmm) cc_final: 0.7741 (mmm) REVERT: C 126 LYS cc_start: 0.8002 (mttm) cc_final: 0.7655 (mtmt) REVERT: F 151 THR cc_start: 0.9020 (t) cc_final: 0.8616 (m) REVERT: F 198 MET cc_start: 0.8806 (mmt) cc_final: 0.8530 (mmm) REVERT: F 247 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8036 (tp30) outliers start: 51 outliers final: 38 residues processed: 302 average time/residue: 0.3400 time to fit residues: 165.4345 Evaluate side-chains 299 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 254 time to evaluate : 2.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 162 CYS Chi-restraints excluded: chain I residue 279 LEU Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 360 HIS Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 126 CYS Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 235 SER Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain H residue 364 MET Chi-restraints excluded: chain H residue 387 ASP Chi-restraints excluded: chain H residue 424 LEU Chi-restraints excluded: chain H residue 427 THR Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 558 MET Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 237 PHE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 267 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 182 optimal weight: 3.9990 chunk 293 optimal weight: 2.9990 chunk 179 optimal weight: 0.4980 chunk 139 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 307 optimal weight: 0.6980 chunk 283 optimal weight: 0.8980 chunk 245 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 189 optimal weight: 0.3980 chunk 150 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 360 HIS C 17 GLN ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25034 Z= 0.164 Angle : 0.576 14.214 34137 Z= 0.271 Chirality : 0.040 0.250 3901 Planarity : 0.004 0.054 4430 Dihedral : 3.879 20.215 3438 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.67 % Allowed : 14.08 % Favored : 84.26 % 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: 0.97 (0.15), residues: 3062 helix: 2.16 (0.17), residues: 981 sheet: -0.16 (0.20), residues: 644 loop : 0.04 (0.17), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP C 238 HIS 0.017 0.001 HIS I 360 PHE 0.022 0.001 PHE F 237 TYR 0.011 0.001 TYR I 489 ARG 0.012 0.000 ARG I 359 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 262 time to evaluate : 2.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 59 ARG cc_start: 0.7490 (ttt180) cc_final: 0.7225 (tpp80) REVERT: I 61 ARG cc_start: 0.7863 (ttp80) cc_final: 0.7436 (ttp80) REVERT: I 66 ASP cc_start: 0.5968 (m-30) cc_final: 0.5557 (m-30) REVERT: I 102 MET cc_start: 0.5290 (ttt) cc_final: 0.5024 (tpp) REVERT: I 279 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.6798 (pp) REVERT: I 326 LYS cc_start: 0.4593 (mmtt) cc_final: 0.3824 (pttp) REVERT: I 519 PHE cc_start: 0.7726 (t80) cc_final: 0.7444 (t80) REVERT: I 547 MET cc_start: 0.8146 (tmm) cc_final: 0.7876 (tmm) REVERT: G 140 TYR cc_start: 0.7105 (m-80) cc_final: 0.6670 (m-10) REVERT: H 67 ASP cc_start: 0.7808 (t0) cc_final: 0.7217 (t0) REVERT: H 333 THR cc_start: 0.8069 (m) cc_final: 0.7635 (p) REVERT: H 364 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.6976 (mtm) REVERT: H 407 THR cc_start: 0.5064 (m) cc_final: 0.4662 (p) REVERT: H 424 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6420 (mm) REVERT: H 465 MET cc_start: 0.8884 (tpp) cc_final: 0.8482 (tpp) REVERT: H 558 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8264 (mmm) REVERT: A 80 ASP cc_start: 0.7800 (t0) cc_final: 0.7450 (t0) REVERT: D 194 SER cc_start: 0.8694 (t) cc_final: 0.8168 (p) REVERT: D 256 MET cc_start: 0.8018 (mmt) cc_final: 0.7809 (mmt) REVERT: B 31 ASP cc_start: 0.8451 (t70) cc_final: 0.8096 (t0) REVERT: B 309 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9078 (mp) REVERT: E 14 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8491 (mp) REVERT: E 198 MET cc_start: 0.8161 (mmm) cc_final: 0.7771 (mmm) REVERT: C 126 LYS cc_start: 0.7990 (mttm) cc_final: 0.7652 (mtmt) REVERT: F 198 MET cc_start: 0.8773 (mmt) cc_final: 0.8432 (mmm) REVERT: F 247 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8000 (tp30) outliers start: 43 outliers final: 36 residues processed: 294 average time/residue: 0.3337 time to fit residues: 158.1846 Evaluate side-chains 299 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 257 time to evaluate : 3.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 162 CYS Chi-restraints excluded: chain I residue 279 LEU Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 126 CYS Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 235 SER Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain H residue 364 MET Chi-restraints excluded: chain H residue 387 ASP Chi-restraints excluded: chain H residue 424 LEU Chi-restraints excluded: chain H residue 427 THR Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 558 MET Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 237 PHE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 267 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 194 optimal weight: 0.0370 chunk 261 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 226 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 245 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 252 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 overall best weight: 1.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 360 HIS ** H 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN C 17 GLN ** C 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.132941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.105688 restraints weight = 45470.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.107310 restraints weight = 26374.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.108115 restraints weight = 20107.424| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 25034 Z= 0.335 Angle : 0.671 14.355 34137 Z= 0.321 Chirality : 0.043 0.265 3901 Planarity : 0.005 0.056 4430 Dihedral : 4.272 23.888 3438 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.90 % Allowed : 14.15 % Favored : 83.95 % 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 (0.15), residues: 3062 helix: 1.96 (0.17), residues: 980 sheet: -0.31 (0.19), residues: 678 loop : -0.21 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 238 HIS 0.007 0.001 HIS H 581 PHE 0.026 0.002 PHE F 237 TYR 0.018 0.002 TYR B 265 ARG 0.005 0.001 ARG H 463 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4773.81 seconds wall clock time: 87 minutes 21.77 seconds (5241.77 seconds total)