Starting phenix.real_space_refine (version: dev) on Sat Feb 25 02:40:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n38_9341/02_2023/6n38_9341.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n38_9341/02_2023/6n38_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_2023/6n38_9341.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n38_9341/02_2023/6n38_9341.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n38_9341/02_2023/6n38_9341.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n38_9341/02_2023/6n38_9341.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 13.70, per 1000 atoms: 0.56 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: 9.26 Conformation dependent library (CDL) restraints added in 3.6 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: 1.49 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: 8.31 Time building geometry restraints manager: 9.96 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 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. 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: 1.240 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: 7.030 Check model and map are aligned: 0.340 Process input model: 60.610 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.240 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 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 % 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 *********************** 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 : 2.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 704 average time/residue: 0.4355 time to fit residues: 448.8861 Evaluate side-chains 308 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 305 time to evaluate : 2.864 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2093 time to fit residues: 5.2578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 280 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 C 17 GLN C 207 HIS F 17 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 25034 Z= 0.240 Angle : 0.680 12.725 34137 Z= 0.341 Chirality : 0.043 0.310 3901 Planarity : 0.005 0.052 4430 Dihedral : 4.498 56.915 3435 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.93 % Favored : 98.04 % Rotamer Outliers : 2.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.15), residues: 3062 helix: 1.89 (0.17), residues: 950 sheet: -0.42 (0.18), residues: 683 loop : 0.22 (0.17), residues: 1429 *********************** 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 417 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 351 time to evaluate : 2.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 36 residues processed: 399 average time/residue: 0.3673 time to fit residues: 229.7902 Evaluate side-chains 296 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 260 time to evaluate : 2.910 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.2375 time to fit residues: 19.6938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 233 optimal weight: 1.9990 chunk 191 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 281 optimal weight: 2.9990 chunk 303 optimal weight: 3.9990 chunk 250 optimal weight: 0.7980 chunk 278 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 225 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 360 HIS G 354 GLN H 263 ASN H 560 GLN H 581 HIS A 148 HIS B 282 HIS E 40 HIS F 17 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3510 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= 0.255 Angle : 0.633 13.394 34137 Z= 0.313 Chirality : 0.042 0.242 3901 Planarity : 0.005 0.048 4430 Dihedral : 4.373 48.600 3435 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.68 % Favored : 97.29 % Rotamer Outliers : 1.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.15), residues: 3062 helix: 2.00 (0.17), residues: 957 sheet: -0.40 (0.19), residues: 688 loop : 0.08 (0.17), residues: 1417 *********************** 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 333 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 296 time to evaluate : 2.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 19 residues processed: 324 average time/residue: 0.3562 time to fit residues: 186.8185 Evaluate side-chains 275 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 256 time to evaluate : 3.122 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2332 time to fit residues: 12.8510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 277 optimal weight: 0.8980 chunk 211 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 31 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 188 optimal weight: 0.1980 chunk 282 optimal weight: 1.9990 chunk 298 optimal weight: 0.6980 chunk 147 optimal weight: 0.0970 chunk 267 optimal weight: 0.0470 chunk 80 optimal weight: 0.9990 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 580 ASN G 361 ASN H 542 HIS C 213 GLN C 297 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3822 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= 0.158 Angle : 0.581 13.506 34137 Z= 0.282 Chirality : 0.040 0.198 3901 Planarity : 0.005 0.048 4430 Dihedral : 4.187 41.654 3435 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.29 % Favored : 97.68 % Rotamer Outliers : 1.20 % 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: 0.88 (0.15), residues: 3062 helix: 2.08 (0.17), residues: 958 sheet: -0.29 (0.19), residues: 682 loop : 0.11 (0.17), residues: 1422 *********************** 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 329 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 298 time to evaluate : 3.488 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 11 residues processed: 320 average time/residue: 0.3479 time to fit residues: 183.0364 Evaluate side-chains 258 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 247 time to evaluate : 3.088 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2780 time to fit residues: 9.2542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 222 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 254 optimal weight: 0.9980 chunk 206 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 152 optimal weight: 0.6980 chunk 268 optimal weight: 0.0030 chunk 75 optimal weight: 1.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 266 GLN H 263 ASN D 40 HIS D 241 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 25034 Z= 0.232 Angle : 0.602 13.900 34137 Z= 0.289 Chirality : 0.041 0.219 3901 Planarity : 0.005 0.052 4430 Dihedral : 4.162 33.333 3435 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.74 % Favored : 97.22 % Rotamer Outliers : 1.28 % 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: 0.77 (0.15), residues: 3062 helix: 1.97 (0.17), residues: 973 sheet: -0.30 (0.19), residues: 655 loop : -0.01 (0.17), residues: 1434 *********************** 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 294 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 261 time to evaluate : 3.000 Fit side-chains outliers start: 33 outliers final: 14 residues processed: 285 average time/residue: 0.3554 time to fit residues: 164.8957 Evaluate side-chains 258 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 244 time to evaluate : 2.910 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2258 time to fit residues: 10.0756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 100 optimal weight: 0.0020 chunk 268 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 175 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 298 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 156 optimal weight: 0.0370 overall best weight: 0.5066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 360 HIS G 283 HIS H 360 HIS A 138 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4315 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= 0.164 Angle : 0.574 13.933 34137 Z= 0.274 Chirality : 0.040 0.231 3901 Planarity : 0.005 0.054 4430 Dihedral : 4.038 26.221 3435 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.25 % Favored : 97.71 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.15), residues: 3062 helix: 2.10 (0.17), residues: 972 sheet: -0.34 (0.19), residues: 645 loop : 0.02 (0.17), residues: 1445 *********************** 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 276 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 255 time to evaluate : 3.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 9 residues processed: 271 average time/residue: 0.3526 time to fit residues: 155.6838 Evaluate side-chains 246 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 237 time to evaluate : 3.015 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2946 time to fit residues: 10.1176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 288 optimal weight: 0.7980 chunk 33 optimal weight: 0.3980 chunk 170 optimal weight: 2.9990 chunk 218 optimal weight: 0.9980 chunk 169 optimal weight: 4.9990 chunk 251 optimal weight: 0.5980 chunk 166 optimal weight: 2.9990 chunk 297 optimal weight: 1.9990 chunk 186 optimal weight: 0.6980 chunk 181 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 282 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 25034 Z= 0.182 Angle : 0.575 13.901 34137 Z= 0.275 Chirality : 0.040 0.153 3901 Planarity : 0.005 0.054 4430 Dihedral : 4.016 22.702 3435 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.84 % Favored : 97.13 % Rotamer Outliers : 0.54 % 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: 0.86 (0.15), residues: 3062 helix: 2.07 (0.17), residues: 979 sheet: -0.27 (0.19), residues: 652 loop : 0.02 (0.17), residues: 1431 *********************** 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 265 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 251 time to evaluate : 2.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 261 average time/residue: 0.3597 time to fit residues: 152.9397 Evaluate side-chains 242 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 237 time to evaluate : 3.214 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2409 time to fit residues: 7.0312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 177 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 189 optimal weight: 0.9990 chunk 202 optimal weight: 0.5980 chunk 147 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 234 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 191 HIS G 359 GLN H 360 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4648 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= 0.208 Angle : 0.588 13.787 34137 Z= 0.279 Chirality : 0.041 0.248 3901 Planarity : 0.005 0.055 4430 Dihedral : 4.042 20.517 3435 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.65 % Favored : 97.32 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.15), residues: 3062 helix: 2.03 (0.17), residues: 977 sheet: -0.25 (0.19), residues: 650 loop : -0.05 (0.17), residues: 1435 *********************** 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 255 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 244 time to evaluate : 2.938 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 249 average time/residue: 0.3726 time to fit residues: 150.2410 Evaluate side-chains 238 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 233 time to evaluate : 2.964 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2425 time to fit residues: 6.2678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 1.9990 chunk 285 optimal weight: 0.5980 chunk 260 optimal weight: 0.7980 chunk 277 optimal weight: 0.6980 chunk 167 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 217 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 250 optimal weight: 0.6980 chunk 262 optimal weight: 1.9990 chunk 276 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 360 HIS A 28 HIS B 297 ASN F 17 GLN F 156 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 25034 Z= 0.174 Angle : 0.575 14.695 34137 Z= 0.273 Chirality : 0.040 0.251 3901 Planarity : 0.005 0.055 4430 Dihedral : 4.001 20.129 3435 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.48 % Favored : 97.49 % Rotamer Outliers : 0.35 % 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: 0.83 (0.15), residues: 3062 helix: 2.04 (0.17), residues: 979 sheet: -0.30 (0.20), residues: 629 loop : -0.00 (0.17), residues: 1454 *********************** 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 267 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 258 time to evaluate : 3.090 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 263 average time/residue: 0.3650 time to fit residues: 157.0321 Evaluate side-chains 241 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 239 time to evaluate : 2.977 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2532 time to fit residues: 4.9387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 182 optimal weight: 0.8980 chunk 293 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 307 optimal weight: 0.9990 chunk 283 optimal weight: 0.9990 chunk 245 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 189 optimal weight: 0.6980 chunk 150 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS B 297 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4904 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= 0.210 Angle : 0.596 14.244 34137 Z= 0.284 Chirality : 0.041 0.255 3901 Planarity : 0.005 0.055 4430 Dihedral : 4.042 20.707 3435 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.81 % Favored : 97.16 % Rotamer Outliers : 0.31 % 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: 0.79 (0.15), residues: 3062 helix: 2.04 (0.17), residues: 976 sheet: -0.33 (0.20), residues: 636 loop : -0.04 (0.17), residues: 1450 ********************** 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 243 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 235 time to evaluate : 2.941 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 240 average time/residue: 0.3696 time to fit residues: 143.9359 Evaluate side-chains 230 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 227 time to evaluate : 3.357 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2388 time to fit residues: 5.5418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 194 optimal weight: 0.0980 chunk 261 optimal weight: 0.0670 chunk 75 optimal weight: 6.9990 chunk 226 optimal weight: 0.0470 chunk 36 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 245 optimal weight: 0.7980 chunk 102 optimal weight: 0.2980 chunk 252 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 overall best weight: 0.2616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.137876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.111820 restraints weight = 45003.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.112838 restraints weight = 27604.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.113415 restraints weight = 21638.458| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 25034 Z= 0.147 Angle : 0.579 16.684 34137 Z= 0.272 Chirality : 0.040 0.255 3901 Planarity : 0.005 0.054 4430 Dihedral : 3.964 22.010 3435 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer Outliers : 0.16 % 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: 0.89 (0.15), residues: 3062 helix: 2.11 (0.17), residues: 979 sheet: -0.26 (0.20), residues: 642 loop : 0.02 (0.17), residues: 1441 =============================================================================== Job complete usr+sys time: 4475.06 seconds wall clock time: 82 minutes 43.73 seconds (4963.73 seconds total)