Starting phenix.real_space_refine (version: dev) on Fri Aug 5 11:54:53 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvy_27021/08_2022/8cvy_27021.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvy_27021/08_2022/8cvy_27021.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvy_27021/08_2022/8cvy_27021.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvy_27021/08_2022/8cvy_27021.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvy_27021/08_2022/8cvy_27021.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvy_27021/08_2022/8cvy_27021.pdb" } resolution = 3.52 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= 0.092 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 89": "NH1" <-> "NH2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 145": "OD1" <-> "OD2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 230": "OD1" <-> "OD2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 303": "NH1" <-> "NH2" Residue "A GLU 306": "OE1" <-> "OE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 321": "OD1" <-> "OD2" Residue "A GLU 359": "OE1" <-> "OE2" Residue "A GLU 378": "OE1" <-> "OE2" Residue "A ARG 386": "NH1" <-> "NH2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ASP 421": "OD1" <-> "OD2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A ASP 424": "OD1" <-> "OD2" Residue "A PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 437": "NH1" <-> "NH2" Residue "A ASP 451": "OD1" <-> "OD2" Residue "A ARG 462": "NH1" <-> "NH2" Residue "A ARG 472": "NH1" <-> "NH2" Residue "A PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 494": "OE1" <-> "OE2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "A GLU 518": "OE1" <-> "OE2" Residue "A TYR 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 555": "NH1" <-> "NH2" Residue "A ARG 586": "NH1" <-> "NH2" Residue "A GLU 590": "OE1" <-> "OE2" Residue "A ASP 597": "OD1" <-> "OD2" Residue "A ARG 603": "NH1" <-> "NH2" Residue "A TYR 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C ARG 89": "NH1" <-> "NH2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 145": "OD1" <-> "OD2" Residue "C GLU 147": "OE1" <-> "OE2" Residue "C PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C ARG 192": "NH1" <-> "NH2" Residue "C TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 230": "OD1" <-> "OD2" Residue "C GLU 232": "OE1" <-> "OE2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C ARG 303": "NH1" <-> "NH2" Residue "C GLU 306": "OE1" <-> "OE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 321": "OD1" <-> "OD2" Residue "C GLU 359": "OE1" <-> "OE2" Residue "C PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 378": "OE1" <-> "OE2" Residue "C ARG 386": "NH1" <-> "NH2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C ASP 421": "OD1" <-> "OD2" Residue "C GLU 423": "OE1" <-> "OE2" Residue "C ASP 424": "OD1" <-> "OD2" Residue "C PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 437": "NH1" <-> "NH2" Residue "C ASP 451": "OD1" <-> "OD2" Residue "C ARG 462": "NH1" <-> "NH2" Residue "C ARG 472": "NH1" <-> "NH2" Residue "C PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 494": "OE1" <-> "OE2" Residue "C GLU 510": "OE1" <-> "OE2" Residue "C GLU 518": "OE1" <-> "OE2" Residue "C TYR 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 555": "NH1" <-> "NH2" Residue "C ARG 586": "NH1" <-> "NH2" Residue "C GLU 590": "OE1" <-> "OE2" Residue "C ARG 603": "NH1" <-> "NH2" Residue "C TYR 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 78": "OE1" <-> "OE2" Residue "D ARG 89": "NH1" <-> "NH2" Residue "D TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 145": "OD1" <-> "OD2" Residue "D GLU 147": "OE1" <-> "OE2" Residue "D PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 230": "OD1" <-> "OD2" Residue "D GLU 232": "OE1" <-> "OE2" Residue "D ARG 246": "NH1" <-> "NH2" Residue "D ARG 303": "NH1" <-> "NH2" Residue "D GLU 306": "OE1" <-> "OE2" Residue "D PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 321": "OD1" <-> "OD2" Residue "D GLU 359": "OE1" <-> "OE2" Residue "D GLU 378": "OE1" <-> "OE2" Residue "D ARG 386": "NH1" <-> "NH2" Residue "D GLU 406": "OE1" <-> "OE2" Residue "D GLU 423": "OE1" <-> "OE2" Residue "D PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 430": "NH1" <-> "NH2" Residue "D PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 437": "NH1" <-> "NH2" Residue "D ASP 454": "OD1" <-> "OD2" Residue "D ARG 462": "NH1" <-> "NH2" Residue "D PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 472": "NH1" <-> "NH2" Residue "D PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 494": "OE1" <-> "OE2" Residue "D GLU 510": "OE1" <-> "OE2" Residue "D GLU 518": "OE1" <-> "OE2" Residue "D TYR 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 555": "NH1" <-> "NH2" Residue "D ARG 586": "NH1" <-> "NH2" Residue "D ARG 603": "NH1" <-> "NH2" Residue "D PHE 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 303": "NH1" <-> "NH2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 321": "OD1" <-> "OD2" Residue "B GLU 359": "OE1" <-> "OE2" Residue "B GLU 378": "OE1" <-> "OE2" Residue "B ARG 386": "NH1" <-> "NH2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B ASP 421": "OD1" <-> "OD2" Residue "B GLU 423": "OE1" <-> "OE2" Residue "B ASP 424": "OD1" <-> "OD2" Residue "B PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 430": "NH1" <-> "NH2" Residue "B ASP 451": "OD1" <-> "OD2" Residue "B ARG 462": "NH1" <-> "NH2" Residue "B ARG 472": "NH1" <-> "NH2" Residue "B PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 494": "OE1" <-> "OE2" Residue "B GLU 510": "OE1" <-> "OE2" Residue "B GLU 518": "OE1" <-> "OE2" Residue "B TYR 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 555": "NH1" <-> "NH2" Residue "B ARG 586": "NH1" <-> "NH2" Residue "B GLU 590": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4680/modules/chem_data/mon_lib" Total number of atoms: 17930 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4862 Classifications: {'peptide': 605} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 580} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 277 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "C" Number of atoms: 4867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4867 Classifications: {'peptide': 605} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 24, 'TRANS': 580} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 285 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "D" Number of atoms: 4851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4851 Classifications: {'peptide': 605} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 24, 'TRANS': 580} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 285 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "B" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2503 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 13, 'TRANS': 296} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 10.25, per 1000 atoms: 0.57 Number of scatterers: 17930 At special positions: 0 Unit cell: (119.76, 126.16, 136.216, 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 88 16.00 O 3260 8.00 N 3092 7.00 C 11490 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: 7.55 Conformation dependent library (CDL) restraints added in 2.7 seconds 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4180 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 12 sheets defined 56.7% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 42 through 59 removed outlier: 4.846A pdb=" N LYS A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL A 53 " --> pdb=" O THR A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 76 Processing helix chain 'A' and resid 84 through 97 removed outlier: 3.525A pdb=" N LYS A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 138 Processing helix chain 'A' and resid 146 through 169 Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 184 through 194 removed outlier: 3.885A pdb=" N LEU A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 217 removed outlier: 3.732A pdb=" N TYR A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ALA A 215 " --> pdb=" O ARG A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 236 Processing helix chain 'A' and resid 238 through 252 Processing helix chain 'A' and resid 259 through 270 Processing helix chain 'A' and resid 292 through 312 removed outlier: 3.617A pdb=" N LEU A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 356 Processing helix chain 'A' and resid 376 through 411 Processing helix chain 'A' and resid 415 through 420 removed outlier: 3.939A pdb=" N LEU A 420 " --> pdb=" O MET A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 435 Processing helix chain 'A' and resid 454 through 464 Processing helix chain 'A' and resid 492 through 500 Processing helix chain 'A' and resid 513 through 523 Processing helix chain 'A' and resid 532 through 542 Processing helix chain 'A' and resid 559 through 576 Processing helix chain 'A' and resid 578 through 590 Processing helix chain 'A' and resid 592 through 597 removed outlier: 3.887A pdb=" N LEU A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 616 removed outlier: 4.612A pdb=" N ARG A 603 " --> pdb=" O LYS A 599 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TYR A 604 " --> pdb=" O TYR A 600 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 616 " --> pdb=" O ALA A 612 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 328 removed outlier: 3.532A pdb=" N LYS E 322 " --> pdb=" O SER E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 347 Processing helix chain 'C' and resid 42 through 59 removed outlier: 4.535A pdb=" N LYS C 52 " --> pdb=" O GLN C 48 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL C 53 " --> pdb=" O THR C 49 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP C 56 " --> pdb=" O LYS C 52 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU C 57 " --> pdb=" O VAL C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 76 Processing helix chain 'C' and resid 84 through 97 removed outlier: 3.504A pdb=" N ARG C 89 " --> pdb=" O PRO C 85 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS C 97 " --> pdb=" O SER C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 136 Processing helix chain 'C' and resid 145 through 169 removed outlier: 3.992A pdb=" N LEU C 166 " --> pdb=" O LEU C 162 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA C 167 " --> pdb=" O GLY C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.631A pdb=" N VAL C 186 " --> pdb=" O TRP C 182 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N GLY C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 217 removed outlier: 3.725A pdb=" N TYR C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ALA C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 236 Processing helix chain 'C' and resid 238 through 252 Processing helix chain 'C' and resid 259 through 270 Processing helix chain 'C' and resid 283 through 288 Processing helix chain 'C' and resid 289 through 291 No H-bonds generated for 'chain 'C' and resid 289 through 291' Processing helix chain 'C' and resid 292 through 312 Processing helix chain 'C' and resid 338 through 356 Processing helix chain 'C' and resid 376 through 411 Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.617A pdb=" N LEU C 420 " --> pdb=" O MET C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 435 Processing helix chain 'C' and resid 454 through 464 Processing helix chain 'C' and resid 492 through 500 Processing helix chain 'C' and resid 513 through 523 Processing helix chain 'C' and resid 532 through 542 Processing helix chain 'C' and resid 559 through 577 Processing helix chain 'C' and resid 578 through 592 removed outlier: 3.531A pdb=" N LEU C 592 " --> pdb=" O ARG C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 597 removed outlier: 3.887A pdb=" N LEU C 596 " --> pdb=" O LEU C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 616 removed outlier: 4.404A pdb=" N ARG C 603 " --> pdb=" O LYS C 599 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N TYR C 604 " --> pdb=" O TYR C 600 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TYR C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA C 616 " --> pdb=" O ALA C 612 " (cutoff:3.500A) Processing helix chain 'G' and resid 317 through 328 Processing helix chain 'G' and resid 337 through 348 removed outlier: 3.761A pdb=" N TYR G 348 " --> pdb=" O LYS G 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 59 removed outlier: 4.851A pdb=" N LYS D 52 " --> pdb=" O GLN D 48 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N VAL D 53 " --> pdb=" O THR D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 76 Processing helix chain 'D' and resid 84 through 97 removed outlier: 3.528A pdb=" N LYS D 97 " --> pdb=" O SER D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 removed outlier: 4.400A pdb=" N TRP D 124 " --> pdb=" O ALA D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 138 Processing helix chain 'D' and resid 146 through 169 Processing helix chain 'D' and resid 184 through 194 removed outlier: 3.963A pdb=" N LEU D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 217 removed outlier: 3.724A pdb=" N TYR D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ALA D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 236 Processing helix chain 'D' and resid 238 through 252 Processing helix chain 'D' and resid 259 through 270 Processing helix chain 'D' and resid 283 through 287 Processing helix chain 'D' and resid 292 through 312 Processing helix chain 'D' and resid 338 through 356 Processing helix chain 'D' and resid 376 through 411 removed outlier: 3.548A pdb=" N GLN D 383 " --> pdb=" O THR D 379 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA D 384 " --> pdb=" O LEU D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 420 removed outlier: 4.474A pdb=" N LEU D 420 " --> pdb=" O MET D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 435 Processing helix chain 'D' and resid 454 through 464 Processing helix chain 'D' and resid 492 through 500 Processing helix chain 'D' and resid 513 through 523 Processing helix chain 'D' and resid 532 through 542 Processing helix chain 'D' and resid 559 through 576 Processing helix chain 'D' and resid 578 through 590 Processing helix chain 'D' and resid 592 through 597 removed outlier: 3.829A pdb=" N LEU D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 616 removed outlier: 4.425A pdb=" N ARG D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N TYR D 604 " --> pdb=" O TYR D 600 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR D 605 " --> pdb=" O LEU D 601 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA D 616 " --> pdb=" O ALA D 612 " (cutoff:3.500A) Processing helix chain 'H' and resid 317 through 328 removed outlier: 3.535A pdb=" N LYS H 322 " --> pdb=" O SER H 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 337 through 348 removed outlier: 3.719A pdb=" N TYR H 348 " --> pdb=" O LYS H 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 312 Processing helix chain 'B' and resid 338 through 356 Processing helix chain 'B' and resid 376 through 411 Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.838A pdb=" N LEU B 420 " --> pdb=" O MET B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 435 Processing helix chain 'B' and resid 454 through 464 Processing helix chain 'B' and resid 492 through 500 Processing helix chain 'B' and resid 513 through 523 Processing helix chain 'B' and resid 532 through 542 Processing helix chain 'B' and resid 559 through 576 Processing helix chain 'B' and resid 578 through 590 Processing helix chain 'B' and resid 592 through 597 removed outlier: 3.886A pdb=" N LEU B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 79 removed outlier: 3.724A pdb=" N LEU A 116 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TYR A 62 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N VAL A 115 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU A 64 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU A 117 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N GLY A 66 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LEU A 29 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL A 65 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLU A 31 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR A 200 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N THR A 256 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N PHE A 202 " --> pdb=" O THR A 256 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N PHE A 255 " --> pdb=" O ILE A 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 473 through 477 removed outlier: 6.511A pdb=" N VAL A 362 " --> pdb=" O LYS A 474 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE A 476 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA A 364 " --> pdb=" O ILE A 476 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU A 324 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N PHE A 365 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE A 326 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE A 367 " --> pdb=" O PHE A 326 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE A 328 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TYR A 325 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL A 504 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N PHE A 327 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLY A 503 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N THR A 529 " --> pdb=" O GLY A 503 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N LEU A 553 " --> pdb=" O SER A 526 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N SER A 528 " --> pdb=" O LEU A 553 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 372 through 375 removed outlier: 4.623A pdb=" N ASN A 447 " --> pdb=" O ASN A 373 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 79 removed outlier: 6.381A pdb=" N TYR C 62 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL C 115 " --> pdb=" O TYR C 62 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU C 64 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU C 117 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N GLY C 66 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU C 29 " --> pdb=" O PHE C 63 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL C 65 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLU C 31 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR C 200 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N THR C 256 " --> pdb=" O THR C 200 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N PHE C 202 " --> pdb=" O THR C 256 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N PHE C 255 " --> pdb=" O ILE C 276 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 473 through 477 removed outlier: 6.507A pdb=" N VAL C 362 " --> pdb=" O LYS C 474 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE C 476 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA C 364 " --> pdb=" O ILE C 476 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU C 324 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N PHE C 365 " --> pdb=" O LEU C 324 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHE C 326 " --> pdb=" O PHE C 365 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE C 367 " --> pdb=" O PHE C 326 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE C 328 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR C 325 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N VAL C 504 " --> pdb=" O TYR C 325 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N PHE C 327 " --> pdb=" O VAL C 504 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLY C 503 " --> pdb=" O ILE C 527 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N THR C 529 " --> pdb=" O GLY C 503 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LEU C 553 " --> pdb=" O SER C 526 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER C 528 " --> pdb=" O LEU C 553 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 372 through 375 removed outlier: 4.977A pdb=" N ASN C 447 " --> pdb=" O ASN C 373 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 62 through 63 removed outlier: 6.050A pdb=" N LEU D 29 " --> pdb=" O PHE D 63 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR D 200 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N THR D 256 " --> pdb=" O THR D 200 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE D 202 " --> pdb=" O THR D 256 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N PHE D 255 " --> pdb=" O ILE D 276 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 66 through 67 Processing sheet with id=AA9, first strand: chain 'D' and resid 473 through 478 removed outlier: 6.323A pdb=" N VAL D 362 " --> pdb=" O LYS D 474 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ILE D 476 " --> pdb=" O VAL D 362 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ALA D 364 " --> pdb=" O ILE D 476 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N HIS D 478 " --> pdb=" O ALA D 364 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N PHE D 366 " --> pdb=" O HIS D 478 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU D 324 " --> pdb=" O VAL D 363 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N PHE D 365 " --> pdb=" O LEU D 324 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE D 326 " --> pdb=" O PHE D 365 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ILE D 367 " --> pdb=" O PHE D 326 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE D 328 " --> pdb=" O ILE D 367 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR D 325 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL D 504 " --> pdb=" O TYR D 325 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N PHE D 327 " --> pdb=" O VAL D 504 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLY D 503 " --> pdb=" O ILE D 527 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N THR D 529 " --> pdb=" O GLY D 503 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N LEU D 553 " --> pdb=" O SER D 526 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N SER D 528 " --> pdb=" O LEU D 553 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 372 through 375 removed outlier: 4.710A pdb=" N ASN D 447 " --> pdb=" O ASN D 373 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 473 through 477 removed outlier: 6.502A pdb=" N VAL B 362 " --> pdb=" O LYS B 474 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE B 476 " --> pdb=" O VAL B 362 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA B 364 " --> pdb=" O ILE B 476 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU B 324 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N PHE B 365 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N PHE B 326 " --> pdb=" O PHE B 365 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ILE B 367 " --> pdb=" O PHE B 326 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE B 328 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TYR B 325 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N VAL B 504 " --> pdb=" O TYR B 325 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N PHE B 327 " --> pdb=" O VAL B 504 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLY B 503 " --> pdb=" O ILE B 527 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N THR B 529 " --> pdb=" O GLY B 503 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU B 553 " --> pdb=" O SER B 526 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N SER B 528 " --> pdb=" O LEU B 553 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 372 through 375 removed outlier: 4.620A pdb=" N ASN B 447 " --> pdb=" O ASN B 373 " (cutoff:3.500A) 890 hydrogen bonds defined for protein. 2631 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: 6.26 Time building geometry restraints manager: 8.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3472 1.33 - 1.45: 5745 1.45 - 1.58: 9050 1.58 - 1.71: 0 1.71 - 1.84: 131 Bond restraints: 18398 Sorted by residual: bond pdb=" CE1 HIS B 311 " pdb=" NE2 HIS B 311 " ideal model delta sigma weight residual 1.321 1.368 -0.047 1.00e-02 1.00e+04 2.23e+01 bond pdb=" C PHE B 440 " pdb=" N PRO B 441 " ideal model delta sigma weight residual 1.331 1.366 -0.034 8.70e-03 1.32e+04 1.55e+01 bond pdb=" CE1 HIS C 501 " pdb=" NE2 HIS C 501 " ideal model delta sigma weight residual 1.321 1.360 -0.039 1.00e-02 1.00e+04 1.51e+01 bond pdb=" C PHE D 440 " pdb=" N PRO D 441 " ideal model delta sigma weight residual 1.331 1.364 -0.033 8.70e-03 1.32e+04 1.45e+01 bond pdb=" CE1 HIS B 446 " pdb=" NE2 HIS B 446 " ideal model delta sigma weight residual 1.321 1.359 -0.038 1.00e-02 1.00e+04 1.43e+01 ... (remaining 18393 not shown) Histogram of bond angle deviations from ideal: 96.13 - 103.82: 167 103.82 - 111.52: 6099 111.52 - 119.21: 8940 119.21 - 126.90: 9525 126.90 - 134.59: 204 Bond angle restraints: 24935 Sorted by residual: angle pdb=" C THR D 49 " pdb=" CA THR D 49 " pdb=" CB THR D 49 " ideal model delta sigma weight residual 109.24 123.32 -14.08 1.75e+00 3.27e-01 6.47e+01 angle pdb=" C THR A 49 " pdb=" CA THR A 49 " pdb=" CB THR A 49 " ideal model delta sigma weight residual 109.29 123.39 -14.10 1.82e+00 3.02e-01 6.00e+01 angle pdb=" CA PHE A 400 " pdb=" CB PHE A 400 " pdb=" CG PHE A 400 " ideal model delta sigma weight residual 113.80 107.20 6.60 1.00e+00 1.00e+00 4.35e+01 angle pdb=" C PHE A 617 " pdb=" CA PHE A 617 " pdb=" CB PHE A 617 " ideal model delta sigma weight residual 111.20 115.41 -4.21 7.10e-01 1.98e+00 3.52e+01 angle pdb=" C PHE D 617 " pdb=" CA PHE D 617 " pdb=" CB PHE D 617 " ideal model delta sigma weight residual 111.20 115.35 -4.15 7.10e-01 1.98e+00 3.41e+01 ... (remaining 24930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.70: 9312 14.70 - 29.41: 997 29.41 - 44.11: 363 44.11 - 58.81: 119 58.81 - 73.52: 23 Dihedral angle restraints: 10814 sinusoidal: 4321 harmonic: 6493 Sorted by residual: dihedral pdb=" C THR D 49 " pdb=" N THR D 49 " pdb=" CA THR D 49 " pdb=" CB THR D 49 " ideal model delta harmonic sigma weight residual -122.00 -141.54 19.54 0 2.50e+00 1.60e-01 6.11e+01 dihedral pdb=" C THR A 49 " pdb=" N THR A 49 " pdb=" CA THR A 49 " pdb=" CB THR A 49 " ideal model delta harmonic sigma weight residual -122.00 -141.26 19.26 0 2.50e+00 1.60e-01 5.94e+01 dihedral pdb=" C ASP A 424 " pdb=" N ASP A 424 " pdb=" CA ASP A 424 " pdb=" CB ASP A 424 " ideal model delta harmonic sigma weight residual -122.60 -135.78 13.18 0 2.50e+00 1.60e-01 2.78e+01 ... (remaining 10811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 2141 0.141 - 0.282: 474 0.282 - 0.423: 50 0.423 - 0.564: 2 0.564 - 0.705: 2 Chirality restraints: 2669 Sorted by residual: chirality pdb=" CA THR D 49 " pdb=" N THR D 49 " pdb=" C THR D 49 " pdb=" CB THR D 49 " both_signs ideal model delta sigma weight residual False 2.53 1.82 0.71 2.00e-01 2.50e+01 1.24e+01 chirality pdb=" CA THR A 49 " pdb=" N THR A 49 " pdb=" C THR A 49 " pdb=" CB THR A 49 " both_signs ideal model delta sigma weight residual False 2.53 1.84 0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" CA ASP B 424 " pdb=" N ASP B 424 " pdb=" C ASP B 424 " pdb=" CB ASP B 424 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.66e+00 ... (remaining 2666 not shown) Planarity restraints: 3222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 143 " 0.040 2.00e-02 2.50e+03 2.47e-02 1.52e+01 pdb=" CG TRP A 143 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP A 143 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP A 143 " -0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP A 143 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TRP A 143 " 0.024 2.00e-02 2.50e+03 pdb=" CE3 TRP A 143 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 143 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 143 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 143 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 44 " 0.042 2.00e-02 2.50e+03 2.36e-02 1.11e+01 pdb=" CG TYR C 44 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR C 44 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 44 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR C 44 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR C 44 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR C 44 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR C 44 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 400 " 0.029 2.00e-02 2.50e+03 2.37e-02 9.80e+00 pdb=" CG PHE A 400 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE A 400 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 400 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 400 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE A 400 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE A 400 " -0.003 2.00e-02 2.50e+03 ... (remaining 3219 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1149 2.75 - 3.29: 18768 3.29 - 3.83: 31457 3.83 - 4.36: 38684 4.36 - 4.90: 63087 Nonbonded interactions: 153145 Sorted by model distance: nonbonded pdb=" OH TYR A 242 " pdb=" O LEU A 269 " model vdw 2.214 2.440 nonbonded pdb=" OH TYR D 242 " pdb=" O LEU D 269 " model vdw 2.216 2.440 nonbonded pdb=" OH TYR C 242 " pdb=" O LEU C 269 " model vdw 2.216 2.440 nonbonded pdb=" O THR A 45 " pdb=" OG1 THR A 49 " model vdw 2.419 2.440 nonbonded pdb=" O THR D 45 " pdb=" OG1 THR D 49 " model vdw 2.428 2.440 ... (remaining 153140 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 22 through 108 or (resid 109 and (name N or name CA or nam \ e C or name O or name CB )) or resid 110 through 145 or (resid 146 and (name N o \ r name CA or name C or name O or name CB )) or resid 147 through 415 or (resid 4 \ 16 and (name N or name CA or name C or name O or name CB )) or resid 417 through \ 421 or (resid 422 and (name N or name CA or name C or name O or name CB )) or r \ esid 423 through 520 or (resid 521 and (name N or name CA or name C or name O or \ name CB )) or resid 522 through 626)) selection = (chain 'C' and (resid 22 through 70 or (resid 71 and (name N or name CA or name \ C or name O or name CB )) or resid 72 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 108 or (resid 109 and \ (name N or name CA or name C or name O or name CB )) or resid 110 through 145 o \ r (resid 146 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 47 through 421 or (resid 422 and (name N or name CA or name C or name O or name \ CB )) or resid 423 through 520 or (resid 521 and (name N or name CA or name C or \ name O or name CB )) or resid 522 through 626)) selection = (chain 'D' and (resid 22 through 70 or (resid 71 and (name N or name CA or name \ C or name O or name CB )) or resid 72 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 626)) } ncs_group { reference = chain 'E' selection = (chain 'G' and resid 316 through 348) selection = (chain 'H' and resid 316 through 348) } 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 88 5.16 5 C 11490 2.51 5 N 3092 2.21 5 O 3260 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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.200 Check model and map are aligned: 0.260 Convert atoms to be neutral: 0.140 Process input model: 47.010 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 62.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 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 : 0.008 0.055 18398 Z= 0.525 Angle : 1.472 14.100 24935 Z= 1.028 Chirality : 0.115 0.705 2669 Planarity : 0.007 0.030 3222 Dihedral : 15.011 73.516 6634 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 6.05 % Cbeta Deviations : 0.77 % 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: 0.51 (0.16), residues: 2212 helix: 1.38 (0.14), residues: 1132 sheet: -0.76 (0.32), residues: 281 loop : -0.67 (0.19), residues: 799 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 652 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 115 outliers final: 23 residues processed: 723 average time/residue: 0.3345 time to fit residues: 346.6130 Evaluate side-chains 376 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 353 time to evaluate : 2.136 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1777 time to fit residues: 10.4425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 0.3980 chunk 166 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 199 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 HIS A 253 HIS A 260 GLN A 283 ASN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 ASN A 446 HIS A 530 ASN A 581 GLN ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 ASN C 38 ASN C 71 GLN C 95 ASN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 HIS C 260 GLN C 283 ASN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 373 ASN C 388 GLN C 530 ASN C 577 GLN C 585 GLN C 587 ASN D 95 ASN ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS D 299 GLN D 388 GLN D 581 GLN D 587 ASN B 297 HIS B 315 HIS B 374 ASN B 530 ASN B 576 GLN ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.090 18398 Z= 0.262 Angle : 0.654 9.065 24935 Z= 0.352 Chirality : 0.045 0.198 2669 Planarity : 0.005 0.108 3222 Dihedral : 4.753 28.443 2457 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer Outliers : 3.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.17), residues: 2212 helix: 2.05 (0.15), residues: 1142 sheet: -0.85 (0.32), residues: 278 loop : -0.63 (0.20), residues: 792 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 374 time to evaluate : 2.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 35 residues processed: 416 average time/residue: 0.3127 time to fit residues: 192.8585 Evaluate side-chains 336 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 301 time to evaluate : 2.034 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.1618 time to fit residues: 13.4603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 216 optimal weight: 10.0000 chunk 178 optimal weight: 1.9990 chunk 198 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 160 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 HIS ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 HIS ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 HIS ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 ASN C 305 GLN C 446 HIS ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 GLN D 438 GLN D 446 HIS B 295 ASN B 541 HIS ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.081 18398 Z= 0.316 Angle : 0.634 9.225 24935 Z= 0.334 Chirality : 0.044 0.215 2669 Planarity : 0.005 0.079 3222 Dihedral : 4.673 24.389 2457 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer Outliers : 3.05 % 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: 0.69 (0.17), residues: 2212 helix: 1.70 (0.15), residues: 1151 sheet: -1.39 (0.30), residues: 283 loop : -0.65 (0.21), residues: 778 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 330 time to evaluate : 2.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 33 residues processed: 365 average time/residue: 0.3032 time to fit residues: 165.7055 Evaluate side-chains 326 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 293 time to evaluate : 2.019 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.1609 time to fit residues: 12.7783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 5.9990 chunk 150 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 190 optimal weight: 8.9990 chunk 57 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 HIS A 305 GLN ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 HIS ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 HIS B 305 GLN ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.096 18398 Z= 0.277 Angle : 0.582 7.456 24935 Z= 0.304 Chirality : 0.042 0.243 2669 Planarity : 0.005 0.114 3222 Dihedral : 4.567 24.065 2457 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 2.42 % 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: 0.67 (0.18), residues: 2212 helix: 1.71 (0.15), residues: 1142 sheet: -1.39 (0.28), residues: 317 loop : -0.60 (0.22), residues: 753 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 308 time to evaluate : 2.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 24 residues processed: 337 average time/residue: 0.3120 time to fit residues: 156.9603 Evaluate side-chains 296 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 272 time to evaluate : 2.033 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1678 time to fit residues: 10.3157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 0.7980 chunk 120 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 181 optimal weight: 0.6980 chunk 146 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 190 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 HIS ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 HIS ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN B 295 ASN B 305 GLN ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.116 18398 Z= 0.230 Angle : 0.569 9.596 24935 Z= 0.295 Chirality : 0.040 0.186 2669 Planarity : 0.005 0.095 3222 Dihedral : 4.500 23.906 2457 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer Outliers : 2.00 % 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: 0.74 (0.18), residues: 2212 helix: 1.77 (0.15), residues: 1133 sheet: -1.37 (0.29), residues: 317 loop : -0.55 (0.22), residues: 762 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 308 time to evaluate : 2.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 19 residues processed: 332 average time/residue: 0.3173 time to fit residues: 158.5860 Evaluate side-chains 306 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 287 time to evaluate : 2.227 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1695 time to fit residues: 9.1195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 0.7980 chunk 191 optimal weight: 9.9990 chunk 42 optimal weight: 0.0010 chunk 124 optimal weight: 7.9990 chunk 52 optimal weight: 0.0970 chunk 212 optimal weight: 7.9990 chunk 176 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 111 optimal weight: 0.3980 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 HIS A 585 GLN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 GLN B 305 GLN ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.126 18398 Z= 0.211 Angle : 0.565 13.478 24935 Z= 0.291 Chirality : 0.041 0.217 2669 Planarity : 0.005 0.116 3222 Dihedral : 4.418 23.981 2457 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer Outliers : 1.68 % 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: 0.87 (0.18), residues: 2212 helix: 1.86 (0.15), residues: 1132 sheet: -1.31 (0.29), residues: 320 loop : -0.45 (0.23), residues: 760 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 310 time to evaluate : 2.379 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 15 residues processed: 326 average time/residue: 0.3158 time to fit residues: 154.1491 Evaluate side-chains 281 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 266 time to evaluate : 2.057 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1857 time to fit residues: 7.9942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 179 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 212 optimal weight: 5.9990 chunk 132 optimal weight: 0.5980 chunk 129 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 HIS ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.5403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.150 18398 Z= 0.230 Angle : 0.569 11.652 24935 Z= 0.296 Chirality : 0.041 0.276 2669 Planarity : 0.005 0.115 3222 Dihedral : 4.367 22.928 2457 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 1.53 % 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 (0.18), residues: 2212 helix: 1.81 (0.15), residues: 1135 sheet: -1.41 (0.29), residues: 320 loop : -0.41 (0.23), residues: 757 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 279 time to evaluate : 2.071 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 15 residues processed: 295 average time/residue: 0.3224 time to fit residues: 142.2694 Evaluate side-chains 279 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 264 time to evaluate : 2.077 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1727 time to fit residues: 7.5856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 134 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 166 optimal weight: 0.9980 chunk 192 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN B 360 GLN ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.5827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.070 18398 Z= 0.462 Angle : 0.698 11.878 24935 Z= 0.361 Chirality : 0.047 0.235 2669 Planarity : 0.005 0.102 3222 Dihedral : 4.770 22.782 2457 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer Outliers : 1.84 % 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: 0.23 (0.18), residues: 2212 helix: 1.33 (0.15), residues: 1145 sheet: -2.00 (0.28), residues: 318 loop : -0.55 (0.24), residues: 749 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 282 time to evaluate : 2.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 21 residues processed: 302 average time/residue: 0.3096 time to fit residues: 140.7967 Evaluate side-chains 278 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 257 time to evaluate : 2.258 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1902 time to fit residues: 10.2120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 10.0000 chunk 185 optimal weight: 0.9980 chunk 197 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 155 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 186 optimal weight: 9.9990 chunk 196 optimal weight: 5.9990 chunk 129 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 530 ASN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.5940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.110 18398 Z= 0.238 Angle : 0.600 12.362 24935 Z= 0.311 Chirality : 0.041 0.234 2669 Planarity : 0.005 0.148 3222 Dihedral : 4.567 24.036 2457 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.30 % Favored : 96.65 % Rotamer Outliers : 0.63 % 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: 0.43 (0.18), residues: 2212 helix: 1.54 (0.15), residues: 1148 sheet: -1.99 (0.27), residues: 324 loop : -0.50 (0.24), residues: 740 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 292 time to evaluate : 2.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 297 average time/residue: 0.3163 time to fit residues: 142.4225 Evaluate side-chains 272 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 268 time to evaluate : 2.095 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1977 time to fit residues: 4.4801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 0.0070 chunk 127 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 219 optimal weight: 20.0000 chunk 201 optimal weight: 0.8980 chunk 174 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.6069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.094 18398 Z= 0.216 Angle : 0.589 12.111 24935 Z= 0.302 Chirality : 0.041 0.286 2669 Planarity : 0.005 0.147 3222 Dihedral : 4.475 23.590 2457 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 0.37 % 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: 0.53 (0.18), residues: 2212 helix: 1.64 (0.15), residues: 1144 sheet: -1.89 (0.28), residues: 318 loop : -0.53 (0.23), residues: 750 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 270 time to evaluate : 2.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 272 average time/residue: 0.3077 time to fit residues: 126.6348 Evaluate side-chains 273 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 269 time to evaluate : 2.015 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2711 time to fit residues: 4.4404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 160 optimal weight: 0.8980 chunk 25 optimal weight: 0.3980 chunk 48 optimal weight: 0.5980 chunk 174 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 chunk 179 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 153 optimal weight: 9.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 HIS ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.187404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.154363 restraints weight = 22340.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.154804 restraints weight = 20514.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.156452 restraints weight = 18959.686| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.6183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.083 18398 Z= 0.202 Angle : 0.582 11.598 24935 Z= 0.297 Chirality : 0.040 0.312 2669 Planarity : 0.005 0.142 3222 Dihedral : 4.370 24.261 2457 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 0.42 % 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: 0.71 (0.18), residues: 2212 helix: 1.73 (0.15), residues: 1144 sheet: -1.65 (0.29), residues: 291 loop : -0.50 (0.23), residues: 777 =============================================================================== Job complete usr+sys time: 3759.25 seconds wall clock time: 69 minutes 23.05 seconds (4163.05 seconds total)