Starting phenix.real_space_refine on Sun Mar 17 13:52:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvy_27021/03_2024/8cvy_27021.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvy_27021/03_2024/8cvy_27021.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvy_27021/03_2024/8cvy_27021.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvy_27021/03_2024/8cvy_27021.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvy_27021/03_2024/8cvy_27021.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvy_27021/03_2024/8cvy_27021.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.092 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 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. 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 8.63, per 1000 atoms: 0.48 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: 6.53 Conformation dependent library (CDL) restraints added in 3.0 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: 2.06 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: 6.51 Time building geometry restraints manager: 7.10 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 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: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 8.630 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 45.950 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 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 % Allowed : 11.37 % Favored : 82.58 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.007 TRP A 143 HIS 0.032 0.005 HIS B 311 PHE 0.053 0.007 PHE A 400 TYR 0.042 0.006 TYR C 44 ARG 0.021 0.002 ARG C 582 *********************** 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 : 2.135 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: A 60 ASP cc_start: 0.8663 (m-30) cc_final: 0.8235 (t70) REVERT: A 227 PHE cc_start: 0.5242 (m-80) cc_final: 0.4742 (m-80) REVERT: A 321 ASP cc_start: 0.8103 (p0) cc_final: 0.7651 (m-30) REVERT: A 375 PHE cc_start: 0.7945 (m-80) cc_final: 0.7729 (m-80) REVERT: A 424 ASP cc_start: 0.8423 (p0) cc_final: 0.8087 (p0) REVERT: A 480 GLU cc_start: 0.8533 (tt0) cc_final: 0.8216 (mm-30) REVERT: A 606 MET cc_start: 0.6653 (mtm) cc_final: 0.6265 (mtp) REVERT: E 317 SER cc_start: 0.7753 (OUTLIER) cc_final: 0.7521 (p) REVERT: C 127 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6550 (tp30) REVERT: C 296 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8106 (mt) REVERT: C 316 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8111 (mp) REVERT: C 403 LYS cc_start: 0.7861 (mmmt) cc_final: 0.7400 (mttm) REVERT: C 409 LEU cc_start: 0.8588 (mt) cc_final: 0.8105 (mt) REVERT: C 425 PHE cc_start: 0.8399 (t80) cc_final: 0.8194 (t80) REVERT: C 509 TYR cc_start: 0.7858 (t80) cc_final: 0.7650 (t80) REVERT: C 552 ILE cc_start: 0.8661 (mm) cc_final: 0.8344 (mm) REVERT: C 554 ASP cc_start: 0.7732 (t0) cc_final: 0.7359 (t0) REVERT: C 579 ARG cc_start: 0.8122 (ttt180) cc_final: 0.7513 (tpp-160) REVERT: C 597 ASP cc_start: 0.8773 (t0) cc_final: 0.8221 (t0) REVERT: G 333 MET cc_start: 0.8728 (mmm) cc_final: 0.7876 (mtm) REVERT: G 346 ASP cc_start: 0.8352 (m-30) cc_final: 0.7743 (m-30) REVERT: D 162 LEU cc_start: 0.8693 (pp) cc_final: 0.7878 (mt) REVERT: D 273 LYS cc_start: 0.8253 (mttt) cc_final: 0.8033 (tptp) REVERT: D 483 SER cc_start: 0.8698 (m) cc_final: 0.8447 (p) REVERT: D 597 ASP cc_start: 0.8439 (t0) cc_final: 0.8023 (t0) REVERT: H 316 VAL cc_start: 0.6247 (OUTLIER) cc_final: 0.5831 (m) REVERT: H 317 SER cc_start: 0.6043 (OUTLIER) cc_final: 0.5185 (p) REVERT: B 299 GLN cc_start: 0.7782 (mt0) cc_final: 0.7334 (tm-30) REVERT: B 319 ASN cc_start: 0.7750 (OUTLIER) cc_final: 0.7494 (m-40) REVERT: B 360 GLN cc_start: 0.3343 (mt0) cc_final: 0.3138 (mm-40) REVERT: B 379 THR cc_start: 0.7962 (m) cc_final: 0.7619 (p) REVERT: B 391 ASP cc_start: 0.8382 (m-30) cc_final: 0.8019 (t0) REVERT: B 414 PRO cc_start: 0.8592 (Cg_endo) cc_final: 0.8032 (Cg_exo) REVERT: B 428 MET cc_start: 0.8283 (mtm) cc_final: 0.8032 (mtt) REVERT: B 443 VAL cc_start: 0.8054 (m) cc_final: 0.7781 (t) REVERT: B 471 ASP cc_start: 0.7130 (m-30) cc_final: 0.6497 (p0) REVERT: B 486 SER cc_start: 0.8580 (m) cc_final: 0.8320 (p) REVERT: B 524 ILE cc_start: 0.5224 (mm) cc_final: 0.4674 (tp) REVERT: B 568 THR cc_start: 0.3951 (p) cc_final: 0.3551 (p) REVERT: B 572 TYR cc_start: 0.6230 (t80) cc_final: 0.5554 (t80) REVERT: B 594 ASP cc_start: 0.6832 (m-30) cc_final: 0.6566 (m-30) outliers start: 115 outliers final: 23 residues processed: 723 average time/residue: 0.3447 time to fit residues: 353.1735 Evaluate side-chains 403 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 373 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 317 SER Chi-restraints excluded: chain B residue 297 HIS Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 492 ASP 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: 0.9980 chunk 92 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 199 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 530 ASN A 581 GLN ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 ASN A 620 HIS 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 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: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18398 Z= 0.264 Angle : 0.622 9.276 24935 Z= 0.334 Chirality : 0.045 0.225 2669 Planarity : 0.004 0.038 3222 Dihedral : 6.535 59.816 2508 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.32 % Allowed : 16.00 % Favored : 79.68 % 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: 1.06 (0.17), residues: 2212 helix: 2.07 (0.14), residues: 1139 sheet: -0.95 (0.32), residues: 278 loop : -0.67 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 34 HIS 0.016 0.001 HIS C 240 PHE 0.031 0.002 PHE B 334 TYR 0.027 0.002 TYR A 493 ARG 0.009 0.001 ARG C 461 *********************** 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 474 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 392 time to evaluate : 1.982 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: A 60 ASP cc_start: 0.8657 (m-30) cc_final: 0.8239 (t70) REVERT: A 89 ARG cc_start: 0.7151 (mtm180) cc_final: 0.6875 (mtm-85) REVERT: A 143 TRP cc_start: 0.6551 (p-90) cc_final: 0.6330 (p-90) REVERT: A 162 LEU cc_start: 0.7935 (pp) cc_final: 0.7685 (tp) REVERT: A 321 ASP cc_start: 0.8163 (p0) cc_final: 0.7939 (m-30) REVERT: A 450 ASP cc_start: 0.8319 (t0) cc_final: 0.7697 (p0) REVERT: A 480 GLU cc_start: 0.8491 (tt0) cc_final: 0.8155 (tp30) REVERT: A 490 PRO cc_start: 0.8643 (Cg_endo) cc_final: 0.8350 (Cg_exo) REVERT: C 81 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8292 (tt0) REVERT: C 94 MET cc_start: 0.7185 (mmm) cc_final: 0.6481 (mmm) REVERT: C 127 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6655 (tp30) REVERT: C 212 TYR cc_start: 0.7878 (m-80) cc_final: 0.7577 (m-80) REVERT: C 225 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8220 (tp30) REVERT: C 245 GLU cc_start: 0.8688 (tp30) cc_final: 0.7912 (tp30) REVERT: C 284 VAL cc_start: 0.8404 (m) cc_final: 0.8010 (m) REVERT: C 293 PHE cc_start: 0.6664 (OUTLIER) cc_final: 0.6186 (t80) REVERT: C 296 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.7863 (mt) REVERT: C 316 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8217 (mp) REVERT: C 333 GLU cc_start: 0.8334 (tt0) cc_final: 0.8093 (tt0) REVERT: C 350 ASN cc_start: 0.7240 (t0) cc_final: 0.6985 (t0) REVERT: C 403 LYS cc_start: 0.7921 (mmmt) cc_final: 0.7428 (mttm) REVERT: C 425 PHE cc_start: 0.8395 (t80) cc_final: 0.8184 (t80) REVERT: C 554 ASP cc_start: 0.7957 (t0) cc_final: 0.7587 (t0) REVERT: C 597 ASP cc_start: 0.8631 (t0) cc_final: 0.8239 (t0) REVERT: G 331 ASP cc_start: 0.6782 (t0) cc_final: 0.6426 (t70) REVERT: D 285 LYS cc_start: 0.8501 (mptt) cc_final: 0.8299 (mmtp) REVERT: D 354 ARG cc_start: 0.7607 (mtp-110) cc_final: 0.7243 (mtm180) REVERT: D 355 VAL cc_start: 0.8685 (p) cc_final: 0.8353 (m) REVERT: D 473 VAL cc_start: 0.9040 (t) cc_final: 0.8572 (p) REVERT: D 483 SER cc_start: 0.8769 (m) cc_final: 0.8456 (p) REVERT: D 562 ASP cc_start: 0.8266 (m-30) cc_final: 0.7878 (t0) REVERT: D 597 ASP cc_start: 0.8576 (t0) cc_final: 0.8117 (t0) REVERT: B 301 LYS cc_start: 0.8204 (ptmt) cc_final: 0.7952 (ptmt) REVERT: B 340 ASP cc_start: 0.6796 (p0) cc_final: 0.6474 (p0) REVERT: B 344 GLU cc_start: 0.8322 (tt0) cc_final: 0.7831 (pp20) REVERT: B 378 GLU cc_start: 0.6283 (tp30) cc_final: 0.5946 (tm-30) REVERT: B 391 ASP cc_start: 0.8397 (m-30) cc_final: 0.8079 (t0) REVERT: B 404 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7591 (pp) REVERT: B 414 PRO cc_start: 0.8150 (Cg_endo) cc_final: 0.7857 (Cg_exo) REVERT: B 419 MET cc_start: 0.6761 (tpp) cc_final: 0.6528 (mpp) REVERT: B 428 MET cc_start: 0.8274 (mtm) cc_final: 0.8006 (mtt) REVERT: B 443 VAL cc_start: 0.8035 (m) cc_final: 0.7813 (t) REVERT: B 486 SER cc_start: 0.8634 (m) cc_final: 0.8350 (p) REVERT: B 524 ILE cc_start: 0.4917 (mm) cc_final: 0.4460 (tp) REVERT: B 538 MET cc_start: 0.7313 (mmt) cc_final: 0.6960 (tpt) outliers start: 82 outliers final: 46 residues processed: 445 average time/residue: 0.3091 time to fit residues: 202.4790 Evaluate side-chains 366 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 315 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 492 ASP Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 491 VAL 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: 0.8980 chunk 166 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 chunk 216 optimal weight: 9.9990 chunk 178 optimal weight: 0.9990 chunk 198 optimal weight: 0.8980 chunk 68 optimal weight: 0.3980 chunk 160 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 HIS ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 HIS C 268 HIS C 283 ASN C 305 GLN ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 HIS D 268 HIS D 299 GLN D 360 GLN B 295 ASN B 305 GLN ** B 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 GLN ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18398 Z= 0.216 Angle : 0.562 8.776 24935 Z= 0.297 Chirality : 0.041 0.192 2669 Planarity : 0.003 0.036 3222 Dihedral : 5.798 58.376 2479 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.89 % Allowed : 17.11 % Favored : 79.00 % 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: 0.99 (0.17), residues: 2212 helix: 1.97 (0.15), residues: 1141 sheet: -1.18 (0.31), residues: 280 loop : -0.54 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 134 HIS 0.009 0.001 HIS C 240 PHE 0.029 0.002 PHE B 334 TYR 0.018 0.002 TYR B 313 ARG 0.012 0.001 ARG A 236 *********************** 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 409 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 335 time to evaluate : 2.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.8653 (m-30) cc_final: 0.8298 (t70) REVERT: A 80 LEU cc_start: 0.6324 (OUTLIER) cc_final: 0.6081 (mt) REVERT: A 106 TRP cc_start: 0.8091 (t60) cc_final: 0.7650 (t60) REVERT: A 108 ILE cc_start: 0.8788 (pp) cc_final: 0.8374 (pp) REVERT: A 143 TRP cc_start: 0.6603 (p-90) cc_final: 0.6350 (p-90) REVERT: A 400 PHE cc_start: 0.7706 (t80) cc_final: 0.7430 (t80) REVERT: A 449 LEU cc_start: 0.9210 (mm) cc_final: 0.8906 (mt) REVERT: A 450 ASP cc_start: 0.8524 (t0) cc_final: 0.8011 (p0) REVERT: A 480 GLU cc_start: 0.8491 (tt0) cc_final: 0.8132 (tp30) REVERT: A 490 PRO cc_start: 0.8698 (Cg_endo) cc_final: 0.8401 (Cg_exo) REVERT: A 599 LYS cc_start: 0.8376 (ttmt) cc_final: 0.8106 (mmmt) REVERT: C 81 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8292 (tt0) REVERT: C 127 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6724 (tp30) REVERT: C 153 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7610 (mm) REVERT: C 225 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8246 (tp30) REVERT: C 293 PHE cc_start: 0.6551 (OUTLIER) cc_final: 0.5882 (t80) REVERT: C 296 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8117 (mt) REVERT: C 316 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8236 (mp) REVERT: C 403 LYS cc_start: 0.7983 (mmmt) cc_final: 0.7535 (mttm) REVERT: C 425 PHE cc_start: 0.8445 (t80) cc_final: 0.8245 (t80) REVERT: C 597 ASP cc_start: 0.8434 (t0) cc_final: 0.8055 (t0) REVERT: G 331 ASP cc_start: 0.6825 (t0) cc_final: 0.6501 (t70) REVERT: D 354 ARG cc_start: 0.7472 (mtp-110) cc_final: 0.7219 (mtm180) REVERT: D 355 VAL cc_start: 0.8645 (p) cc_final: 0.8357 (t) REVERT: D 473 VAL cc_start: 0.8871 (t) cc_final: 0.8630 (p) REVERT: D 483 SER cc_start: 0.8721 (m) cc_final: 0.8421 (p) REVERT: D 562 ASP cc_start: 0.8317 (m-30) cc_final: 0.7789 (t0) REVERT: D 597 ASP cc_start: 0.8435 (t0) cc_final: 0.7979 (t0) REVERT: B 324 LEU cc_start: 0.6818 (mt) cc_final: 0.6595 (mt) REVERT: B 391 ASP cc_start: 0.8376 (m-30) cc_final: 0.8076 (t0) REVERT: B 404 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.7829 (pp) REVERT: B 409 LEU cc_start: 0.8509 (mp) cc_final: 0.8255 (mp) REVERT: B 428 MET cc_start: 0.8249 (mtm) cc_final: 0.7911 (mtt) REVERT: B 443 VAL cc_start: 0.8136 (m) cc_final: 0.7848 (t) REVERT: B 486 SER cc_start: 0.8606 (m) cc_final: 0.8278 (p) REVERT: B 495 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8303 (mp0) REVERT: B 524 ILE cc_start: 0.4811 (mm) cc_final: 0.4390 (tp) REVERT: B 538 MET cc_start: 0.7461 (mmt) cc_final: 0.7116 (tpt) REVERT: B 568 THR cc_start: 0.3695 (p) cc_final: 0.3413 (p) outliers start: 74 outliers final: 53 residues processed: 381 average time/residue: 0.2991 time to fit residues: 170.7277 Evaluate side-chains 371 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 311 time to evaluate : 2.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 492 ASP Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 491 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 0.1980 chunk 150 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 chunk 212 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 190 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 228 ASN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 HIS ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 446 HIS B 383 GLN ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18398 Z= 0.201 Angle : 0.544 9.807 24935 Z= 0.284 Chirality : 0.041 0.203 2669 Planarity : 0.003 0.044 3222 Dihedral : 5.709 59.332 2479 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.84 % Allowed : 18.42 % Favored : 77.74 % 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: 0.92 (0.18), residues: 2212 helix: 1.90 (0.15), residues: 1145 sheet: -1.13 (0.29), residues: 307 loop : -0.55 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 134 HIS 0.009 0.001 HIS A 240 PHE 0.031 0.002 PHE B 334 TYR 0.019 0.001 TYR A 493 ARG 0.007 0.000 ARG A 591 *********************** 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 408 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 335 time to evaluate : 2.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.8607 (m-30) cc_final: 0.8299 (t70) REVERT: A 80 LEU cc_start: 0.6214 (OUTLIER) cc_final: 0.5956 (mt) REVERT: A 108 ILE cc_start: 0.8786 (pp) cc_final: 0.8177 (pt) REVERT: A 143 TRP cc_start: 0.6727 (p-90) cc_final: 0.6477 (p-90) REVERT: A 227 PHE cc_start: 0.7176 (m-10) cc_final: 0.6938 (m-10) REVERT: A 228 ASN cc_start: 0.8498 (t0) cc_final: 0.8120 (t0) REVERT: A 237 GLN cc_start: 0.8038 (mt0) cc_final: 0.7605 (tt0) REVERT: A 449 LEU cc_start: 0.9252 (mm) cc_final: 0.9015 (mt) REVERT: A 450 ASP cc_start: 0.8662 (t0) cc_final: 0.8220 (p0) REVERT: A 480 GLU cc_start: 0.8508 (tt0) cc_final: 0.8155 (tp30) REVERT: A 490 PRO cc_start: 0.8751 (Cg_endo) cc_final: 0.8510 (Cg_exo) REVERT: A 599 LYS cc_start: 0.8426 (ttmt) cc_final: 0.8125 (mmmt) REVERT: C 70 GLU cc_start: 0.7147 (tm-30) cc_final: 0.6935 (tm-30) REVERT: C 81 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8266 (tt0) REVERT: C 95 ASN cc_start: 0.8129 (m-40) cc_final: 0.7909 (m110) REVERT: C 127 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6713 (tp30) REVERT: C 132 GLU cc_start: 0.8258 (tp30) cc_final: 0.7786 (tm-30) REVERT: C 153 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7587 (mm) REVERT: C 293 PHE cc_start: 0.6490 (OUTLIER) cc_final: 0.5874 (t80) REVERT: C 296 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7843 (mt) REVERT: C 403 LYS cc_start: 0.7966 (mmmt) cc_final: 0.7651 (mtmm) REVERT: C 597 ASP cc_start: 0.8359 (t0) cc_final: 0.8039 (t0) REVERT: G 331 ASP cc_start: 0.6864 (t0) cc_final: 0.6502 (t70) REVERT: D 156 PHE cc_start: 0.8298 (m-80) cc_final: 0.8048 (m-80) REVERT: D 354 ARG cc_start: 0.7468 (mtp-110) cc_final: 0.7223 (mtm180) REVERT: D 355 VAL cc_start: 0.8643 (p) cc_final: 0.8379 (t) REVERT: D 466 PHE cc_start: 0.8269 (m-80) cc_final: 0.8040 (m-80) REVERT: D 473 VAL cc_start: 0.8919 (t) cc_final: 0.8686 (p) REVERT: D 483 SER cc_start: 0.8731 (m) cc_final: 0.8467 (p) REVERT: D 562 ASP cc_start: 0.8352 (m-30) cc_final: 0.7834 (t0) REVERT: D 597 ASP cc_start: 0.8384 (t0) cc_final: 0.7964 (t0) REVERT: B 324 LEU cc_start: 0.6805 (mt) cc_final: 0.6561 (mt) REVERT: B 391 ASP cc_start: 0.8374 (m-30) cc_final: 0.8080 (t0) REVERT: B 428 MET cc_start: 0.8200 (mtm) cc_final: 0.7898 (mtt) REVERT: B 443 VAL cc_start: 0.8161 (m) cc_final: 0.7900 (t) REVERT: B 486 SER cc_start: 0.8560 (m) cc_final: 0.8237 (p) REVERT: B 495 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8242 (mp0) REVERT: B 538 MET cc_start: 0.7424 (mmt) cc_final: 0.7156 (tpt) REVERT: B 568 THR cc_start: 0.3718 (p) cc_final: 0.3470 (p) outliers start: 73 outliers final: 53 residues processed: 383 average time/residue: 0.3080 time to fit residues: 175.4377 Evaluate side-chains 360 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 302 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 492 ASP Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain H residue 348 TYR Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 491 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 181 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 190 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 446 HIS ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 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: 0.7908 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 18398 Z= 0.276 Angle : 0.555 8.294 24935 Z= 0.289 Chirality : 0.042 0.188 2669 Planarity : 0.003 0.048 3222 Dihedral : 5.509 59.543 2474 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.21 % Allowed : 18.26 % Favored : 77.53 % 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: 0.84 (0.18), residues: 2212 helix: 1.86 (0.15), residues: 1142 sheet: -1.32 (0.29), residues: 310 loop : -0.55 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 182 HIS 0.007 0.001 HIS A 240 PHE 0.025 0.002 PHE B 307 TYR 0.017 0.002 TYR E 348 ARG 0.008 0.001 ARG A 591 *********************** 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 392 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 312 time to evaluate : 1.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LEU cc_start: 0.6463 (OUTLIER) cc_final: 0.6228 (mt) REVERT: A 227 PHE cc_start: 0.7217 (m-10) cc_final: 0.6858 (m-10) REVERT: A 228 ASN cc_start: 0.8498 (t0) cc_final: 0.8082 (t0) REVERT: A 449 LEU cc_start: 0.9252 (mm) cc_final: 0.9018 (mt) REVERT: A 450 ASP cc_start: 0.8711 (t0) cc_final: 0.8429 (p0) REVERT: A 480 GLU cc_start: 0.8558 (tt0) cc_final: 0.8167 (tp30) REVERT: A 599 LYS cc_start: 0.8516 (ttmt) cc_final: 0.8270 (mmmt) REVERT: C 70 GLU cc_start: 0.7138 (tm-30) cc_final: 0.6864 (tm-30) REVERT: C 81 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8305 (tt0) REVERT: C 94 MET cc_start: 0.7632 (mmm) cc_final: 0.7400 (mmm) REVERT: C 127 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6643 (tp30) REVERT: C 132 GLU cc_start: 0.8299 (tp30) cc_final: 0.7856 (tm-30) REVERT: C 153 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7679 (mm) REVERT: C 245 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.7860 (tp30) REVERT: C 293 PHE cc_start: 0.6634 (OUTLIER) cc_final: 0.6052 (t80) REVERT: C 296 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.7934 (mt) REVERT: C 403 LYS cc_start: 0.8089 (mmmt) cc_final: 0.7629 (mttt) REVERT: C 597 ASP cc_start: 0.8385 (t0) cc_final: 0.8060 (t0) REVERT: G 331 ASP cc_start: 0.6867 (t0) cc_final: 0.6610 (t70) REVERT: D 195 ARG cc_start: 0.9177 (tpp80) cc_final: 0.8815 (tpp80) REVERT: D 227 PHE cc_start: 0.6765 (m-80) cc_final: 0.6518 (m-80) REVERT: D 354 ARG cc_start: 0.7530 (mtp-110) cc_final: 0.7270 (mtm180) REVERT: D 355 VAL cc_start: 0.8680 (p) cc_final: 0.8399 (t) REVERT: D 473 VAL cc_start: 0.9035 (t) cc_final: 0.8793 (p) REVERT: D 483 SER cc_start: 0.8721 (m) cc_final: 0.8484 (p) REVERT: D 597 ASP cc_start: 0.8454 (t0) cc_final: 0.8018 (t0) REVERT: B 324 LEU cc_start: 0.6947 (mt) cc_final: 0.6741 (mt) REVERT: B 391 ASP cc_start: 0.8361 (m-30) cc_final: 0.8027 (t0) REVERT: B 428 MET cc_start: 0.8206 (mtm) cc_final: 0.7932 (mtt) REVERT: B 443 VAL cc_start: 0.8224 (m) cc_final: 0.7949 (t) REVERT: B 486 SER cc_start: 0.8516 (m) cc_final: 0.8213 (p) REVERT: B 524 ILE cc_start: 0.5098 (mp) cc_final: 0.4426 (tt) REVERT: B 538 MET cc_start: 0.7686 (mmt) cc_final: 0.7407 (tpt) outliers start: 80 outliers final: 62 residues processed: 366 average time/residue: 0.3051 time to fit residues: 165.9694 Evaluate side-chains 358 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 290 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 492 ASP Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 491 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 0.9990 chunk 191 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 212 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 446 HIS ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 GLN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 ASN D 48 GLN ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 GLN ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 18398 Z= 0.306 Angle : 0.576 9.355 24935 Z= 0.301 Chirality : 0.042 0.253 2669 Planarity : 0.004 0.048 3222 Dihedral : 5.427 57.983 2472 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.21 % Allowed : 18.42 % Favored : 76.37 % 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: 0.69 (0.18), residues: 2212 helix: 1.76 (0.15), residues: 1139 sheet: -1.57 (0.29), residues: 307 loop : -0.56 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 325 HIS 0.007 0.001 HIS C 240 PHE 0.027 0.002 PHE B 307 TYR 0.024 0.002 TYR A 493 ARG 0.007 0.001 ARG C 462 *********************** 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 405 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 306 time to evaluate : 2.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.5797 (mmt) cc_final: 0.5282 (mmt) REVERT: A 143 TRP cc_start: 0.6866 (p-90) cc_final: 0.6656 (p-90) REVERT: A 228 ASN cc_start: 0.8485 (t0) cc_final: 0.8016 (t0) REVERT: A 237 GLN cc_start: 0.7827 (mt0) cc_final: 0.7531 (tt0) REVERT: A 333 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7203 (mt-10) REVERT: A 425 PHE cc_start: 0.6896 (OUTLIER) cc_final: 0.6573 (t80) REVERT: A 449 LEU cc_start: 0.9213 (mm) cc_final: 0.8898 (mt) REVERT: A 480 GLU cc_start: 0.8534 (tt0) cc_final: 0.8093 (tp30) REVERT: A 494 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7786 (mm-30) REVERT: A 599 LYS cc_start: 0.8743 (ttmt) cc_final: 0.8438 (mmmt) REVERT: C 60 ASP cc_start: 0.7789 (t0) cc_final: 0.7225 (t0) REVERT: C 70 GLU cc_start: 0.7191 (tm-30) cc_final: 0.6870 (tm-30) REVERT: C 81 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8332 (tt0) REVERT: C 94 MET cc_start: 0.7788 (mmm) cc_final: 0.7212 (mtp) REVERT: C 127 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6652 (tp30) REVERT: C 132 GLU cc_start: 0.8325 (tp30) cc_final: 0.7784 (tm-30) REVERT: C 134 TRP cc_start: 0.8120 (t60) cc_final: 0.7785 (t-100) REVERT: C 153 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7697 (mm) REVERT: C 245 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.7829 (tp30) REVERT: C 293 PHE cc_start: 0.6547 (OUTLIER) cc_final: 0.6042 (t80) REVERT: C 296 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7842 (mt) REVERT: C 333 GLU cc_start: 0.8559 (tt0) cc_final: 0.8305 (tt0) REVERT: C 403 LYS cc_start: 0.8064 (mmmt) cc_final: 0.7553 (mttm) REVERT: C 554 ASP cc_start: 0.7743 (t0) cc_final: 0.7471 (t0) REVERT: C 597 ASP cc_start: 0.8436 (t0) cc_final: 0.8061 (t0) REVERT: G 331 ASP cc_start: 0.6984 (t0) cc_final: 0.6720 (t70) REVERT: D 195 ARG cc_start: 0.9144 (tpp80) cc_final: 0.8777 (tpp80) REVERT: D 354 ARG cc_start: 0.7565 (mtp-110) cc_final: 0.7301 (mtm180) REVERT: D 355 VAL cc_start: 0.8698 (p) cc_final: 0.8421 (t) REVERT: D 483 SER cc_start: 0.8728 (m) cc_final: 0.8497 (p) REVERT: D 597 ASP cc_start: 0.8519 (t0) cc_final: 0.8070 (t0) REVERT: B 391 ASP cc_start: 0.8383 (m-30) cc_final: 0.8037 (t0) REVERT: B 428 MET cc_start: 0.8276 (mtm) cc_final: 0.8006 (mtt) REVERT: B 443 VAL cc_start: 0.8231 (m) cc_final: 0.7971 (t) REVERT: B 486 SER cc_start: 0.8509 (m) cc_final: 0.8178 (p) REVERT: B 524 ILE cc_start: 0.4948 (mp) cc_final: 0.4148 (tt) REVERT: B 538 MET cc_start: 0.7538 (mmt) cc_final: 0.7259 (tpt) REVERT: B 568 THR cc_start: 0.3878 (p) cc_final: 0.3615 (p) outliers start: 99 outliers final: 75 residues processed: 374 average time/residue: 0.3002 time to fit residues: 169.2689 Evaluate side-chains 362 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 281 time to evaluate : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 492 ASP Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 421 ASP Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 509 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 20.0000 chunk 23 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 212 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 GLN B 576 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: 0.7944 moved from start: 0.5347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 18398 Z= 0.248 Angle : 0.541 9.457 24935 Z= 0.283 Chirality : 0.041 0.187 2669 Planarity : 0.003 0.050 3222 Dihedral : 5.339 56.748 2472 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.53 % Allowed : 19.37 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.18), residues: 2212 helix: 1.82 (0.15), residues: 1148 sheet: -1.71 (0.28), residues: 313 loop : -0.47 (0.23), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 182 HIS 0.006 0.001 HIS C 240 PHE 0.025 0.002 PHE B 307 TYR 0.020 0.001 TYR B 313 ARG 0.007 0.001 ARG C 462 *********************** 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 379 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 293 time to evaluate : 2.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.5753 (mmt) cc_final: 0.5069 (mmt) REVERT: A 237 GLN cc_start: 0.7750 (mt0) cc_final: 0.7513 (tt0) REVERT: A 275 ASP cc_start: 0.7417 (t0) cc_final: 0.7200 (m-30) REVERT: A 425 PHE cc_start: 0.6886 (OUTLIER) cc_final: 0.6560 (t80) REVERT: A 449 LEU cc_start: 0.9273 (mm) cc_final: 0.8951 (mt) REVERT: A 480 GLU cc_start: 0.8491 (tt0) cc_final: 0.8042 (tp30) REVERT: A 494 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7795 (mm-30) REVERT: A 599 LYS cc_start: 0.8754 (ttmt) cc_final: 0.8452 (mmmt) REVERT: C 60 ASP cc_start: 0.7790 (t0) cc_final: 0.7266 (t0) REVERT: C 70 GLU cc_start: 0.7160 (tm-30) cc_final: 0.6807 (tm-30) REVERT: C 81 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8311 (tt0) REVERT: C 94 MET cc_start: 0.7862 (mmm) cc_final: 0.7418 (mtp) REVERT: C 127 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6642 (tp30) REVERT: C 132 GLU cc_start: 0.8278 (tp30) cc_final: 0.7955 (tm-30) REVERT: C 153 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7767 (mm) REVERT: C 245 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.7853 (tp30) REVERT: C 296 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7829 (mt) REVERT: C 333 GLU cc_start: 0.8561 (tt0) cc_final: 0.8312 (tt0) REVERT: C 403 LYS cc_start: 0.8007 (mmmt) cc_final: 0.7571 (mttt) REVERT: C 597 ASP cc_start: 0.8464 (t0) cc_final: 0.8088 (t0) REVERT: G 331 ASP cc_start: 0.6951 (t0) cc_final: 0.6727 (t70) REVERT: G 336 ASP cc_start: 0.8421 (t0) cc_final: 0.8169 (t0) REVERT: D 195 ARG cc_start: 0.9134 (tpp80) cc_final: 0.8763 (tpp80) REVERT: D 227 PHE cc_start: 0.6489 (m-80) cc_final: 0.6248 (m-80) REVERT: D 277 VAL cc_start: 0.8954 (OUTLIER) cc_final: 0.8684 (m) REVERT: D 354 ARG cc_start: 0.7580 (mtp-110) cc_final: 0.7340 (mtm180) REVERT: D 355 VAL cc_start: 0.8678 (p) cc_final: 0.8384 (t) REVERT: D 483 SER cc_start: 0.8650 (m) cc_final: 0.8447 (p) REVERT: D 539 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7245 (tm-30) REVERT: D 597 ASP cc_start: 0.8522 (t0) cc_final: 0.8099 (t0) REVERT: D 622 THR cc_start: 0.8065 (t) cc_final: 0.7773 (m) REVERT: B 391 ASP cc_start: 0.8379 (m-30) cc_final: 0.8025 (t0) REVERT: B 428 MET cc_start: 0.8271 (mtm) cc_final: 0.7988 (mtm) REVERT: B 443 VAL cc_start: 0.8268 (m) cc_final: 0.8022 (t) REVERT: B 486 SER cc_start: 0.8453 (m) cc_final: 0.8101 (p) REVERT: B 524 ILE cc_start: 0.5170 (mp) cc_final: 0.4345 (tt) REVERT: B 538 MET cc_start: 0.7598 (mmt) cc_final: 0.7268 (tpt) REVERT: B 568 THR cc_start: 0.3935 (p) cc_final: 0.3647 (p) outliers start: 86 outliers final: 66 residues processed: 355 average time/residue: 0.3125 time to fit residues: 165.8006 Evaluate side-chains 345 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 272 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 492 ASP Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 421 ASP Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 539 GLU Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 491 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 0.0980 chunk 84 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 chunk 192 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 HIS ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** 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: 0.7995 moved from start: 0.5585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 18398 Z= 0.339 Angle : 0.604 10.850 24935 Z= 0.313 Chirality : 0.043 0.386 2669 Planarity : 0.004 0.108 3222 Dihedral : 5.314 56.330 2470 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.74 % Allowed : 20.05 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.18), residues: 2212 helix: 1.65 (0.15), residues: 1154 sheet: -1.93 (0.28), residues: 318 loop : -0.54 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 182 HIS 0.009 0.001 HIS A 240 PHE 0.023 0.002 PHE B 366 TYR 0.021 0.002 TYR C 68 ARG 0.009 0.001 ARG C 211 *********************** 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 383 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 293 time to evaluate : 2.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.5735 (mmt) cc_final: 0.4981 (mmt) REVERT: A 156 PHE cc_start: 0.7249 (OUTLIER) cc_final: 0.6665 (m-10) REVERT: A 227 PHE cc_start: 0.7290 (m-10) cc_final: 0.6653 (m-80) REVERT: A 237 GLN cc_start: 0.7768 (mt0) cc_final: 0.7532 (tt0) REVERT: A 275 ASP cc_start: 0.7587 (t0) cc_final: 0.7385 (m-30) REVERT: A 333 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7302 (mt-10) REVERT: A 425 PHE cc_start: 0.6894 (OUTLIER) cc_final: 0.6551 (t80) REVERT: A 444 CYS cc_start: 0.7970 (p) cc_final: 0.7746 (p) REVERT: A 449 LEU cc_start: 0.9246 (mm) cc_final: 0.8967 (mt) REVERT: A 480 GLU cc_start: 0.8450 (tt0) cc_final: 0.8009 (tp30) REVERT: A 599 LYS cc_start: 0.8811 (ttmt) cc_final: 0.8492 (mmmt) REVERT: C 60 ASP cc_start: 0.7894 (t0) cc_final: 0.7340 (t0) REVERT: C 70 GLU cc_start: 0.7209 (tm-30) cc_final: 0.6843 (tm-30) REVERT: C 81 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8296 (tt0) REVERT: C 94 MET cc_start: 0.7897 (mmm) cc_final: 0.7523 (mtp) REVERT: C 127 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6657 (tp30) REVERT: C 132 GLU cc_start: 0.8334 (tp30) cc_final: 0.7957 (tm-30) REVERT: C 245 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.7858 (tp30) REVERT: C 296 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8108 (mm) REVERT: C 450 ASP cc_start: 0.8009 (t0) cc_final: 0.7705 (t0) REVERT: C 484 SER cc_start: 0.7901 (p) cc_final: 0.7581 (t) REVERT: G 331 ASP cc_start: 0.7009 (t0) cc_final: 0.6766 (t70) REVERT: D 195 ARG cc_start: 0.9111 (tpp80) cc_final: 0.8731 (tpp80) REVERT: D 227 PHE cc_start: 0.6866 (m-80) cc_final: 0.6193 (m-80) REVERT: D 228 ASN cc_start: 0.8618 (t0) cc_final: 0.8282 (t0) REVERT: D 277 VAL cc_start: 0.8966 (OUTLIER) cc_final: 0.8719 (m) REVERT: D 354 ARG cc_start: 0.7630 (mtp-110) cc_final: 0.7386 (mtm180) REVERT: D 355 VAL cc_start: 0.8703 (p) cc_final: 0.8397 (t) REVERT: D 483 SER cc_start: 0.8703 (m) cc_final: 0.8483 (p) REVERT: D 524 ILE cc_start: 0.9106 (mm) cc_final: 0.8825 (mm) REVERT: D 539 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7420 (tt0) REVERT: D 597 ASP cc_start: 0.8574 (t0) cc_final: 0.8170 (t0) REVERT: B 391 ASP cc_start: 0.8384 (m-30) cc_final: 0.7996 (t0) REVERT: B 404 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8542 (tt) REVERT: B 428 MET cc_start: 0.8333 (mtm) cc_final: 0.8034 (mtm) REVERT: B 443 VAL cc_start: 0.8289 (m) cc_final: 0.8030 (t) REVERT: B 486 SER cc_start: 0.8386 (m) cc_final: 0.8008 (p) REVERT: B 524 ILE cc_start: 0.5242 (mp) cc_final: 0.4398 (tt) REVERT: B 538 MET cc_start: 0.7616 (mmt) cc_final: 0.7264 (tpt) REVERT: B 568 THR cc_start: 0.3999 (p) cc_final: 0.3751 (p) outliers start: 90 outliers final: 72 residues processed: 355 average time/residue: 0.2920 time to fit residues: 155.9408 Evaluate side-chains 358 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 278 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 492 ASP Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 421 ASP Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 539 GLU Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 509 TYR 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: 0.0040 chunk 197 optimal weight: 0.5980 chunk 118 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 chunk 186 optimal weight: 20.0000 chunk 196 optimal weight: 0.9980 chunk 129 optimal weight: 0.4980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 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: 0.7934 moved from start: 0.5715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 18398 Z= 0.201 Angle : 0.549 10.885 24935 Z= 0.284 Chirality : 0.041 0.378 2669 Planarity : 0.003 0.051 3222 Dihedral : 5.206 56.522 2470 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.74 % Allowed : 21.21 % Favored : 75.05 % 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: 0.72 (0.18), residues: 2212 helix: 1.81 (0.15), residues: 1153 sheet: -1.86 (0.28), residues: 324 loop : -0.46 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 134 HIS 0.010 0.001 HIS A 240 PHE 0.018 0.002 PHE E 338 TYR 0.037 0.001 TYR B 313 ARG 0.008 0.001 ARG C 211 *********************** 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 375 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 304 time to evaluate : 2.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.5642 (mmt) cc_final: 0.5066 (mmt) REVERT: A 135 ASP cc_start: 0.8366 (m-30) cc_final: 0.8131 (m-30) REVERT: A 143 TRP cc_start: 0.7104 (p-90) cc_final: 0.6864 (p-90) REVERT: A 227 PHE cc_start: 0.7121 (m-10) cc_final: 0.6910 (m-10) REVERT: A 231 LYS cc_start: 0.8571 (pttt) cc_final: 0.7414 (tttm) REVERT: A 237 GLN cc_start: 0.7812 (mt0) cc_final: 0.7582 (tt0) REVERT: A 425 PHE cc_start: 0.6883 (OUTLIER) cc_final: 0.6587 (t80) REVERT: A 449 LEU cc_start: 0.9274 (mm) cc_final: 0.9014 (mt) REVERT: A 480 GLU cc_start: 0.8459 (tt0) cc_final: 0.8018 (tp30) REVERT: A 599 LYS cc_start: 0.8779 (ttmt) cc_final: 0.8467 (mmmt) REVERT: C 60 ASP cc_start: 0.7749 (t0) cc_final: 0.7157 (t0) REVERT: C 70 GLU cc_start: 0.7113 (tm-30) cc_final: 0.6781 (tm-30) REVERT: C 81 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8349 (tt0) REVERT: C 94 MET cc_start: 0.7902 (mmm) cc_final: 0.7558 (mtp) REVERT: C 127 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6553 (tp30) REVERT: C 132 GLU cc_start: 0.8236 (tp30) cc_final: 0.7990 (tm-30) REVERT: C 153 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7719 (mm) REVERT: C 245 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.7832 (tp30) REVERT: C 403 LYS cc_start: 0.8093 (mmmt) cc_final: 0.7668 (mttt) REVERT: C 450 ASP cc_start: 0.8013 (t0) cc_final: 0.7713 (t0) REVERT: C 484 SER cc_start: 0.7918 (p) cc_final: 0.7629 (t) REVERT: C 597 ASP cc_start: 0.8298 (t0) cc_final: 0.7872 (m-30) REVERT: G 336 ASP cc_start: 0.8438 (t0) cc_final: 0.8144 (t0) REVERT: D 195 ARG cc_start: 0.9097 (tpp80) cc_final: 0.8716 (tpp80) REVERT: D 227 PHE cc_start: 0.6528 (m-80) cc_final: 0.6035 (m-80) REVERT: D 228 ASN cc_start: 0.8590 (t0) cc_final: 0.8249 (t0) REVERT: D 277 VAL cc_start: 0.8887 (OUTLIER) cc_final: 0.8660 (m) REVERT: D 355 VAL cc_start: 0.8700 (p) cc_final: 0.8448 (t) REVERT: D 483 SER cc_start: 0.8628 (m) cc_final: 0.8412 (p) REVERT: D 524 ILE cc_start: 0.9134 (mm) cc_final: 0.8840 (mm) REVERT: D 539 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7410 (tm-30) REVERT: D 597 ASP cc_start: 0.8548 (t0) cc_final: 0.8155 (t0) REVERT: B 391 ASP cc_start: 0.8346 (m-30) cc_final: 0.7988 (t0) REVERT: B 404 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8299 (tt) REVERT: B 428 MET cc_start: 0.8291 (mtm) cc_final: 0.8001 (mtm) REVERT: B 443 VAL cc_start: 0.8331 (m) cc_final: 0.8089 (t) REVERT: B 486 SER cc_start: 0.8393 (m) cc_final: 0.8020 (p) REVERT: B 505 PHE cc_start: 0.2669 (m-80) cc_final: 0.2430 (m-80) REVERT: B 524 ILE cc_start: 0.5250 (mp) cc_final: 0.4353 (tt) REVERT: B 538 MET cc_start: 0.7586 (mmt) cc_final: 0.7223 (tpt) REVERT: B 568 THR cc_start: 0.3886 (p) cc_final: 0.3645 (p) outliers start: 71 outliers final: 54 residues processed: 350 average time/residue: 0.3077 time to fit residues: 161.9482 Evaluate side-chains 348 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 287 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 492 ASP Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 421 ASP Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 539 GLU Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 491 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 0.6980 chunk 127 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 219 optimal weight: 7.9990 chunk 201 optimal weight: 0.0060 chunk 174 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 107 optimal weight: 0.0570 chunk 138 optimal weight: 0.6980 overall best weight: 0.4114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.5849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 18398 Z= 0.179 Angle : 0.548 11.370 24935 Z= 0.283 Chirality : 0.040 0.300 2669 Planarity : 0.004 0.052 3222 Dihedral : 4.960 56.707 2467 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.16 % Allowed : 22.05 % Favored : 74.79 % 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 (0.18), residues: 2212 helix: 1.90 (0.15), residues: 1150 sheet: -1.73 (0.29), residues: 309 loop : -0.40 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 134 HIS 0.010 0.001 HIS A 240 PHE 0.033 0.002 PHE B 534 TYR 0.033 0.001 TYR B 313 ARG 0.010 0.000 ARG C 211 ********************** 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 360 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 300 time to evaluate : 1.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.5548 (mmt) cc_final: 0.5160 (mmt) REVERT: A 135 ASP cc_start: 0.8406 (m-30) cc_final: 0.8153 (m-30) REVERT: A 143 TRP cc_start: 0.7142 (p-90) cc_final: 0.6926 (p-90) REVERT: A 231 LYS cc_start: 0.8522 (pttt) cc_final: 0.7321 (tttm) REVERT: A 237 GLN cc_start: 0.7764 (mt0) cc_final: 0.7542 (tt0) REVERT: A 425 PHE cc_start: 0.6890 (OUTLIER) cc_final: 0.6603 (t80) REVERT: A 449 LEU cc_start: 0.9272 (mm) cc_final: 0.9028 (mt) REVERT: A 480 GLU cc_start: 0.8427 (tt0) cc_final: 0.8001 (tp30) REVERT: A 599 LYS cc_start: 0.8826 (ttmt) cc_final: 0.8509 (mmmt) REVERT: C 60 ASP cc_start: 0.7717 (t0) cc_final: 0.7067 (t0) REVERT: C 81 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8293 (tt0) REVERT: C 94 MET cc_start: 0.7862 (mmm) cc_final: 0.7521 (mtp) REVERT: C 127 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6487 (tp30) REVERT: C 153 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7752 (mm) REVERT: C 245 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.7839 (tp30) REVERT: C 403 LYS cc_start: 0.8058 (mmmt) cc_final: 0.7648 (mttt) REVERT: C 450 ASP cc_start: 0.8044 (t0) cc_final: 0.7740 (t0) REVERT: C 484 SER cc_start: 0.7894 (p) cc_final: 0.7626 (t) REVERT: C 597 ASP cc_start: 0.8231 (t0) cc_final: 0.7910 (m-30) REVERT: D 195 ARG cc_start: 0.9081 (tpp80) cc_final: 0.8701 (tpp80) REVERT: D 228 ASN cc_start: 0.8557 (t0) cc_final: 0.8237 (t0) REVERT: D 277 VAL cc_start: 0.8772 (OUTLIER) cc_final: 0.8563 (m) REVERT: D 355 VAL cc_start: 0.8655 (p) cc_final: 0.8389 (t) REVERT: D 483 SER cc_start: 0.8578 (m) cc_final: 0.8371 (p) REVERT: D 524 ILE cc_start: 0.9117 (mm) cc_final: 0.8846 (mm) REVERT: D 539 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7395 (mt-10) REVERT: D 597 ASP cc_start: 0.8480 (t0) cc_final: 0.8108 (t0) REVERT: H 332 TYR cc_start: 0.7992 (p90) cc_final: 0.7705 (p90) REVERT: B 391 ASP cc_start: 0.8346 (m-30) cc_final: 0.7995 (t0) REVERT: B 428 MET cc_start: 0.8284 (mtm) cc_final: 0.7992 (mtm) REVERT: B 443 VAL cc_start: 0.8337 (m) cc_final: 0.8075 (t) REVERT: B 486 SER cc_start: 0.8401 (m) cc_final: 0.8040 (p) REVERT: B 505 PHE cc_start: 0.2741 (m-80) cc_final: 0.2374 (m-80) REVERT: B 524 ILE cc_start: 0.5116 (mp) cc_final: 0.4169 (tt) REVERT: B 538 MET cc_start: 0.7569 (mmt) cc_final: 0.7307 (tpt) REVERT: B 542 ILE cc_start: -0.0879 (tp) cc_final: -0.1331 (tt) REVERT: B 568 THR cc_start: 0.3981 (p) cc_final: 0.3725 (p) outliers start: 60 outliers final: 50 residues processed: 339 average time/residue: 0.3008 time to fit residues: 152.8545 Evaluate side-chains 343 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 287 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 492 ASP Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 421 ASP Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 539 GLU Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 491 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 160 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 174 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 179 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 GLN ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.204212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.169134 restraints weight = 22966.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.171688 restraints weight = 17788.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.173778 restraints weight = 13523.673| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.5961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18398 Z= 0.201 Angle : 0.553 12.792 24935 Z= 0.284 Chirality : 0.041 0.336 2669 Planarity : 0.004 0.056 3222 Dihedral : 4.932 57.100 2467 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.42 % Allowed : 22.26 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.18), residues: 2212 helix: 1.91 (0.15), residues: 1150 sheet: -1.77 (0.29), residues: 309 loop : -0.37 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 134 HIS 0.010 0.001 HIS A 240 PHE 0.031 0.002 PHE B 534 TYR 0.033 0.001 TYR B 313 ARG 0.010 0.001 ARG C 211 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4135.31 seconds wall clock time: 75 minutes 28.52 seconds (4528.52 seconds total)