Starting phenix.real_space_refine on Fri Mar 22 03:17:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pp6_20420/03_2024/6pp6_20420_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pp6_20420/03_2024/6pp6_20420.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pp6_20420/03_2024/6pp6_20420.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pp6_20420/03_2024/6pp6_20420.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pp6_20420/03_2024/6pp6_20420_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pp6_20420/03_2024/6pp6_20420_trim_updated.pdb" } resolution = 4.28 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= 1.000 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: 6 Type Number sf(0) Gaussians P 17 5.49 5 S 35 5.16 5 C 10050 2.51 5 N 2691 2.21 5 O 3187 1.98 5 H 16126 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 187": "OD1" <-> "OD2" Residue "B ASP 194": "OD1" <-> "OD2" Residue "B ASP 201": "OD1" <-> "OD2" Residue "B ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 352": "OD1" <-> "OD2" Residue "B ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C ASP 194": "OD1" <-> "OD2" Residue "C ASP 201": "OD1" <-> "OD2" Residue "C PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 352": "OD1" <-> "OD2" Residue "C ASP 356": "OD1" <-> "OD2" Residue "C ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 109": "OE1" <-> "OE2" Residue "D ASP 157": "OD1" <-> "OD2" Residue "D ASP 194": "OD1" <-> "OD2" Residue "D ARG 200": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 392": "OD1" <-> "OD2" Residue "E TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 103": "OD1" <-> "OD2" Residue "E ASP 137": "OD1" <-> "OD2" Residue "E ASP 170": "OD1" <-> "OD2" Residue "E TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 184": "OD1" <-> "OD2" Residue "E ARG 200": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 201": "OD1" <-> "OD2" Residue "E ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 279": "OD1" <-> "OD2" Residue "E ASP 347": "OD1" <-> "OD2" Residue "E PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 382": "OD1" <-> "OD2" Residue "F TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 279": "OD1" <-> "OD2" Residue "F ASP 294": "OD1" <-> "OD2" Residue "F PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 352": "OD1" <-> "OD2" Residue "F ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 392": "OD1" <-> "OD2" Residue "F TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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: 32106 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 5330 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 13, 'TRANS': 330} Chain breaks: 2 Chain: "B" Number of atoms: 5353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 5353 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 13, 'TRANS': 332} Chain breaks: 1 Chain: "C" Number of atoms: 5353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 5353 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 13, 'TRANS': 332} Chain breaks: 1 Chain: "D" Number of atoms: 5380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 5380 Classifications: {'peptide': 349} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 335} Chain breaks: 1 Chain: "E" Number of atoms: 5336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 5336 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 13, 'TRANS': 331} Chain breaks: 1 Chain: "F" Number of atoms: 5125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 5125 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 12, 'TRANS': 318} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 47 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.71, per 1000 atoms: 0.46 Number of scatterers: 32106 At special positions: 0 Unit cell: (147.32, 140.36, 104.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 35 16.00 P 17 15.00 O 3187 8.00 N 2691 7.00 C 10050 6.00 H 16126 1.00 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: 26.39 Conformation dependent library (CDL) restraints added in 3.8 seconds 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3796 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 99 helices and 15 sheets defined 44.7% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.61 Creating SS restraints... Processing helix chain 'A' and resid 67 through 77 removed outlier: 3.813A pdb=" N TYR A 77 " --> pdb=" O HIS A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 100 removed outlier: 3.585A pdb=" N LYS A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 135 removed outlier: 3.549A pdb=" N ALA A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 169 removed outlier: 3.671A pdb=" N LYS A 164 " --> pdb=" O ILE A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 176 No H-bonds generated for 'chain 'A' and resid 173 through 176' Processing helix chain 'A' and resid 186 through 189 Processing helix chain 'A' and resid 205 through 216 Processing helix chain 'A' and resid 224 through 226 No H-bonds generated for 'chain 'A' and resid 224 through 226' Processing helix chain 'A' and resid 254 through 261 Processing helix chain 'A' and resid 285 through 288 No H-bonds generated for 'chain 'A' and resid 285 through 288' Processing helix chain 'A' and resid 292 through 298 removed outlier: 3.711A pdb=" N LYS A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 Processing helix chain 'A' and resid 319 through 327 Processing helix chain 'A' and resid 333 through 344 Processing helix chain 'A' and resid 352 through 365 Processing helix chain 'A' and resid 369 through 379 removed outlier: 4.173A pdb=" N ARG A 373 " --> pdb=" O ARG A 370 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A 377 " --> pdb=" O SER A 374 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A 378 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 379 " --> pdb=" O VAL A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 387 Processing helix chain 'A' and resid 400 through 404 removed outlier: 3.719A pdb=" N ASP A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 400 through 404' Processing helix chain 'B' and resid 67 through 76 removed outlier: 3.810A pdb=" N ASP B 76 " --> pdb=" O ASN B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 98 removed outlier: 3.886A pdb=" N VAL B 87 " --> pdb=" O GLN B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 135 removed outlier: 3.570A pdb=" N ALA B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 169 removed outlier: 3.529A pdb=" N LYS B 164 " --> pdb=" O ILE B 161 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS B 168 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 176 No H-bonds generated for 'chain 'B' and resid 173 through 176' Processing helix chain 'B' and resid 187 through 189 No H-bonds generated for 'chain 'B' and resid 187 through 189' Processing helix chain 'B' and resid 207 through 216 removed outlier: 3.572A pdb=" N LEU B 212 " --> pdb=" O GLN B 208 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 262 Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'B' and resid 292 through 298 removed outlier: 3.655A pdb=" N ILE B 296 " --> pdb=" O PRO B 292 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS B 297 " --> pdb=" O GLU B 293 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 292 through 298' Processing helix chain 'B' and resid 302 through 306 Processing helix chain 'B' and resid 319 through 327 removed outlier: 3.612A pdb=" N LYS B 327 " --> pdb=" O ILE B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 344 removed outlier: 3.903A pdb=" N GLU B 344 " --> pdb=" O LEU B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 365 removed outlier: 3.727A pdb=" N ALA B 357 " --> pdb=" O GLU B 353 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 364 " --> pdb=" O LYS B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 379 removed outlier: 3.502A pdb=" N ALA B 378 " --> pdb=" O ILE B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 387 Processing helix chain 'B' and resid 400 through 404 removed outlier: 3.675A pdb=" N ASP B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 400 through 404' Processing helix chain 'C' and resid 67 through 76 removed outlier: 3.685A pdb=" N ASP C 76 " --> pdb=" O ASN C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 100 removed outlier: 3.502A pdb=" N LYS C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 87 " --> pdb=" O GLN C 83 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR C 96 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS C 97 " --> pdb=" O TYR C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 135 removed outlier: 3.704A pdb=" N ALA C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU C 135 " --> pdb=" O THR C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 169 Processing helix chain 'C' and resid 173 through 176 No H-bonds generated for 'chain 'C' and resid 173 through 176' Processing helix chain 'C' and resid 186 through 189 Processing helix chain 'C' and resid 205 through 216 removed outlier: 4.477A pdb=" N LYS C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU C 216 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 262 removed outlier: 3.597A pdb=" N ARG C 261 " --> pdb=" O VAL C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 292 through 298 removed outlier: 3.770A pdb=" N LYS C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 307 removed outlier: 3.823A pdb=" N ARG C 307 " --> pdb=" O GLU C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 327 removed outlier: 3.530A pdb=" N ILE C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN C 324 " --> pdb=" O GLU C 320 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 326 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS C 327 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 344 removed outlier: 4.006A pdb=" N GLU C 344 " --> pdb=" O LEU C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 365 removed outlier: 3.834A pdb=" N ALA C 357 " --> pdb=" O GLU C 353 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE C 358 " --> pdb=" O ALA C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 387 removed outlier: 3.504A pdb=" N GLU C 377 " --> pdb=" O SER C 374 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA C 378 " --> pdb=" O ILE C 375 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASP C 382 " --> pdb=" O ALA C 379 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR C 383 " --> pdb=" O LEU C 380 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET C 384 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU C 387 " --> pdb=" O MET C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 404 removed outlier: 3.602A pdb=" N ASP C 404 " --> pdb=" O GLU C 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 400 through 404' Processing helix chain 'D' and resid 67 through 76 Processing helix chain 'D' and resid 82 through 100 removed outlier: 3.983A pdb=" N VAL D 87 " --> pdb=" O GLN D 83 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 88 " --> pdb=" O ALA D 84 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS D 97 " --> pdb=" O TYR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 135 removed outlier: 3.617A pdb=" N ALA D 129 " --> pdb=" O LYS D 125 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU D 135 " --> pdb=" O THR D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 169 Processing helix chain 'D' and resid 173 through 176 No H-bonds generated for 'chain 'D' and resid 173 through 176' Processing helix chain 'D' and resid 186 through 188 No H-bonds generated for 'chain 'D' and resid 186 through 188' Processing helix chain 'D' and resid 206 through 216 removed outlier: 4.490A pdb=" N LYS D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 262 removed outlier: 3.521A pdb=" N HIS D 260 " --> pdb=" O LYS D 256 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG D 261 " --> pdb=" O VAL D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 285 No H-bonds generated for 'chain 'D' and resid 282 through 285' Processing helix chain 'D' and resid 292 through 298 removed outlier: 3.951A pdb=" N LYS D 297 " --> pdb=" O GLU D 293 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE D 298 " --> pdb=" O ASP D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 306 Processing helix chain 'D' and resid 319 through 327 removed outlier: 3.703A pdb=" N ILE D 323 " --> pdb=" O GLU D 319 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 344 removed outlier: 3.623A pdb=" N GLU D 344 " --> pdb=" O LEU D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 365 removed outlier: 3.505A pdb=" N ASP D 356 " --> pdb=" O ASP D 352 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA D 364 " --> pdb=" O LYS D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 387 removed outlier: 3.764A pdb=" N GLU D 377 " --> pdb=" O SER D 374 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA D 378 " --> pdb=" O ILE D 375 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D 381 " --> pdb=" O ALA D 378 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASP D 382 " --> pdb=" O ALA D 379 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR D 385 " --> pdb=" O ASP D 382 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU D 387 " --> pdb=" O MET D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 404 removed outlier: 3.659A pdb=" N ASP D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 400 through 404' Processing helix chain 'E' and resid 67 through 77 removed outlier: 3.637A pdb=" N HIS E 73 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP E 76 " --> pdb=" O ASN E 72 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR E 77 " --> pdb=" O HIS E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 101 Processing helix chain 'E' and resid 125 through 136 removed outlier: 3.551A pdb=" N ALA E 129 " --> pdb=" O LYS E 125 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU E 130 " --> pdb=" O THR E 126 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA E 133 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG E 134 " --> pdb=" O GLU E 130 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU E 135 " --> pdb=" O THR E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 169 removed outlier: 3.581A pdb=" N LYS E 164 " --> pdb=" O ILE E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 176 No H-bonds generated for 'chain 'E' and resid 173 through 176' Processing helix chain 'E' and resid 186 through 188 No H-bonds generated for 'chain 'E' and resid 186 through 188' Processing helix chain 'E' and resid 205 through 216 removed outlier: 4.454A pdb=" N LYS E 213 " --> pdb=" O GLN E 209 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 263 Processing helix chain 'E' and resid 283 through 289 removed outlier: 3.758A pdb=" N LEU E 287 " --> pdb=" O GLU E 283 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA E 288 " --> pdb=" O GLY E 284 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN E 289 " --> pdb=" O GLU E 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 283 through 289' Processing helix chain 'E' and resid 292 through 298 removed outlier: 3.710A pdb=" N LYS E 297 " --> pdb=" O GLU E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 306 Processing helix chain 'E' and resid 321 through 327 Processing helix chain 'E' and resid 333 through 343 Processing helix chain 'E' and resid 352 through 365 Processing helix chain 'E' and resid 369 through 379 removed outlier: 3.982A pdb=" N ARG E 373 " --> pdb=" O ARG E 370 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA E 378 " --> pdb=" O ILE E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 385 No H-bonds generated for 'chain 'E' and resid 383 through 385' Processing helix chain 'E' and resid 400 through 404 Processing helix chain 'F' and resid 67 through 77 removed outlier: 3.792A pdb=" N TYR F 77 " --> pdb=" O HIS F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 101 removed outlier: 3.630A pdb=" N LEU F 99 " --> pdb=" O HIS F 95 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG F 100 " --> pdb=" O TYR F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 136 removed outlier: 3.742A pdb=" N ALA F 129 " --> pdb=" O LYS F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 168 removed outlier: 3.656A pdb=" N ILE F 162 " --> pdb=" O VAL F 158 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU F 165 " --> pdb=" O ILE F 161 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU F 166 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS F 168 " --> pdb=" O LYS F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 215 removed outlier: 4.507A pdb=" N LYS F 213 " --> pdb=" O GLN F 209 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU F 214 " --> pdb=" O ALA F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 226 No H-bonds generated for 'chain 'F' and resid 224 through 226' Processing helix chain 'F' and resid 254 through 261 removed outlier: 3.642A pdb=" N ARG F 261 " --> pdb=" O VAL F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 289 Processing helix chain 'F' and resid 292 through 298 removed outlier: 3.583A pdb=" N ILE F 296 " --> pdb=" O PRO F 292 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS F 297 " --> pdb=" O GLU F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 306 Processing helix chain 'F' and resid 319 through 327 removed outlier: 3.632A pdb=" N ILE F 323 " --> pdb=" O GLU F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 344 Processing helix chain 'F' and resid 352 through 365 removed outlier: 3.530A pdb=" N ALA F 357 " --> pdb=" O GLU F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 387 removed outlier: 3.682A pdb=" N VAL F 376 " --> pdb=" O LEU F 372 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP F 382 " --> pdb=" O ALA F 378 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N THR F 383 " --> pdb=" O ALA F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 404 Processing sheet with id= A, first strand: chain 'A' and resid 311 through 313 removed outlier: 6.899A pdb=" N LEU A 116 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 220 through 222 removed outlier: 3.744A pdb=" N ALA A 220 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL A 238 " --> pdb=" O ALA A 220 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 347 through 350 removed outlier: 3.549A pdb=" N VAL A 397 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 410 " --> pdb=" O VAL A 397 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 140 through 142 removed outlier: 6.955A pdb=" N ILE B 180 " --> pdb=" O THR B 141 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU B 244 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ILE B 183 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE B 246 " --> pdb=" O ILE B 183 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 219 through 223 removed outlier: 4.066A pdb=" N ALA B 220 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL B 238 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 236 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 347 through 350 removed outlier: 3.533A pdb=" N LYS B 395 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 312 through 314 Processing sheet with id= H, first strand: chain 'C' and resid 347 through 350 removed outlier: 3.616A pdb=" N ILE C 398 " --> pdb=" O GLU C 349 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE C 412 " --> pdb=" O GLU C 394 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL C 396 " --> pdb=" O LEU C 410 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU C 410 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 180 through 184 removed outlier: 6.388A pdb=" N LEU D 244 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ILE D 183 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE D 246 " --> pdb=" O ILE D 183 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'D' and resid 347 through 350 removed outlier: 3.518A pdb=" N ILE D 398 " --> pdb=" O GLU D 349 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 312 through 314 removed outlier: 3.503A pdb=" N ILE E 115 " --> pdb=" O PHE E 245 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 219 through 222 removed outlier: 4.036A pdb=" N ALA E 220 " --> pdb=" O VAL E 238 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL E 238 " --> pdb=" O ALA E 220 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 347 through 350 removed outlier: 3.522A pdb=" N GLU E 349 " --> pdb=" O VAL E 396 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 140 through 142 removed outlier: 6.485A pdb=" N ILE F 180 " --> pdb=" O THR F 141 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU F 244 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N ILE F 183 " --> pdb=" O LEU F 244 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE F 246 " --> pdb=" O ILE F 183 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'F' and resid 347 through 350 removed outlier: 3.696A pdb=" N ILE F 398 " --> pdb=" O GLU F 349 " (cutoff:3.500A) 484 hydrogen bonds defined for protein. 1164 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: 11.18 Time building geometry restraints manager: 27.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 16120 1.06 - 1.28: 2857 1.28 - 1.50: 6187 1.50 - 1.73: 7088 1.73 - 1.95: 59 Bond restraints: 32311 Sorted by residual: bond pdb=" C ILE D 301 " pdb=" N PRO D 302 " ideal model delta sigma weight residual 1.334 1.366 -0.032 1.51e-02 4.39e+03 4.47e+00 bond pdb=" N LEU A 64 " pdb=" CA LEU A 64 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.90e-02 2.77e+03 3.92e+00 bond pdb=" N LEU F 64 " pdb=" CA LEU F 64 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.90e-02 2.77e+03 3.70e+00 bond pdb=" C PRO D 223 " pdb=" N PRO D 224 " ideal model delta sigma weight residual 1.335 1.350 -0.015 8.70e-03 1.32e+04 2.95e+00 bond pdb=" N UNK S 1 " pdb=" CA UNK S 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.79e+00 ... (remaining 32306 not shown) Histogram of bond angle deviations from ideal: 100.53 - 107.65: 3063 107.65 - 114.78: 39670 114.78 - 121.90: 10479 121.90 - 129.02: 5472 129.02 - 136.15: 86 Bond angle restraints: 58770 Sorted by residual: angle pdb=" CA GLY F 206 " pdb=" C GLY F 206 " pdb=" N VAL F 207 " ideal model delta sigma weight residual 116.81 111.26 5.55 1.00e+00 1.00e+00 3.08e+01 angle pdb=" C ASN C 101 " pdb=" N GLY C 102 " pdb=" CA GLY C 102 " ideal model delta sigma weight residual 121.41 132.11 -10.70 1.96e+00 2.60e-01 2.98e+01 angle pdb=" N SER C 105 " pdb=" CA SER C 105 " pdb=" C SER C 105 " ideal model delta sigma weight residual 109.59 101.92 7.67 1.61e+00 3.86e-01 2.27e+01 angle pdb=" C GLY F 204 " pdb=" N GLU F 205 " pdb=" CA GLU F 205 " ideal model delta sigma weight residual 121.54 129.14 -7.60 1.91e+00 2.74e-01 1.58e+01 angle pdb=" C GLU F 205 " pdb=" N GLY F 206 " pdb=" CA GLY F 206 " ideal model delta sigma weight residual 119.94 124.18 -4.24 1.11e+00 8.12e-01 1.46e+01 ... (remaining 58765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 13421 17.32 - 34.63: 1152 34.63 - 51.95: 310 51.95 - 69.26: 84 69.26 - 86.58: 11 Dihedral angle restraints: 14978 sinusoidal: 8519 harmonic: 6459 Sorted by residual: dihedral pdb=" CA LYS C 366 " pdb=" CB LYS C 366 " pdb=" CG LYS C 366 " pdb=" CD LYS C 366 " ideal model delta sinusoidal sigma weight residual -60.00 -119.14 59.14 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ASP A 194 " pdb=" CB ASP A 194 " pdb=" CG ASP A 194 " pdb=" OD1 ASP A 194 " ideal model delta sinusoidal sigma weight residual -30.00 -82.13 52.13 1 2.00e+01 2.50e-03 9.27e+00 dihedral pdb=" N ARG E 370 " pdb=" CA ARG E 370 " pdb=" CB ARG E 370 " pdb=" CG ARG E 370 " ideal model delta sinusoidal sigma weight residual -180.00 -129.30 -50.70 3 1.50e+01 4.44e-03 8.93e+00 ... (remaining 14975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1961 0.041 - 0.083: 441 0.083 - 0.124: 164 0.124 - 0.166: 31 0.166 - 0.207: 1 Chirality restraints: 2598 Sorted by residual: chirality pdb=" CA ASP C 103 " pdb=" N ASP C 103 " pdb=" C ASP C 103 " pdb=" CB ASP C 103 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ILE B 301 " pdb=" N ILE B 301 " pdb=" C ILE B 301 " pdb=" CB ILE B 301 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA SER C 105 " pdb=" N SER C 105 " pdb=" C SER C 105 " pdb=" CB SER C 105 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.81e-01 ... (remaining 2595 not shown) Planarity restraints: 4789 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 370 " 0.090 9.50e-02 1.11e+02 9.25e-02 1.73e+02 pdb=" NE ARG B 370 " 0.074 2.00e-02 2.50e+03 pdb=" CZ ARG B 370 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG B 370 " -0.025 2.00e-02 2.50e+03 pdb=" NH2 ARG B 370 " 0.003 2.00e-02 2.50e+03 pdb="HH11 ARG B 370 " -0.016 2.00e-02 2.50e+03 pdb="HH12 ARG B 370 " -0.058 2.00e-02 2.50e+03 pdb="HH21 ARG B 370 " -0.172 2.00e-02 2.50e+03 pdb="HH22 ARG B 370 " 0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN E 195 " -0.043 5.00e-02 4.00e+02 6.43e-02 6.61e+00 pdb=" N PRO E 196 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO E 196 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 196 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 328 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.19e+00 pdb=" N PRO F 329 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO F 329 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 329 " 0.028 5.00e-02 4.00e+02 ... (remaining 4786 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.01: 161 2.01 - 2.65: 45151 2.65 - 3.30: 91772 3.30 - 3.95: 112184 3.95 - 4.60: 176602 Nonbonded interactions: 425870 Sorted by model distance: nonbonded pdb=" OD1 ASP C 399 " pdb=" HG SER C 401 " model vdw 1.357 1.850 nonbonded pdb=" HZ2 LYS C 112 " pdb=" O SER C 241 " model vdw 1.397 1.850 nonbonded pdb=" OD1 ASP E 144 " pdb=" HG1 THR E 146 " model vdw 1.425 1.850 nonbonded pdb=" O GLU F 263 " pdb=" HG1 THR F 264 " model vdw 1.429 1.850 nonbonded pdb=" O LEU C 326 " pdb=" HG1 THR C 334 " model vdw 1.434 1.850 ... (remaining 425865 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 64 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 149 or resid 157 through 194 or resid 202 through 225 or resid 233 thr \ ough 413)) selection = (chain 'B' and (resid 64 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 149 or resid 157 through 194 or resid 202 through 225 or resid 233 thr \ ough 413)) selection = (chain 'C' and (resid 64 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 149 or resid 157 through 194 or resid 202 through 225 or resid 233 thr \ ough 413)) selection = (chain 'D' and (resid 64 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 149 or resid 157 through 194 or resid 202 through 225 or resid 233 thr \ ough 413)) selection = (chain 'E' and (resid 64 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 149 or resid 157 through 194 or resid 202 through 225 or resid 233 thr \ ough 413)) selection = (chain 'F' and (resid 64 through 225 or resid 233 through 259 or (resid 260 and \ (name N or name CA or name C or name O or name CB or name CG or name ND1 or name \ CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or nam \ e HD1 or name HD2 or name HE1)) or resid 261 through 413)) } 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: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.460 Extract box with map and model: 3.260 Check model and map are aligned: 0.550 Set scattering table: 0.320 Process input model: 104.980 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16185 Z= 0.235 Angle : 0.713 10.700 21919 Z= 0.392 Chirality : 0.042 0.207 2598 Planarity : 0.004 0.076 2819 Dihedral : 12.431 81.962 6147 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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: -1.13 (0.17), residues: 2031 helix: -0.21 (0.16), residues: 770 sheet: -0.40 (0.30), residues: 272 loop : -1.23 (0.18), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 95 PHE 0.014 0.001 PHE A 270 TYR 0.010 0.001 TYR E 93 ARG 0.013 0.001 ARG E 261 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 400 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 400 time to evaluate : 2.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 137 ASP cc_start: 0.8301 (p0) cc_final: 0.8074 (t0) REVERT: B 141 THR cc_start: 0.8912 (t) cc_final: 0.8584 (m) REVERT: B 160 ASN cc_start: 0.9086 (t0) cc_final: 0.8836 (t0) REVERT: B 162 ILE cc_start: 0.9360 (mm) cc_final: 0.9043 (mt) REVERT: B 245 PHE cc_start: 0.8262 (m-80) cc_final: 0.7928 (m-80) REVERT: B 289 GLN cc_start: 0.9303 (mt0) cc_final: 0.9027 (mp10) REVERT: C 205 GLU cc_start: 0.8375 (tt0) cc_final: 0.7573 (tm-30) REVERT: D 363 MET cc_start: 0.9302 (mtm) cc_final: 0.9072 (mmm) REVERT: E 341 PHE cc_start: 0.8935 (m-10) cc_final: 0.8735 (m-10) REVERT: E 366 LYS cc_start: 0.9242 (mmtt) cc_final: 0.8881 (tptp) REVERT: E 384 MET cc_start: 0.8725 (mtm) cc_final: 0.7790 (mtp) REVERT: F 225 GLN cc_start: 0.5795 (tt0) cc_final: 0.5234 (tt0) REVERT: F 381 LEU cc_start: 0.9518 (tp) cc_final: 0.9237 (pp) outliers start: 0 outliers final: 0 residues processed: 400 average time/residue: 0.6297 time to fit residues: 370.1640 Evaluate side-chains 243 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 2.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 103 optimal weight: 0.5980 chunk 82 optimal weight: 6.9990 chunk 159 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 118 optimal weight: 0.0010 chunk 184 optimal weight: 8.9990 overall best weight: 1.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 195 ASN A 225 GLN B 68 HIS B 167 GLN B 185 GLN B 208 GLN C 101 ASN D 260 HIS F 114 ASN ** F 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 ASN F 336 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16185 Z= 0.175 Angle : 0.520 5.471 21919 Z= 0.277 Chirality : 0.040 0.166 2598 Planarity : 0.004 0.043 2819 Dihedral : 7.460 60.846 2294 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.06 % Allowed : 1.99 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.17), residues: 2031 helix: 0.49 (0.17), residues: 808 sheet: -0.26 (0.31), residues: 271 loop : -1.03 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 68 PHE 0.017 0.001 PHE E 298 TYR 0.016 0.001 TYR E 93 ARG 0.006 0.000 ARG F 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 282 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 281 time to evaluate : 2.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 137 ASP cc_start: 0.8440 (p0) cc_final: 0.8153 (t0) REVERT: A 191 ARG cc_start: 0.8847 (ttp80) cc_final: 0.8607 (ttp80) REVERT: A 356 ASP cc_start: 0.8900 (p0) cc_final: 0.8657 (p0) REVERT: B 160 ASN cc_start: 0.9182 (t0) cc_final: 0.8036 (t0) REVERT: B 245 PHE cc_start: 0.7827 (m-80) cc_final: 0.7445 (m-80) REVERT: B 289 GLN cc_start: 0.9235 (mt0) cc_final: 0.9008 (mp10) REVERT: C 205 GLU cc_start: 0.8126 (tt0) cc_final: 0.7715 (tm-30) REVERT: C 247 CYS cc_start: 0.9056 (m) cc_final: 0.8668 (m) REVERT: C 384 MET cc_start: 0.9455 (mtm) cc_final: 0.9233 (mtm) REVERT: D 170 ASP cc_start: 0.9035 (t0) cc_final: 0.8714 (t0) REVERT: D 205 GLU cc_start: 0.8806 (pm20) cc_final: 0.8563 (pm20) REVERT: E 245 PHE cc_start: 0.8877 (m-80) cc_final: 0.8553 (m-80) REVERT: E 293 GLU cc_start: 0.9168 (pt0) cc_final: 0.8921 (pm20) REVERT: E 366 LYS cc_start: 0.9334 (mmtt) cc_final: 0.8944 (tptp) REVERT: E 384 MET cc_start: 0.8794 (mtm) cc_final: 0.7872 (mtp) outliers start: 1 outliers final: 1 residues processed: 281 average time/residue: 0.6243 time to fit residues: 261.1134 Evaluate side-chains 218 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 217 time to evaluate : 2.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 102 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 153 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 184 optimal weight: 7.9990 chunk 199 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 chunk 183 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 GLN C 95 HIS C 101 ASN F 237 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16185 Z= 0.257 Angle : 0.558 7.780 21919 Z= 0.286 Chirality : 0.039 0.152 2598 Planarity : 0.003 0.028 2819 Dihedral : 7.349 66.714 2294 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.18), residues: 2031 helix: 0.18 (0.17), residues: 841 sheet: -0.06 (0.31), residues: 269 loop : -1.09 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 73 PHE 0.017 0.001 PHE E 298 TYR 0.013 0.001 TYR D 385 ARG 0.008 0.001 ARG F 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 250 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 2.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8590 (p0) cc_final: 0.8203 (t0) REVERT: A 144 ASP cc_start: 0.8220 (m-30) cc_final: 0.7866 (p0) REVERT: A 283 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7106 (pm20) REVERT: B 142 MET cc_start: 0.7806 (tmm) cc_final: 0.7540 (tmm) REVERT: B 160 ASN cc_start: 0.8886 (t0) cc_final: 0.8638 (t0) REVERT: B 289 GLN cc_start: 0.9249 (mt0) cc_final: 0.9025 (mp10) REVERT: B 323 ILE cc_start: 0.9671 (tp) cc_final: 0.9060 (tp) REVERT: C 205 GLU cc_start: 0.8279 (tt0) cc_final: 0.7818 (tm-30) REVERT: C 247 CYS cc_start: 0.9108 (m) cc_final: 0.8694 (m) REVERT: C 384 MET cc_start: 0.9467 (mtm) cc_final: 0.9231 (mtm) REVERT: D 78 VAL cc_start: 0.7809 (t) cc_final: 0.7472 (m) REVERT: D 170 ASP cc_start: 0.9136 (t0) cc_final: 0.8780 (t0) REVERT: E 157 ASP cc_start: 0.8415 (p0) cc_final: 0.8166 (p0) REVERT: E 245 PHE cc_start: 0.9026 (m-80) cc_final: 0.8811 (m-80) REVERT: E 293 GLU cc_start: 0.9249 (pt0) cc_final: 0.8924 (pm20) REVERT: E 366 LYS cc_start: 0.9415 (mmtt) cc_final: 0.9047 (tptp) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.5822 time to fit residues: 220.6900 Evaluate side-chains 191 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 182 optimal weight: 20.0000 chunk 138 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 chunk 88 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 185 optimal weight: 20.0000 chunk 196 optimal weight: 10.0000 chunk 96 optimal weight: 0.6980 chunk 175 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 338 GLN C 101 ASN D 225 GLN D 260 HIS F 114 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 16185 Z= 0.276 Angle : 0.547 5.351 21919 Z= 0.284 Chirality : 0.040 0.148 2598 Planarity : 0.004 0.055 2819 Dihedral : 7.073 72.155 2294 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.17), residues: 2031 helix: -0.18 (0.17), residues: 850 sheet: -0.13 (0.31), residues: 272 loop : -1.11 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.002 HIS S 3 PHE 0.028 0.001 PHE B 245 TYR 0.020 0.001 TYR A 182 ARG 0.010 0.001 ARG F 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 220 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 2.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 137 ASP cc_start: 0.8619 (p0) cc_final: 0.8299 (t70) REVERT: A 142 MET cc_start: 0.8827 (mmt) cc_final: 0.8515 (mmm) REVERT: A 144 ASP cc_start: 0.8287 (m-30) cc_final: 0.7780 (p0) REVERT: A 148 LEU cc_start: 0.9195 (mt) cc_final: 0.8943 (mt) REVERT: B 142 MET cc_start: 0.7968 (tmm) cc_final: 0.7525 (tmm) REVERT: B 160 ASN cc_start: 0.8906 (t0) cc_final: 0.8658 (t0) REVERT: B 162 ILE cc_start: 0.9320 (mm) cc_final: 0.9065 (mt) REVERT: B 244 LEU cc_start: 0.8913 (tp) cc_final: 0.8584 (tt) REVERT: B 323 ILE cc_start: 0.9660 (tp) cc_final: 0.9078 (tp) REVERT: C 247 CYS cc_start: 0.9209 (m) cc_final: 0.8814 (m) REVERT: C 286 LEU cc_start: 0.9138 (tt) cc_final: 0.8891 (tt) REVERT: D 78 VAL cc_start: 0.8042 (t) cc_final: 0.7735 (m) REVERT: D 170 ASP cc_start: 0.9150 (t0) cc_final: 0.8775 (t0) REVERT: E 157 ASP cc_start: 0.8484 (p0) cc_final: 0.8213 (p0) REVERT: E 293 GLU cc_start: 0.9333 (pt0) cc_final: 0.9035 (pm20) REVERT: E 366 LYS cc_start: 0.9418 (mmtt) cc_final: 0.9108 (tptp) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.5694 time to fit residues: 191.8334 Evaluate side-chains 182 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 2.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 163 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 167 optimal weight: 9.9990 chunk 135 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 176 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 HIS C 331 ASN D 177 GLN D 225 GLN E 94 ASN E 338 GLN F 114 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 16185 Z= 0.353 Angle : 0.619 7.768 21919 Z= 0.318 Chirality : 0.040 0.171 2598 Planarity : 0.004 0.035 2819 Dihedral : 7.166 77.426 2294 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % 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: -1.53 (0.17), residues: 2031 helix: -0.72 (0.16), residues: 874 sheet: -0.39 (0.30), residues: 277 loop : -1.42 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 73 PHE 0.042 0.002 PHE B 245 TYR 0.014 0.002 TYR D 171 ARG 0.007 0.001 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 2.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 ASP cc_start: 0.8233 (m-30) cc_final: 0.8015 (p0) REVERT: A 182 TYR cc_start: 0.8096 (t80) cc_final: 0.7145 (t80) REVERT: B 118 ILE cc_start: 0.9346 (mt) cc_final: 0.9009 (pt) REVERT: B 160 ASN cc_start: 0.8876 (t0) cc_final: 0.8424 (t0) REVERT: B 162 ILE cc_start: 0.9411 (mm) cc_final: 0.9162 (mt) REVERT: B 323 ILE cc_start: 0.9666 (tp) cc_final: 0.9086 (tp) REVERT: C 202 VAL cc_start: 0.8895 (p) cc_final: 0.8409 (p) REVERT: D 78 VAL cc_start: 0.8234 (t) cc_final: 0.8006 (m) REVERT: D 130 GLU cc_start: 0.9227 (tt0) cc_final: 0.8486 (tm-30) REVERT: D 170 ASP cc_start: 0.9212 (t0) cc_final: 0.8865 (t0) REVERT: E 157 ASP cc_start: 0.8544 (p0) cc_final: 0.8289 (p0) REVERT: E 293 GLU cc_start: 0.9372 (pt0) cc_final: 0.9129 (pm20) REVERT: E 366 LYS cc_start: 0.9446 (mmtt) cc_final: 0.9160 (tptp) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.5312 time to fit residues: 174.6130 Evaluate side-chains 174 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 66 optimal weight: 0.8980 chunk 176 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 196 optimal weight: 9.9990 chunk 163 optimal weight: 6.9990 chunk 90 optimal weight: 0.0570 chunk 16 optimal weight: 20.0000 chunk 64 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 overall best weight: 2.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 HIS F 114 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16185 Z= 0.199 Angle : 0.497 5.338 21919 Z= 0.256 Chirality : 0.039 0.142 2598 Planarity : 0.003 0.030 2819 Dihedral : 7.065 78.508 2294 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.06 % Allowed : 0.70 % Favored : 99.24 % 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: -1.13 (0.17), residues: 2031 helix: -0.30 (0.17), residues: 866 sheet: -0.19 (0.30), residues: 275 loop : -1.28 (0.19), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 73 PHE 0.033 0.001 PHE B 245 TYR 0.014 0.001 TYR D 385 ARG 0.006 0.000 ARG E 370 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 211 time to evaluate : 2.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8947 (p0) cc_final: 0.8550 (t70) REVERT: A 144 ASP cc_start: 0.8329 (m-30) cc_final: 0.7965 (p0) REVERT: A 150 GLU cc_start: 0.7558 (tp30) cc_final: 0.7171 (tp30) REVERT: B 118 ILE cc_start: 0.9348 (mt) cc_final: 0.8992 (pt) REVERT: B 160 ASN cc_start: 0.8913 (t0) cc_final: 0.8502 (t0) REVERT: B 162 ILE cc_start: 0.9416 (mm) cc_final: 0.9161 (mt) REVERT: B 323 ILE cc_start: 0.9679 (tp) cc_final: 0.9114 (tp) REVERT: D 78 VAL cc_start: 0.8237 (t) cc_final: 0.7997 (m) REVERT: D 170 ASP cc_start: 0.9256 (t0) cc_final: 0.8966 (t0) REVERT: D 363 MET cc_start: 0.9191 (tpp) cc_final: 0.8929 (tpp) REVERT: E 142 MET cc_start: 0.8359 (tmm) cc_final: 0.7805 (tmm) REVERT: E 293 GLU cc_start: 0.9316 (pt0) cc_final: 0.9104 (pm20) REVERT: E 366 LYS cc_start: 0.9428 (mmtt) cc_final: 0.9132 (tptp) outliers start: 1 outliers final: 1 residues processed: 211 average time/residue: 0.5266 time to fit residues: 174.9098 Evaluate side-chains 177 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 176 time to evaluate : 2.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 189 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 111 optimal weight: 7.9990 chunk 143 optimal weight: 7.9990 chunk 165 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 195 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 HIS F 114 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 16185 Z= 0.172 Angle : 0.480 5.352 21919 Z= 0.245 Chirality : 0.039 0.140 2598 Planarity : 0.003 0.026 2819 Dihedral : 6.964 86.737 2294 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % 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: 2031 helix: -0.03 (0.17), residues: 859 sheet: -0.16 (0.30), residues: 272 loop : -1.17 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 73 PHE 0.028 0.001 PHE E 245 TYR 0.012 0.001 TYR D 385 ARG 0.004 0.000 ARG D 307 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 2.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 137 ASP cc_start: 0.8945 (p0) cc_final: 0.8531 (t70) REVERT: A 142 MET cc_start: 0.8870 (mmt) cc_final: 0.8486 (mmm) REVERT: A 144 ASP cc_start: 0.8361 (m-30) cc_final: 0.7975 (p0) REVERT: A 150 GLU cc_start: 0.7506 (tp30) cc_final: 0.7135 (tp30) REVERT: A 182 TYR cc_start: 0.8000 (t80) cc_final: 0.7121 (t80) REVERT: B 160 ASN cc_start: 0.8914 (t0) cc_final: 0.8495 (t0) REVERT: B 162 ILE cc_start: 0.9442 (mm) cc_final: 0.9193 (mt) REVERT: B 323 ILE cc_start: 0.9677 (tp) cc_final: 0.9116 (tp) REVERT: C 286 LEU cc_start: 0.9157 (tt) cc_final: 0.8859 (tt) REVERT: D 78 VAL cc_start: 0.8360 (t) cc_final: 0.8016 (m) REVERT: D 170 ASP cc_start: 0.9254 (t0) cc_final: 0.8961 (t0) REVERT: D 363 MET cc_start: 0.9162 (tpp) cc_final: 0.8903 (tpp) REVERT: E 142 MET cc_start: 0.8365 (tmm) cc_final: 0.7812 (tmm) REVERT: E 157 ASP cc_start: 0.8469 (p0) cc_final: 0.8246 (p0) REVERT: E 293 GLU cc_start: 0.9326 (pt0) cc_final: 0.9093 (pm20) REVERT: E 366 LYS cc_start: 0.9450 (mmtt) cc_final: 0.9125 (tptp) REVERT: F 94 ASN cc_start: 0.9491 (m-40) cc_final: 0.9232 (m-40) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.5803 time to fit residues: 195.6109 Evaluate side-chains 172 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 78 optimal weight: 0.7980 chunk 116 optimal weight: 0.8980 chunk 58 optimal weight: 0.3980 chunk 38 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 153 optimal weight: 3.9990 chunk 177 optimal weight: 8.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 HIS D 208 GLN F 114 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16185 Z= 0.165 Angle : 0.473 5.337 21919 Z= 0.242 Chirality : 0.039 0.140 2598 Planarity : 0.003 0.029 2819 Dihedral : 6.917 87.443 2294 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.06 % Allowed : 0.47 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.18), residues: 2031 helix: 0.06 (0.17), residues: 861 sheet: -0.10 (0.30), residues: 272 loop : -1.15 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS B 73 PHE 0.026 0.001 PHE B 245 TYR 0.010 0.001 TYR D 385 ARG 0.004 0.000 ARG D 307 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 211 time to evaluate : 2.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 137 ASP cc_start: 0.8927 (p0) cc_final: 0.8516 (t70) REVERT: A 142 MET cc_start: 0.8889 (mmt) cc_final: 0.8589 (mmm) REVERT: A 144 ASP cc_start: 0.8307 (m-30) cc_final: 0.7909 (p0) REVERT: A 150 GLU cc_start: 0.7535 (tp30) cc_final: 0.7168 (tp30) REVERT: B 162 ILE cc_start: 0.9466 (mm) cc_final: 0.9212 (mt) REVERT: B 323 ILE cc_start: 0.9670 (tp) cc_final: 0.9124 (tp) REVERT: C 202 VAL cc_start: 0.8853 (m) cc_final: 0.8606 (p) REVERT: C 286 LEU cc_start: 0.9149 (tt) cc_final: 0.8844 (tt) REVERT: D 78 VAL cc_start: 0.8278 (t) cc_final: 0.8039 (m) REVERT: D 130 GLU cc_start: 0.9213 (tt0) cc_final: 0.8382 (tm-30) REVERT: D 170 ASP cc_start: 0.9240 (t0) cc_final: 0.8932 (t0) REVERT: E 142 MET cc_start: 0.8339 (tmm) cc_final: 0.7808 (tmm) REVERT: E 293 GLU cc_start: 0.9300 (pt0) cc_final: 0.9078 (pm20) REVERT: E 366 LYS cc_start: 0.9447 (mmtt) cc_final: 0.9042 (tptp) REVERT: F 94 ASN cc_start: 0.9515 (m-40) cc_final: 0.9311 (m-40) outliers start: 1 outliers final: 1 residues processed: 211 average time/residue: 0.5345 time to fit residues: 177.8088 Evaluate side-chains 177 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 176 time to evaluate : 2.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 9.9990 chunk 171 optimal weight: 9.9990 chunk 182 optimal weight: 20.0000 chunk 109 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 143 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 164 optimal weight: 1.9990 chunk 172 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 GLN F 114 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 16185 Z= 0.157 Angle : 0.463 5.866 21919 Z= 0.236 Chirality : 0.039 0.142 2598 Planarity : 0.003 0.029 2819 Dihedral : 6.870 89.334 2294 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.18), residues: 2031 helix: 0.15 (0.17), residues: 863 sheet: -0.05 (0.30), residues: 272 loop : -1.10 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS B 73 PHE 0.023 0.001 PHE B 245 TYR 0.010 0.001 TYR D 385 ARG 0.004 0.000 ARG D 307 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 2.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 137 ASP cc_start: 0.8931 (p0) cc_final: 0.8507 (t70) REVERT: A 142 MET cc_start: 0.8888 (mmt) cc_final: 0.8489 (mmm) REVERT: A 144 ASP cc_start: 0.8335 (m-30) cc_final: 0.7926 (p0) REVERT: A 150 GLU cc_start: 0.7532 (tp30) cc_final: 0.7148 (tp30) REVERT: A 182 TYR cc_start: 0.8077 (t80) cc_final: 0.7184 (t80) REVERT: B 118 ILE cc_start: 0.9334 (mt) cc_final: 0.8995 (pt) REVERT: B 323 ILE cc_start: 0.9665 (tp) cc_final: 0.9132 (tp) REVERT: C 202 VAL cc_start: 0.8858 (m) cc_final: 0.8600 (p) REVERT: C 286 LEU cc_start: 0.9132 (tt) cc_final: 0.8821 (tt) REVERT: D 78 VAL cc_start: 0.8269 (t) cc_final: 0.8038 (m) REVERT: D 130 GLU cc_start: 0.9212 (tt0) cc_final: 0.8583 (tm-30) REVERT: D 170 ASP cc_start: 0.9238 (t0) cc_final: 0.8927 (t0) REVERT: E 293 GLU cc_start: 0.9284 (pt0) cc_final: 0.9039 (pm20) REVERT: E 366 LYS cc_start: 0.9447 (mmtt) cc_final: 0.9063 (tptp) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.5324 time to fit residues: 177.1488 Evaluate side-chains 178 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 2.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 192 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 134 optimal weight: 0.2980 chunk 202 optimal weight: 0.9980 chunk 186 optimal weight: 9.9990 chunk 161 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 chunk 124 optimal weight: 0.5980 chunk 98 optimal weight: 0.0970 chunk 127 optimal weight: 4.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 HIS D 208 GLN D 260 HIS F 114 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 16185 Z= 0.117 Angle : 0.449 5.519 21919 Z= 0.226 Chirality : 0.039 0.150 2598 Planarity : 0.002 0.031 2819 Dihedral : 6.655 88.964 2294 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.06 % Allowed : 0.18 % Favored : 99.77 % 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: -0.21 (0.18), residues: 2031 helix: 0.57 (0.18), residues: 851 sheet: 0.15 (0.31), residues: 272 loop : -0.84 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 260 PHE 0.021 0.001 PHE E 245 TYR 0.014 0.001 TYR E 93 ARG 0.004 0.000 ARG D 307 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 222 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 221 time to evaluate : 2.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 137 ASP cc_start: 0.8935 (p0) cc_final: 0.8493 (t70) REVERT: A 142 MET cc_start: 0.8804 (mmt) cc_final: 0.8408 (mmm) REVERT: A 144 ASP cc_start: 0.8382 (m-30) cc_final: 0.8041 (p0) REVERT: A 150 GLU cc_start: 0.7528 (tp30) cc_final: 0.7134 (tp30) REVERT: A 182 TYR cc_start: 0.7930 (t80) cc_final: 0.7042 (t80) REVERT: A 390 MET cc_start: 0.9211 (mmp) cc_final: 0.8973 (mmp) REVERT: B 118 ILE cc_start: 0.9314 (mt) cc_final: 0.8948 (pt) REVERT: B 160 ASN cc_start: 0.8914 (t0) cc_final: 0.8465 (t0) REVERT: B 162 ILE cc_start: 0.9487 (mm) cc_final: 0.9244 (mt) REVERT: B 197 SER cc_start: 0.8702 (m) cc_final: 0.8255 (t) REVERT: B 323 ILE cc_start: 0.9661 (tp) cc_final: 0.9149 (tp) REVERT: C 247 CYS cc_start: 0.9317 (m) cc_final: 0.9025 (m) REVERT: C 286 LEU cc_start: 0.9087 (tt) cc_final: 0.8793 (tt) REVERT: D 130 GLU cc_start: 0.9182 (tt0) cc_final: 0.8411 (tm-30) REVERT: D 170 ASP cc_start: 0.9219 (t0) cc_final: 0.8911 (t0) REVERT: D 384 MET cc_start: 0.9320 (mtt) cc_final: 0.8912 (mtm) REVERT: E 366 LYS cc_start: 0.9427 (mmtt) cc_final: 0.9019 (tptp) REVERT: F 94 ASN cc_start: 0.9485 (m-40) cc_final: 0.9244 (m-40) outliers start: 1 outliers final: 1 residues processed: 221 average time/residue: 0.5165 time to fit residues: 181.2975 Evaluate side-chains 182 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 181 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 23 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 165 optimal weight: 0.8980 chunk 20 optimal weight: 20.0000 chunk 29 optimal weight: 4.9990 chunk 141 optimal weight: 0.0670 overall best weight: 1.6722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 GLN F 114 ASN F 331 ASN F 336 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.083648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.061379 restraints weight = 173019.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.064308 restraints weight = 85106.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.066309 restraints weight = 53587.129| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.5297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16185 Z= 0.144 Angle : 0.455 5.375 21919 Z= 0.231 Chirality : 0.039 0.144 2598 Planarity : 0.003 0.032 2819 Dihedral : 6.620 88.193 2294 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % 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: -0.16 (0.18), residues: 2031 helix: 0.58 (0.17), residues: 856 sheet: 0.19 (0.30), residues: 269 loop : -0.79 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.001 HIS B 73 PHE 0.020 0.001 PHE B 245 TYR 0.010 0.001 TYR E 93 ARG 0.004 0.000 ARG D 307 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6016.13 seconds wall clock time: 107 minutes 10.52 seconds (6430.52 seconds total)