Starting phenix.real_space_refine on Mon Mar 25 02:34:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr3_27669/03_2024/8dr3_27669_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr3_27669/03_2024/8dr3_27669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr3_27669/03_2024/8dr3_27669.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr3_27669/03_2024/8dr3_27669.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr3_27669/03_2024/8dr3_27669_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr3_27669/03_2024/8dr3_27669_trim.pdb" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.048 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: 7 Type Number sf(0) Gaussians P 77 5.49 5 Mg 4 5.21 5 S 103 5.16 5 C 14394 2.51 5 N 3951 2.21 5 O 4600 1.98 5 H 22825 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 294": "OE1" <-> "OE2" Residue "A ASP 381": "OD1" <-> "OD2" Residue "A ASP 397": "OD1" <-> "OD2" Residue "A PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 736": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 31": "OD1" <-> "OD2" Residue "B ASP 39": "OD1" <-> "OD2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B ASP 222": "OD1" <-> "OD2" Residue "B GLU 287": "OE1" <-> "OE2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C GLU 43": "OE1" <-> "OE2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C GLU 194": "OE1" <-> "OE2" Residue "C ASP 276": "OD1" <-> "OD2" Residue "C GLU 279": "OE1" <-> "OE2" Residue "D ASP 86": "OD1" <-> "OD2" Residue "D ASP 178": "OD1" <-> "OD2" Residue "D GLU 258": "OE1" <-> "OE2" Residue "D GLU 306": "OE1" <-> "OE2" Residue "E ASP 172": "OD1" <-> "OD2" Residue "E ASP 195": "OD1" <-> "OD2" Residue "F GLU 7": "OE1" <-> "OE2" Residue "F ASP 93": "OD1" <-> "OD2" Residue "F GLU 104": "OE1" <-> "OE2" Residue "F GLU 113": "OE1" <-> "OE2" Residue "F ASP 150": "OD1" <-> "OD2" Residue "G PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 17": "OD1" <-> "OD2" Residue "H GLU 55": "OE1" <-> "OE2" Residue "H GLU 143": "OE1" <-> "OE2" Residue "H GLU 192": "OE1" <-> "OE2" Residue "H ASP 214": "OD1" <-> "OD2" 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: 45954 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 10168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 10168 Classifications: {'peptide': 643} Link IDs: {'PTRANS': 25, 'TRANS': 617} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 5084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 5084 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 9, 'TRANS': 308} Chain: "C" Number of atoms: 5262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5262 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain: "D" Number of atoms: 5457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 5457 Classifications: {'peptide': 343} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 330} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 5698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5698 Classifications: {'peptide': 354} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 339} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 4055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 4055 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 8, 'TRANS': 249} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 4047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 4047 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 8, 'TRANS': 248} Chain: "H" Number of atoms: 4023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 4023 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "I" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 616 Classifications: {'DNA': 19} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 18} Chain: "J" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 553 Classifications: {'DNA': 18} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 17} Chain: "K" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 426 Classifications: {'DNA': 13} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 12} Chain: "L" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 397 Classifications: {'DNA': 13} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 20.33, per 1000 atoms: 0.44 Number of scatterers: 45954 At special positions: 0 Unit cell: (146.202, 119.77, 144.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 103 16.00 P 77 15.00 Mg 4 11.99 O 4600 8.00 N 3951 7.00 C 14394 6.00 H 22825 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: 37.21 Conformation dependent library (CDL) restraints added in 4.9 seconds 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5236 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 16 sheets defined 55.4% alpha, 15.8% beta 17 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 21.39 Creating SS restraints... Processing helix chain 'A' and resid 105 through 113 Processing helix chain 'A' and resid 173 through 184 removed outlier: 3.653A pdb=" N TYR A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 222 through 232 Processing helix chain 'A' and resid 240 through 281 removed outlier: 3.673A pdb=" N GLU A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 313 through 326 Processing helix chain 'A' and resid 326 through 333 Processing helix chain 'A' and resid 342 through 346 removed outlier: 4.197A pdb=" N VAL A 345 " --> pdb=" O GLY A 342 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE A 346 " --> pdb=" O SER A 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 342 through 346' Processing helix chain 'A' and resid 358 through 370 Processing helix chain 'A' and resid 384 through 391 Processing helix chain 'A' and resid 392 through 396 Processing helix chain 'A' and resid 400 through 406 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.599A pdb=" N MET A 429 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 445 removed outlier: 3.609A pdb=" N ARG A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 467 Proline residue: A 465 - end of helix Processing helix chain 'A' and resid 479 through 494 removed outlier: 3.950A pdb=" N ILE A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER A 485 " --> pdb=" O ASN A 481 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ARG A 486 " --> pdb=" O SER A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 511 Processing helix chain 'A' and resid 513 through 526 removed outlier: 3.665A pdb=" N THR A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 543 Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 561 through 564 Processing helix chain 'A' and resid 565 through 572 removed outlier: 3.795A pdb=" N ARG A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN A 571 " --> pdb=" O ILE A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 removed outlier: 4.207A pdb=" N ASP A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 596 Processing helix chain 'A' and resid 609 through 632 Processing helix chain 'A' and resid 637 through 639 No H-bonds generated for 'chain 'A' and resid 637 through 639' Processing helix chain 'A' and resid 640 through 649 Processing helix chain 'A' and resid 649 through 656 Processing helix chain 'A' and resid 668 through 690 Processing helix chain 'A' and resid 697 through 704 Processing helix chain 'A' and resid 704 through 714 removed outlier: 4.210A pdb=" N THR A 708 " --> pdb=" O ASP A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 721 Processing helix chain 'A' and resid 724 through 735 Processing helix chain 'A' and resid 738 through 747 Processing helix chain 'A' and resid 750 through 754 removed outlier: 3.559A pdb=" N VAL A 754 " --> pdb=" O GLY A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 762 Processing helix chain 'A' and resid 763 through 776 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 19 through 23 Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 85 through 99 removed outlier: 3.941A pdb=" N ILE B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LYS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 134 removed outlier: 3.639A pdb=" N ARG B 128 " --> pdb=" O GLN B 124 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 201 through 217 Processing helix chain 'B' and resid 220 through 228 Processing helix chain 'B' and resid 231 through 241 removed outlier: 3.749A pdb=" N ILE B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 256 removed outlier: 3.555A pdb=" N LEU B 256 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 276 Processing helix chain 'B' and resid 281 through 302 Processing helix chain 'B' and resid 305 through 321 removed outlier: 3.527A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 13 Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 27 removed outlier: 3.610A pdb=" N VAL C 27 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 58 through 72 Processing helix chain 'C' and resid 75 through 77 No H-bonds generated for 'chain 'C' and resid 75 through 77' Processing helix chain 'C' and resid 89 through 103 removed outlier: 3.932A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 123 through 137 removed outlier: 3.605A pdb=" N ARG C 131 " --> pdb=" O GLN C 127 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.603A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 160 removed outlier: 3.613A pdb=" N ARG C 160 " --> pdb=" O ALA C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.695A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 240 through 254 Processing helix chain 'C' and resid 255 through 271 removed outlier: 4.080A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 287 removed outlier: 4.031A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 312 removed outlier: 3.978A pdb=" N ARG C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS C 312 " --> pdb=" O TYR C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 332 Processing helix chain 'C' and resid 333 through 335 No H-bonds generated for 'chain 'C' and resid 333 through 335' Processing helix chain 'D' and resid 17 through 24 removed outlier: 3.657A pdb=" N GLN D 24 " --> pdb=" O GLN D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 35 through 39 Processing helix chain 'D' and resid 42 through 56 removed outlier: 4.452A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR D 52 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 84 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.879A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 141 through 145 Processing helix chain 'D' and resid 146 through 152 Processing helix chain 'D' and resid 153 through 160 removed outlier: 3.576A pdb=" N GLU D 158 " --> pdb=" O ARG D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 177 through 184 Processing helix chain 'D' and resid 193 through 209 removed outlier: 3.759A pdb=" N ILE D 198 " --> pdb=" O ALA D 194 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ASP D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ARG D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 225 Processing helix chain 'D' and resid 227 through 246 Processing helix chain 'D' and resid 252 through 261 Processing helix chain 'D' and resid 264 through 278 Processing helix chain 'D' and resid 279 through 292 removed outlier: 3.844A pdb=" N LYS D 292 " --> pdb=" O ASN D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 310 Processing helix chain 'D' and resid 315 through 334 removed outlier: 3.544A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 12 through 16 Processing helix chain 'E' and resid 19 through 32 removed outlier: 4.319A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 36 Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 62 through 67 Processing helix chain 'E' and resid 97 through 103 removed outlier: 7.024A pdb=" N ASN E 103 " --> pdb=" O ASP E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 111 removed outlier: 3.795A pdb=" N VAL E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 118 Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 147 through 161 removed outlier: 4.260A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 184 Processing helix chain 'E' and resid 194 through 210 Processing helix chain 'E' and resid 216 through 227 Processing helix chain 'E' and resid 229 through 244 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 292 removed outlier: 3.716A pdb=" N HIS E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 308 Processing helix chain 'E' and resid 314 through 335 Processing helix chain 'E' and resid 337 through 354 removed outlier: 3.982A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 20 removed outlier: 4.489A pdb=" N PHE F 12 " --> pdb=" O GLU F 8 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 57 No H-bonds generated for 'chain 'F' and resid 55 through 57' Processing helix chain 'F' and resid 72 through 80 Processing helix chain 'F' and resid 141 through 155 removed outlier: 3.809A pdb=" N GLN F 153 " --> pdb=" O ARG F 149 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU F 154 " --> pdb=" O ASP F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 194 Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 217 through 221 removed outlier: 4.190A pdb=" N SER F 220 " --> pdb=" O LYS F 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 19 removed outlier: 3.879A pdb=" N PHE G 19 " --> pdb=" O ILE G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 57 No H-bonds generated for 'chain 'G' and resid 55 through 57' Processing helix chain 'G' and resid 72 through 80 Processing helix chain 'G' and resid 141 through 153 removed outlier: 3.614A pdb=" N GLN G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 194 Processing helix chain 'G' and resid 209 through 216 Processing helix chain 'G' and resid 217 through 221 removed outlier: 4.390A pdb=" N SER G 220 " --> pdb=" O LYS G 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 19 removed outlier: 4.341A pdb=" N PHE H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE H 19 " --> pdb=" O ILE H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 57 No H-bonds generated for 'chain 'H' and resid 55 through 57' Processing helix chain 'H' and resid 72 through 80 Processing helix chain 'H' and resid 141 through 155 removed outlier: 3.768A pdb=" N GLN H 153 " --> pdb=" O ARG H 149 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU H 154 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 216 Processing helix chain 'H' and resid 217 through 221 removed outlier: 4.025A pdb=" N SER H 220 " --> pdb=" O LYS H 217 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 163 through 166 removed outlier: 6.926A pdb=" N VAL A 164 " --> pdb=" O VAL A 200 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 373 through 377 removed outlier: 8.214A pdb=" N ILE A 452 " --> pdb=" O PHE A 419 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE A 421 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ILE A 454 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N MET A 423 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA A 349 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N CYS A 455 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU A 351 " --> pdb=" O CYS A 455 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 497 through 498 removed outlier: 6.549A pdb=" N LYS A 497 " --> pdb=" O ILE A 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 599 through 601 Processing sheet with id=AA5, first strand: chain 'B' and resid 75 through 78 removed outlier: 6.292A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N MET B 45 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N CYS B 144 " --> pdb=" O MET B 45 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE B 47 " --> pdb=" O CYS B 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.473A pdb=" N LEU C 49 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N ALA C 147 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE C 51 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.550A pdb=" N MET D 61 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N CYS D 170 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE D 63 " --> pdb=" O CYS D 170 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU D 62 " --> pdb=" O PHE D 187 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 69 through 76 removed outlier: 6.662A pdb=" N LEU E 94 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU E 40 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 212 through 213 removed outlier: 6.406A pdb=" N GLN E 212 " --> pdb=" O LEU E 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 59 through 62 removed outlier: 4.083A pdb=" N GLU F 59 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE F 111 " --> pdb=" O ILE H 181 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ASP H 172 " --> pdb=" O SER H 157 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N SER H 157 " --> pdb=" O ASP H 172 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 66 through 71 removed outlier: 6.508A pdb=" N LEU F 25 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL F 40 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASN F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLN F 38 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N SER F 230 " --> pdb=" O PRO F 234 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ASP F 240 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ARG F 224 " --> pdb=" O ASP F 240 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 203 through 208 removed outlier: 6.009A pdb=" N SER F 157 " --> pdb=" O ASP F 172 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ASP F 172 " --> pdb=" O SER F 157 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE G 111 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU G 59 " --> pdb=" O LYS G 5 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 66 through 71 removed outlier: 6.594A pdb=" N LEU G 25 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL G 40 " --> pdb=" O LEU G 25 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASN G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN G 38 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ASP G 240 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ARG G 224 " --> pdb=" O ASP G 240 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 203 through 208 removed outlier: 5.680A pdb=" N SER G 157 " --> pdb=" O ASP G 172 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASP G 172 " --> pdb=" O SER G 157 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE G 181 " --> pdb=" O ILE H 111 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ILE H 111 " --> pdb=" O ILE G 181 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 203 through 208 removed outlier: 5.680A pdb=" N SER G 157 " --> pdb=" O ASP G 172 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASP G 172 " --> pdb=" O SER G 157 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE G 181 " --> pdb=" O ILE H 111 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ILE H 111 " --> pdb=" O ILE G 181 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 66 through 71 removed outlier: 8.050A pdb=" N LEU H 25 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL H 40 " --> pdb=" O LEU H 25 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ASN H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLN H 38 " --> pdb=" O ASN H 27 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE H 36 " --> pdb=" O GLN H 29 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ASP H 240 " --> pdb=" O ARG H 224 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ARG H 224 " --> pdb=" O ASP H 240 " (cutoff:3.500A) 1243 hydrogen bonds defined for protein. 3501 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 19.78 Time building geometry restraints manager: 38.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 22785 1.05 - 1.27: 3832 1.27 - 1.49: 9294 1.49 - 1.70: 10361 1.70 - 1.92: 162 Bond restraints: 46434 Sorted by residual: bond pdb=" C2' AGS A1001 " pdb=" C3' AGS A1001 " ideal model delta sigma weight residual 1.530 1.239 0.291 1.30e-02 5.92e+03 5.01e+02 bond pdb=" C2' AGS B 402 " pdb=" C3' AGS B 402 " ideal model delta sigma weight residual 1.530 1.239 0.291 1.30e-02 5.92e+03 5.00e+02 bond pdb=" C2' AGS D 402 " pdb=" C3' AGS D 402 " ideal model delta sigma weight residual 1.530 1.241 0.289 1.30e-02 5.92e+03 4.95e+02 bond pdb=" C2' AGS C 402 " pdb=" C3' AGS C 402 " ideal model delta sigma weight residual 1.530 1.241 0.289 1.30e-02 5.92e+03 4.95e+02 bond pdb=" C6 AGS A1001 " pdb=" N6 AGS A1001 " ideal model delta sigma weight residual 1.335 1.469 -0.134 1.00e-02 1.00e+04 1.78e+02 ... (remaining 46429 not shown) Histogram of bond angle deviations from ideal: 99.39 - 106.31: 810 106.31 - 113.23: 56042 113.23 - 120.14: 13938 120.14 - 127.06: 13196 127.06 - 133.98: 298 Bond angle restraints: 84284 Sorted by residual: angle pdb=" N1 AGS D 402 " pdb=" C2 AGS D 402 " pdb=" N3 AGS D 402 " ideal model delta sigma weight residual 128.80 120.08 8.72 8.41e-01 1.41e+00 1.08e+02 angle pdb=" N1 AGS B 402 " pdb=" C2 AGS B 402 " pdb=" N3 AGS B 402 " ideal model delta sigma weight residual 128.80 120.08 8.72 8.41e-01 1.41e+00 1.07e+02 angle pdb=" N1 AGS A1001 " pdb=" C2 AGS A1001 " pdb=" N3 AGS A1001 " ideal model delta sigma weight residual 128.80 120.12 8.68 8.41e-01 1.41e+00 1.07e+02 angle pdb=" N1 AGS C 402 " pdb=" C2 AGS C 402 " pdb=" N3 AGS C 402 " ideal model delta sigma weight residual 128.80 120.17 8.63 8.41e-01 1.41e+00 1.05e+02 angle pdb=" C5 AGS D 402 " pdb=" N7 AGS D 402 " pdb=" C8 AGS D 402 " ideal model delta sigma weight residual 103.67 108.01 -4.34 4.26e-01 5.51e+00 1.04e+02 ... (remaining 84279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.32: 20365 35.32 - 70.64: 906 70.64 - 105.95: 42 105.95 - 141.27: 3 141.27 - 176.59: 4 Dihedral angle restraints: 21320 sinusoidal: 12237 harmonic: 9083 Sorted by residual: dihedral pdb=" O2B GDP E 401 " pdb=" O3A GDP E 401 " pdb=" PB GDP E 401 " pdb=" PA GDP E 401 " ideal model delta sinusoidal sigma weight residual 180.00 12.70 167.30 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C5' GDP E 401 " pdb=" O5' GDP E 401 " pdb=" PA GDP E 401 " pdb=" O3A GDP E 401 " ideal model delta sinusoidal sigma weight residual 179.98 -72.13 -107.89 1 2.00e+01 2.50e-03 3.14e+01 dihedral pdb=" CA GLU G 7 " pdb=" C GLU G 7 " pdb=" N GLU G 8 " pdb=" CA GLU G 8 " ideal model delta harmonic sigma weight residual 180.00 157.02 22.98 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 21317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3290 0.060 - 0.120: 417 0.120 - 0.181: 35 0.181 - 0.241: 4 0.241 - 0.301: 4 Chirality restraints: 3750 Sorted by residual: chirality pdb=" C2' AGS C 402 " pdb=" C1' AGS C 402 " pdb=" C3' AGS C 402 " pdb=" O2' AGS C 402 " both_signs ideal model delta sigma weight residual False -2.67 -2.37 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C2' AGS D 402 " pdb=" C1' AGS D 402 " pdb=" C3' AGS D 402 " pdb=" O2' AGS D 402 " both_signs ideal model delta sigma weight residual False -2.67 -2.38 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C2' AGS B 402 " pdb=" C1' AGS B 402 " pdb=" C3' AGS B 402 " pdb=" O2' AGS B 402 " both_signs ideal model delta sigma weight residual False -2.67 -2.38 -0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 3747 not shown) Planarity restraints: 6573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 14 " -0.150 9.50e-02 1.11e+02 5.03e-02 2.94e+00 pdb=" NE ARG G 14 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG G 14 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG G 14 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG G 14 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG G 14 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG G 14 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG G 14 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG G 14 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 663 " -0.145 9.50e-02 1.11e+02 4.84e-02 2.74e+00 pdb=" NE ARG A 663 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 663 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 663 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 663 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 663 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG A 663 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 663 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A 663 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 149 " -0.132 9.50e-02 1.11e+02 4.41e-02 2.31e+00 pdb=" NE ARG G 149 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG G 149 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG G 149 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG G 149 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG G 149 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG G 149 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG G 149 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG G 149 " 0.000 2.00e-02 2.50e+03 ... (remaining 6570 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 1277 2.14 - 2.76: 85785 2.76 - 3.37: 130793 3.37 - 3.99: 171891 3.99 - 4.60: 265359 Nonbonded interactions: 655105 Sorted by model distance: nonbonded pdb=" OE1 GLU H 55 " pdb=" H GLU H 55 " model vdw 1.530 1.850 nonbonded pdb=" OD1 ASN B 79 " pdb=" HG SER B 81 " model vdw 1.604 1.850 nonbonded pdb=" O SER F 0 " pdb="HH12 ARG F 61 " model vdw 1.605 1.850 nonbonded pdb=" O HIS A 644 " pdb=" HG SER A 648 " model vdw 1.616 1.850 nonbonded pdb=" OD1 ASN D 96 " pdb=" HG SER D 98 " model vdw 1.624 1.850 ... (remaining 655100 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 'F' and resid 0 through 254) selection = (chain 'G' and ((resid 0 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 1 through 254)) selection = (chain 'H' and ((resid 0 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 1 through 254)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.770 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: 0.610 Extract box with map and model: 14.000 Check model and map are aligned: 0.650 Set scattering table: 0.380 Process input model: 161.440 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.120 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:11.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 192.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 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 : 0.007 0.291 23609 Z= 0.345 Angle : 0.539 8.896 32176 Z= 0.374 Chirality : 0.040 0.301 3750 Planarity : 0.003 0.066 3867 Dihedral : 18.830 176.591 9071 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.15 % Allowed : 20.29 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.17), residues: 2736 helix: 2.53 (0.15), residues: 1314 sheet: 1.01 (0.22), residues: 534 loop : 0.69 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 742 HIS 0.012 0.001 HIS B 232 PHE 0.019 0.001 PHE G 245 TYR 0.009 0.001 TYR D 64 ARG 0.007 0.000 ARG G 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 281 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 362 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 334 time to evaluate : 3.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 16 residues processed: 358 average time/residue: 3.5175 time to fit residues: 1415.0910 Evaluate side-chains 222 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 206 time to evaluate : 3.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 185 PHE Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain H residue 185 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 3.9990 chunk 209 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 111 optimal weight: 0.5980 chunk 216 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 131 optimal weight: 0.7980 chunk 161 optimal weight: 1.9990 chunk 250 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 ASN A 398 ASN A 442 GLN A 537 ASN B 232 HIS B 244 ASN C 171 GLN C 192 ASN C 202 ASN C 333 ASN E 224 GLN H 84 ASN H 153 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23609 Z= 0.171 Angle : 0.502 6.628 32176 Z= 0.268 Chirality : 0.039 0.155 3750 Planarity : 0.004 0.056 3867 Dihedral : 15.359 177.380 3687 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.69 % Allowed : 21.19 % Favored : 77.12 % 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: 2.33 (0.17), residues: 2736 helix: 2.43 (0.15), residues: 1316 sheet: 1.00 (0.22), residues: 535 loop : 0.63 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.009 0.001 HIS B 232 PHE 0.011 0.001 PHE E 328 TYR 0.011 0.001 TYR A 735 ARG 0.010 0.000 ARG A 468 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 281 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 252 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 211 time to evaluate : 3.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 24 residues processed: 245 average time/residue: 3.3496 time to fit residues: 928.2635 Evaluate side-chains 218 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 194 time to evaluate : 3.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 185 PHE Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain H residue 201 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 139 optimal weight: 0.0470 chunk 77 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 251 optimal weight: 8.9990 chunk 271 optimal weight: 4.9990 chunk 223 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN A 575 ASN B 244 ASN H 153 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 23609 Z= 0.363 Angle : 0.561 7.861 32176 Z= 0.302 Chirality : 0.043 0.166 3750 Planarity : 0.004 0.069 3867 Dihedral : 15.333 172.883 3681 Min Nonbonded Distance : 1.614 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.55 % Allowed : 19.09 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.16), residues: 2736 helix: 2.00 (0.14), residues: 1313 sheet: 0.92 (0.21), residues: 539 loop : 0.39 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 669 HIS 0.008 0.001 HIS E 18 PHE 0.018 0.001 PHE E 328 TYR 0.015 0.002 TYR A 688 ARG 0.010 0.001 ARG A 468 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 281 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 269 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 207 time to evaluate : 3.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.8032 (mm) REVERT: B 77 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.7052 (tt0) REVERT: F 94 ASN cc_start: 0.7654 (OUTLIER) cc_final: 0.7447 (m-40) outliers start: 62 outliers final: 30 residues processed: 256 average time/residue: 3.4275 time to fit residues: 993.0349 Evaluate side-chains 227 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 194 time to evaluate : 3.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 333 SER Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain F residue 143 GLU Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 185 PHE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 174 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 248 optimal weight: 6.9990 chunk 188 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 168 optimal weight: 0.8980 chunk 251 optimal weight: 7.9990 chunk 266 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 238 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN B 244 ASN ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 153 GLN G 83 ASN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 153 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23609 Z= 0.223 Angle : 0.505 6.238 32176 Z= 0.271 Chirality : 0.040 0.160 3750 Planarity : 0.004 0.063 3867 Dihedral : 15.254 175.092 3677 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.77 % Allowed : 20.37 % Favored : 77.86 % 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: 1.99 (0.16), residues: 2736 helix: 2.12 (0.14), residues: 1313 sheet: 1.01 (0.21), residues: 550 loop : 0.39 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 669 HIS 0.005 0.001 HIS E 18 PHE 0.013 0.001 PHE E 328 TYR 0.011 0.001 TYR D 286 ARG 0.010 0.000 ARG A 468 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 281 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 241 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 198 time to evaluate : 3.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.8026 (mm) REVERT: F 143 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.6338 (mp0) outliers start: 43 outliers final: 23 residues processed: 230 average time/residue: 3.5168 time to fit residues: 925.8412 Evaluate side-chains 214 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 189 time to evaluate : 3.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain F residue 143 GLU Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 185 PHE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 165 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 222 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 198 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 227 optimal weight: 0.8980 chunk 184 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 chunk 239 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN B 244 ASN D 124 HIS ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 153 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 23609 Z= 0.331 Angle : 0.535 6.398 32176 Z= 0.288 Chirality : 0.042 0.158 3750 Planarity : 0.004 0.050 3867 Dihedral : 15.294 175.965 3671 Min Nonbonded Distance : 1.665 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.18 % Allowed : 19.71 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.16), residues: 2736 helix: 1.99 (0.14), residues: 1312 sheet: 1.03 (0.21), residues: 548 loop : 0.36 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 669 HIS 0.006 0.001 HIS E 18 PHE 0.014 0.001 PHE E 328 TYR 0.013 0.002 TYR A 688 ARG 0.007 0.001 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 281 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 250 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 197 time to evaluate : 3.687 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: D 108 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6683 (mp0) REVERT: H 29 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.7233 (mt0) outliers start: 53 outliers final: 28 residues processed: 234 average time/residue: 3.4545 time to fit residues: 911.0787 Evaluate side-chains 216 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 186 time to evaluate : 3.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain E residue 333 SER Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain F residue 143 GLU Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 185 PHE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 29 GLN Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 165 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 89 optimal weight: 2.9990 chunk 240 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 267 optimal weight: 4.9990 chunk 221 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 140 optimal weight: 0.7980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN A 442 GLN B 244 ASN ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 153 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23609 Z= 0.238 Angle : 0.506 6.115 32176 Z= 0.273 Chirality : 0.040 0.170 3750 Planarity : 0.004 0.048 3867 Dihedral : 15.275 176.275 3671 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.06 % Allowed : 19.71 % Favored : 78.23 % 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: 1.98 (0.16), residues: 2736 helix: 2.09 (0.14), residues: 1318 sheet: 1.08 (0.21), residues: 549 loop : 0.36 (0.22), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 669 HIS 0.004 0.001 HIS E 18 PHE 0.015 0.001 PHE H 245 TYR 0.011 0.001 TYR A 184 ARG 0.005 0.000 ARG A 468 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 281 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 239 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 189 time to evaluate : 3.703 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: D 108 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6689 (mp0) REVERT: F 143 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6455 (mp0) REVERT: H 29 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.7165 (mt0) outliers start: 50 outliers final: 32 residues processed: 224 average time/residue: 3.5602 time to fit residues: 898.8789 Evaluate side-chains 220 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 185 time to evaluate : 3.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 143 GLU Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 70 MET Chi-restraints excluded: chain G residue 153 GLN Chi-restraints excluded: chain G residue 185 PHE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 29 GLN Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 165 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 257 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 195 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 266 optimal weight: 0.9980 chunk 166 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 HIS A 398 ASN B 244 ASN ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 153 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23609 Z= 0.215 Angle : 0.505 7.381 32176 Z= 0.270 Chirality : 0.039 0.162 3750 Planarity : 0.004 0.068 3867 Dihedral : 15.236 175.711 3670 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.98 % Allowed : 19.96 % Favored : 78.07 % 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: 2.07 (0.16), residues: 2736 helix: 2.21 (0.14), residues: 1312 sheet: 1.07 (0.21), residues: 547 loop : 0.39 (0.22), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 669 HIS 0.005 0.001 HIS A 254 PHE 0.012 0.001 PHE E 328 TYR 0.011 0.001 TYR A 184 ARG 0.008 0.000 ARG H 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 281 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 242 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 194 time to evaluate : 3.541 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: D 108 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6687 (mp0) REVERT: F 143 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6422 (mp0) REVERT: H 29 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.7160 (mt0) outliers start: 48 outliers final: 30 residues processed: 229 average time/residue: 3.5385 time to fit residues: 921.3102 Evaluate side-chains 218 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 185 time to evaluate : 3.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 143 GLU Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 70 MET Chi-restraints excluded: chain G residue 185 PHE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 29 GLN Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 165 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 164 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 158 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 181 optimal weight: 0.1980 chunk 131 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 209 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN B 244 ASN H 153 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23609 Z= 0.211 Angle : 0.501 6.847 32176 Z= 0.267 Chirality : 0.039 0.159 3750 Planarity : 0.004 0.060 3867 Dihedral : 15.215 175.852 3670 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.89 % Allowed : 19.67 % Favored : 78.44 % 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: 2.12 (0.16), residues: 2736 helix: 2.26 (0.14), residues: 1312 sheet: 1.09 (0.21), residues: 547 loop : 0.39 (0.22), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 669 HIS 0.005 0.001 HIS G 64 PHE 0.012 0.001 PHE E 328 TYR 0.012 0.001 TYR A 184 ARG 0.011 0.000 ARG H 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 281 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 240 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 194 time to evaluate : 3.695 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: D 108 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6694 (mp0) REVERT: F 143 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6431 (mp0) REVERT: H 29 GLN cc_start: 0.7421 (OUTLIER) cc_final: 0.7142 (mt0) outliers start: 46 outliers final: 32 residues processed: 229 average time/residue: 3.5105 time to fit residues: 909.3533 Evaluate side-chains 219 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 184 time to evaluate : 3.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain F residue 143 GLU Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 70 MET Chi-restraints excluded: chain G residue 153 GLN Chi-restraints excluded: chain G residue 185 PHE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 29 GLN Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 153 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 241 optimal weight: 3.9990 chunk 254 optimal weight: 6.9990 chunk 232 optimal weight: 2.9990 chunk 247 optimal weight: 9.9990 chunk 149 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 chunk 234 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 HIS A 398 ASN B 244 ASN ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN ** H 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 153 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 23609 Z= 0.329 Angle : 0.537 7.720 32176 Z= 0.286 Chirality : 0.041 0.172 3750 Planarity : 0.004 0.090 3867 Dihedral : 15.262 175.644 3669 Min Nonbonded Distance : 1.666 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.69 % Allowed : 19.79 % Favored : 78.52 % 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: 1.98 (0.16), residues: 2736 helix: 2.10 (0.14), residues: 1320 sheet: 1.07 (0.21), residues: 549 loop : 0.35 (0.22), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 669 HIS 0.005 0.001 HIS B 232 PHE 0.014 0.001 PHE E 328 TYR 0.012 0.002 TYR A 688 ARG 0.014 0.001 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 281 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 229 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 188 time to evaluate : 3.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 108 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6687 (mp0) REVERT: F 143 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6421 (mp0) REVERT: H 29 GLN cc_start: 0.7434 (OUTLIER) cc_final: 0.7104 (mt0) outliers start: 41 outliers final: 29 residues processed: 220 average time/residue: 3.5426 time to fit residues: 879.1757 Evaluate side-chains 216 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 184 time to evaluate : 3.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain F residue 143 GLU Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 70 MET Chi-restraints excluded: chain G residue 185 PHE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 29 GLN Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 152 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 262 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 182 optimal weight: 0.8980 chunk 274 optimal weight: 5.9990 chunk 253 optimal weight: 6.9990 chunk 218 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23609 Z= 0.275 Angle : 0.530 7.754 32176 Z= 0.282 Chirality : 0.041 0.164 3750 Planarity : 0.004 0.096 3867 Dihedral : 15.286 175.580 3668 Min Nonbonded Distance : 1.666 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.44 % Allowed : 20.00 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.16), residues: 2736 helix: 2.12 (0.14), residues: 1311 sheet: 1.11 (0.22), residues: 542 loop : 0.38 (0.22), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 669 HIS 0.005 0.001 HIS E 18 PHE 0.013 0.001 PHE E 328 TYR 0.011 0.001 TYR A 688 ARG 0.012 0.000 ARG B 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 281 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 192 time to evaluate : 3.695 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: D 108 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6687 (mp0) REVERT: F 143 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6433 (mp0) REVERT: G 185 PHE cc_start: 0.7454 (OUTLIER) cc_final: 0.6637 (p90) REVERT: H 29 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.7092 (mt0) outliers start: 35 outliers final: 27 residues processed: 221 average time/residue: 3.4668 time to fit residues: 868.1930 Evaluate side-chains 219 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 188 time to evaluate : 3.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain F residue 143 GLU Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 70 MET Chi-restraints excluded: chain G residue 185 PHE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 29 GLN Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 201 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 219 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 225 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.102469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.061111 restraints weight = 94921.685| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 2.14 r_work: 0.2635 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2522 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23609 Z= 0.262 Angle : 0.532 11.033 32176 Z= 0.282 Chirality : 0.040 0.156 3750 Planarity : 0.004 0.094 3867 Dihedral : 15.302 175.701 3668 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.40 % Allowed : 19.92 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.16), residues: 2736 helix: 2.14 (0.14), residues: 1311 sheet: 1.10 (0.22), residues: 541 loop : 0.34 (0.22), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 669 HIS 0.004 0.001 HIS C 260 PHE 0.012 0.001 PHE E 328 TYR 0.012 0.001 TYR G 211 ARG 0.013 0.001 ARG B 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17067.08 seconds wall clock time: 297 minutes 35.77 seconds (17855.77 seconds total)