Starting phenix.real_space_refine on Mon Nov 20 02:06:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etw_28601/11_2023/8etw_28601_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etw_28601/11_2023/8etw_28601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etw_28601/11_2023/8etw_28601.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etw_28601/11_2023/8etw_28601.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etw_28601/11_2023/8etw_28601_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etw_28601/11_2023/8etw_28601_neut_updated.pdb" } resolution = 2.64 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= 0.001 sd= 0.023 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 95 5.16 5 C 18039 2.51 5 N 4942 2.21 5 O 5578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Q ASP 1072": "OD1" <-> "OD2" Residue "Q TYR 1083": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 1103": "OD1" <-> "OD2" Residue "Q TYR 1122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 1167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 138": "OE1" <-> "OE2" Residue "R PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 201": "OD1" <-> "OD2" Residue "R ASP 585": "OD1" <-> "OD2" Residue "R ASP 602": "OD1" <-> "OD2" Residue "R GLU 623": "OE1" <-> "OE2" Residue "R ASP 634": "OD1" <-> "OD2" Residue "R GLU 643": "OE1" <-> "OE2" Residue "R ASP 663": "OD1" <-> "OD2" Residue "R PHE 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 95": "OE1" <-> "OE2" Residue "T GLU 119": "OE1" <-> "OE2" Residue "T GLU 203": "OE1" <-> "OE2" Residue "T GLU 225": "OE1" <-> "OE2" Residue "T GLU 227": "OE1" <-> "OE2" Residue "T GLU 242": "OE1" <-> "OE2" Residue "T ASP 253": "OD1" <-> "OD2" Residue "T GLU 279": "OE1" <-> "OE2" Residue "T GLU 287": "OE1" <-> "OE2" Residue "T TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 365": "OD1" <-> "OD2" Residue "T GLU 385": "OE1" <-> "OE2" Residue "T ASP 401": "OD1" <-> "OD2" Residue "T GLU 433": "OE1" <-> "OE2" Residue "T ASP 448": "OD1" <-> "OD2" Residue "U PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 115": "OE1" <-> "OE2" Residue "U ASP 193": "OD1" <-> "OD2" Residue "U PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 271": "OD1" <-> "OD2" Residue "U GLU 304": "OE1" <-> "OE2" Residue "U ASP 349": "OD1" <-> "OD2" Residue "U TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 374": "OE1" <-> "OE2" Residue "U GLU 375": "OE1" <-> "OE2" Residue "U ASP 385": "OD1" <-> "OD2" Residue "U GLU 442": "OE1" <-> "OE2" Residue "U TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 135": "OE1" <-> "OE2" Residue "V GLU 141": "OE1" <-> "OE2" Residue "V GLU 146": "OE1" <-> "OE2" Residue "V GLU 150": "OE1" <-> "OE2" Residue "V TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 198": "OD1" <-> "OD2" Residue "V GLU 203": "OE1" <-> "OE2" Residue "V ASP 223": "OD1" <-> "OD2" Residue "V ASP 251": "OD1" <-> "OD2" Residue "V GLU 312": "OE1" <-> "OE2" Residue "V TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 365": "OD1" <-> "OD2" Residue "V ASP 376": "OD1" <-> "OD2" Residue "V PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 448": "OD1" <-> "OD2" Residue "V GLU 457": "OE1" <-> "OE2" Residue "W PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 142": "OE1" <-> "OE2" Residue "W GLU 166": "OE1" <-> "OE2" Residue "W ASP 193": "OD1" <-> "OD2" Residue "W ASP 245": "OD1" <-> "OD2" Residue "W ASP 271": "OD1" <-> "OD2" Residue "W ASP 296": "OD1" <-> "OD2" Residue "W ASP 302": "OD1" <-> "OD2" Residue "W ASP 349": "OD1" <-> "OD2" Residue "W GLU 375": "OE1" <-> "OE2" Residue "W GLU 419": "OE1" <-> "OE2" Residue "W GLU 442": "OE1" <-> "OE2" Residue "W TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 450": "OD1" <-> "OD2" Residue "X ASP 36": "OD1" <-> "OD2" Residue "X GLU 45": "OE1" <-> "OE2" Residue "X GLU 119": "OE1" <-> "OE2" Residue "X PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 141": "OE1" <-> "OE2" Residue "X ASP 216": "OD1" <-> "OD2" Residue "X GLU 221": "OE1" <-> "OE2" Residue "X ASP 223": "OD1" <-> "OD2" Residue "X GLU 242": "OE1" <-> "OE2" Residue "X GLU 385": "OE1" <-> "OE2" Residue "X GLU 441": "OE1" <-> "OE2" Residue "Y GLU 131": "OE1" <-> "OE2" Residue "Y ASP 164": "OD1" <-> "OD2" Residue "Y GLU 170": "OE1" <-> "OE2" Residue "Y ASP 213": "OD1" <-> "OD2" Residue "Y GLU 243": "OE1" <-> "OE2" Residue "Y GLU 314": "OE1" <-> "OE2" Residue "Y PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 450": "OD1" <-> "OD2" Residue "Z PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 303": "OE1" <-> "OE2" Residue "Z GLU 313": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 28666 Number of models: 1 Model: "" Number of chains: 16 Chain: "Q" Number of atoms: 3385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3385 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 22, 'TRANS': 395} Chain breaks: 5 Chain: "R" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3548 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain breaks: 1 Chain: "S" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1014 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 9, 'TRANS': 115} Chain breaks: 1 Chain: "T" Number of atoms: 3339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3339 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 417} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3350 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 425} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "V" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3404 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 18, 'TRANS': 424} Chain: "W" Number of atoms: 3398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3398 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 431} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 3397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3397 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 18, 'TRANS': 423} Chain: "Y" Number of atoms: 3421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3421 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 434} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Z" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 248 Classifications: {'peptide': 28} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 25} Chain: "T" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.63, per 1000 atoms: 0.51 Number of scatterers: 28666 At special positions: 0 Unit cell: (128.59, 158.65, 197.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 95 16.00 P 12 15.00 O 5578 8.00 N 4942 7.00 C 18039 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.73 Conformation dependent library (CDL) restraints added in 5.2 seconds 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6820 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 151 helices and 30 sheets defined 38.3% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.17 Creating SS restraints... Processing helix chain 'Q' and resid 958 through 970 Processing helix chain 'Q' and resid 975 through 984 Processing helix chain 'Q' and resid 1001 through 1012 removed outlier: 3.960A pdb=" N GLN Q1006 " --> pdb=" O ASN Q1002 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE Q1007 " --> pdb=" O ALA Q1003 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1014 through 1017 No H-bonds generated for 'chain 'Q' and resid 1014 through 1017' Processing helix chain 'Q' and resid 1087 through 1093 Processing helix chain 'Q' and resid 1102 through 1110 Processing helix chain 'Q' and resid 1122 through 1132 Processing helix chain 'Q' and resid 1139 through 1145 Processing helix chain 'Q' and resid 1148 through 1153 Processing helix chain 'Q' and resid 1170 through 1179 removed outlier: 3.605A pdb=" N VAL Q1177 " --> pdb=" O GLU Q1173 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR Q1178 " --> pdb=" O LEU Q1174 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG Q1179 " --> pdb=" O LEU Q1175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1186 through 1190 Processing helix chain 'Q' and resid 1193 through 1200 Processing helix chain 'Q' and resid 1227 through 1237 Processing helix chain 'Q' and resid 1240 through 1245 Processing helix chain 'Q' and resid 1251 through 1258 Processing helix chain 'Q' and resid 1265 through 1267 No H-bonds generated for 'chain 'Q' and resid 1265 through 1267' Processing helix chain 'Q' and resid 1293 through 1296 No H-bonds generated for 'chain 'Q' and resid 1293 through 1296' Processing helix chain 'Q' and resid 1299 through 1314 removed outlier: 3.827A pdb=" N VAL Q1309 " --> pdb=" O ASP Q1305 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS Q1310 " --> pdb=" O GLU Q1306 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU Q1311 " --> pdb=" O LEU Q1307 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1326 through 1338 Processing helix chain 'Q' and resid 1358 through 1363 Processing helix chain 'Q' and resid 1398 through 1407 removed outlier: 3.701A pdb=" N GLN Q1403 " --> pdb=" O THR Q1399 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1428 through 1431 No H-bonds generated for 'chain 'Q' and resid 1428 through 1431' Processing helix chain 'R' and resid 31 through 33 No H-bonds generated for 'chain 'R' and resid 31 through 33' Processing helix chain 'R' and resid 83 through 85 No H-bonds generated for 'chain 'R' and resid 83 through 85' Processing helix chain 'R' and resid 90 through 94 Processing helix chain 'R' and resid 109 through 121 Processing helix chain 'R' and resid 144 through 157 Processing helix chain 'R' and resid 168 through 176 Processing helix chain 'R' and resid 216 through 230 Processing helix chain 'R' and resid 240 through 249 Processing helix chain 'R' and resid 257 through 261 removed outlier: 3.504A pdb=" N ILE R 261 " --> pdb=" O TYR R 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 257 through 261' Processing helix chain 'R' and resid 267 through 270 No H-bonds generated for 'chain 'R' and resid 267 through 270' Processing helix chain 'R' and resid 586 through 588 No H-bonds generated for 'chain 'R' and resid 586 through 588' Processing helix chain 'R' and resid 590 through 595 Processing helix chain 'R' and resid 607 through 610 Processing helix chain 'R' and resid 617 through 620 No H-bonds generated for 'chain 'R' and resid 617 through 620' Processing helix chain 'R' and resid 622 through 625 removed outlier: 3.845A pdb=" N ILE R 625 " --> pdb=" O PRO R 622 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 622 through 625' Processing helix chain 'R' and resid 638 through 647 Processing helix chain 'R' and resid 659 through 667 removed outlier: 3.771A pdb=" N ASN R 667 " --> pdb=" O ASP R 663 " (cutoff:3.500A) Processing helix chain 'R' and resid 673 through 675 No H-bonds generated for 'chain 'R' and resid 673 through 675' Processing helix chain 'R' and resid 680 through 691 Processing helix chain 'R' and resid 709 through 719 Processing helix chain 'R' and resid 721 through 724 No H-bonds generated for 'chain 'R' and resid 721 through 724' Processing helix chain 'R' and resid 731 through 737 Processing helix chain 'S' and resid 29 through 39 removed outlier: 4.323A pdb=" N LEU S 33 " --> pdb=" O ARG S 29 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ARG S 34 " --> pdb=" O LEU S 30 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER S 35 " --> pdb=" O LEU S 31 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL S 36 " --> pdb=" O PHE S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 82 removed outlier: 4.076A pdb=" N ILE S 67 " --> pdb=" O ALA S 63 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER S 68 " --> pdb=" O ARG S 64 " (cutoff:3.500A) Processing helix chain 'S' and resid 100 through 103 No H-bonds generated for 'chain 'S' and resid 100 through 103' Processing helix chain 'S' and resid 137 through 142 Processing helix chain 'S' and resid 151 through 156 Processing helix chain 'T' and resid 52 through 67 Processing helix chain 'T' and resid 85 through 96 Processing helix chain 'T' and resid 107 through 110 removed outlier: 3.805A pdb=" N LEU T 110 " --> pdb=" O GLY T 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 107 through 110' Processing helix chain 'T' and resid 117 through 128 removed outlier: 3.925A pdb=" N ALA T 128 " --> pdb=" O ASN T 124 " (cutoff:3.500A) Processing helix chain 'T' and resid 183 through 191 Processing helix chain 'T' and resid 216 through 218 No H-bonds generated for 'chain 'T' and resid 216 through 218' Processing helix chain 'T' and resid 249 through 255 Processing helix chain 'T' and resid 282 through 297 Processing helix chain 'T' and resid 313 through 315 No H-bonds generated for 'chain 'T' and resid 313 through 315' Processing helix chain 'T' and resid 318 through 327 removed outlier: 3.827A pdb=" N ASN T 325 " --> pdb=" O PHE T 321 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS T 326 " --> pdb=" O THR T 322 " (cutoff:3.500A) Processing helix chain 'T' and resid 356 through 358 No H-bonds generated for 'chain 'T' and resid 356 through 358' Processing helix chain 'T' and resid 361 through 366 removed outlier: 3.661A pdb=" N ASP T 365 " --> pdb=" O PRO T 361 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG T 366 " --> pdb=" O ASP T 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 361 through 366' Processing helix chain 'T' and resid 377 through 390 Processing helix chain 'T' and resid 397 through 409 Processing helix chain 'T' and resid 412 through 428 removed outlier: 3.516A pdb=" N LEU T 416 " --> pdb=" O LEU T 412 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ALA T 420 " --> pdb=" O LEU T 416 " (cutoff:3.500A) Proline residue: T 421 - end of helix Processing helix chain 'T' and resid 436 through 445 Processing helix chain 'T' and resid 449 through 457 Processing helix chain 'U' and resid 48 through 63 Processing helix chain 'U' and resid 81 through 92 Processing helix chain 'U' and resid 113 through 124 removed outlier: 3.987A pdb=" N SER U 124 " --> pdb=" O ALA U 120 " (cutoff:3.500A) Processing helix chain 'U' and resid 173 through 180 Processing helix chain 'U' and resid 241 through 248 Processing helix chain 'U' and resid 254 through 259 removed outlier: 4.001A pdb=" N THR U 259 " --> pdb=" O ALA U 256 " (cutoff:3.500A) Processing helix chain 'U' and resid 267 through 283 Processing helix chain 'U' and resid 298 through 300 No H-bonds generated for 'chain 'U' and resid 298 through 300' Processing helix chain 'U' and resid 303 through 312 removed outlier: 3.779A pdb=" N ARG U 311 " --> pdb=" O SER U 307 " (cutoff:3.500A) Processing helix chain 'U' and resid 340 through 342 No H-bonds generated for 'chain 'U' and resid 340 through 342' Processing helix chain 'U' and resid 345 through 349 Processing helix chain 'U' and resid 361 through 374 Processing helix chain 'U' and resid 381 through 393 Processing helix chain 'U' and resid 396 through 413 removed outlier: 4.217A pdb=" N SER U 404 " --> pdb=" O SER U 400 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL U 405 " --> pdb=" O ASN U 401 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLN U 407 " --> pdb=" O ILE U 403 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLN U 408 " --> pdb=" O SER U 404 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE U 409 " --> pdb=" O VAL U 405 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG U 413 " --> pdb=" O ILE U 409 " (cutoff:3.500A) Processing helix chain 'U' and resid 420 through 429 Processing helix chain 'U' and resid 433 through 446 removed outlier: 6.716A pdb=" N SER U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N GLN U 446 " --> pdb=" O GLU U 442 " (cutoff:3.500A) Processing helix chain 'V' and resid 52 through 67 Processing helix chain 'V' and resid 85 through 96 Processing helix chain 'V' and resid 107 through 110 removed outlier: 3.856A pdb=" N LEU V 110 " --> pdb=" O GLY V 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 107 through 110' Processing helix chain 'V' and resid 117 through 127 Processing helix chain 'V' and resid 183 through 191 removed outlier: 3.694A pdb=" N SER V 188 " --> pdb=" O THR V 184 " (cutoff:3.500A) Processing helix chain 'V' and resid 249 through 257 Processing helix chain 'V' and resid 265 through 270 Processing helix chain 'V' and resid 282 through 297 Processing helix chain 'V' and resid 313 through 315 No H-bonds generated for 'chain 'V' and resid 313 through 315' Processing helix chain 'V' and resid 318 through 329 removed outlier: 3.777A pdb=" N LYS V 326 " --> pdb=" O THR V 322 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLU V 329 " --> pdb=" O ASN V 325 " (cutoff:3.500A) Processing helix chain 'V' and resid 356 through 358 No H-bonds generated for 'chain 'V' and resid 356 through 358' Processing helix chain 'V' and resid 361 through 366 removed outlier: 4.524A pdb=" N ARG V 366 " --> pdb=" O ASP V 362 " (cutoff:3.500A) Processing helix chain 'V' and resid 377 through 390 Processing helix chain 'V' and resid 397 through 409 Processing helix chain 'V' and resid 412 through 429 removed outlier: 4.292A pdb=" N LEU V 419 " --> pdb=" O ALA V 415 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ALA V 420 " --> pdb=" O LEU V 416 " (cutoff:3.500A) Proline residue: V 421 - end of helix removed outlier: 3.831A pdb=" N SER V 429 " --> pdb=" O LEU V 425 " (cutoff:3.500A) Processing helix chain 'V' and resid 436 through 445 Processing helix chain 'V' and resid 449 through 457 Processing helix chain 'W' and resid 48 through 63 Processing helix chain 'W' and resid 81 through 92 Processing helix chain 'W' and resid 113 through 124 removed outlier: 4.055A pdb=" N SER W 124 " --> pdb=" O ALA W 120 " (cutoff:3.500A) Processing helix chain 'W' and resid 173 through 180 Processing helix chain 'W' and resid 241 through 249 Processing helix chain 'W' and resid 253 through 259 removed outlier: 4.112A pdb=" N PHE W 258 " --> pdb=" O PHE W 254 " (cutoff:3.500A) Processing helix chain 'W' and resid 267 through 282 Processing helix chain 'W' and resid 303 through 314 removed outlier: 3.936A pdb=" N ARG W 311 " --> pdb=" O SER W 307 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLU W 314 " --> pdb=" O ASN W 310 " (cutoff:3.500A) Processing helix chain 'W' and resid 340 through 342 No H-bonds generated for 'chain 'W' and resid 340 through 342' Processing helix chain 'W' and resid 345 through 349 Processing helix chain 'W' and resid 361 through 374 Processing helix chain 'W' and resid 381 through 393 Processing helix chain 'W' and resid 396 through 412 removed outlier: 4.028A pdb=" N ILE W 403 " --> pdb=" O SER W 399 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N SER W 404 " --> pdb=" O SER W 400 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL W 405 " --> pdb=" O ASN W 401 " (cutoff:3.500A) Processing helix chain 'W' and resid 420 through 429 Processing helix chain 'W' and resid 433 through 441 Processing helix chain 'X' and resid 52 through 67 Processing helix chain 'X' and resid 85 through 96 Processing helix chain 'X' and resid 107 through 110 removed outlier: 3.692A pdb=" N LEU X 110 " --> pdb=" O GLY X 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 107 through 110' Processing helix chain 'X' and resid 117 through 128 removed outlier: 3.795A pdb=" N ALA X 128 " --> pdb=" O ASN X 124 " (cutoff:3.500A) Processing helix chain 'X' and resid 183 through 192 removed outlier: 4.068A pdb=" N GLU X 187 " --> pdb=" O THR X 184 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU X 192 " --> pdb=" O ILE X 189 " (cutoff:3.500A) Processing helix chain 'X' and resid 216 through 218 No H-bonds generated for 'chain 'X' and resid 216 through 218' Processing helix chain 'X' and resid 249 through 257 Processing helix chain 'X' and resid 265 through 271 Processing helix chain 'X' and resid 282 through 297 Processing helix chain 'X' and resid 313 through 315 No H-bonds generated for 'chain 'X' and resid 313 through 315' Processing helix chain 'X' and resid 318 through 329 removed outlier: 4.478A pdb=" N GLU X 329 " --> pdb=" O ASN X 325 " (cutoff:3.500A) Processing helix chain 'X' and resid 356 through 358 No H-bonds generated for 'chain 'X' and resid 356 through 358' Processing helix chain 'X' and resid 361 through 366 removed outlier: 3.869A pdb=" N ARG X 366 " --> pdb=" O ASP X 362 " (cutoff:3.500A) Processing helix chain 'X' and resid 377 through 390 Processing helix chain 'X' and resid 397 through 409 Processing helix chain 'X' and resid 412 through 417 Processing helix chain 'X' and resid 420 through 428 Processing helix chain 'X' and resid 436 through 445 Processing helix chain 'X' and resid 449 through 457 Processing helix chain 'Y' and resid 48 through 63 Processing helix chain 'Y' and resid 81 through 91 Processing helix chain 'Y' and resid 103 through 106 removed outlier: 4.014A pdb=" N ILE Y 106 " --> pdb=" O GLY Y 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 103 through 106' Processing helix chain 'Y' and resid 113 through 124 removed outlier: 3.853A pdb=" N SER Y 124 " --> pdb=" O ALA Y 120 " (cutoff:3.500A) Processing helix chain 'Y' and resid 173 through 180 Processing helix chain 'Y' and resid 206 through 208 No H-bonds generated for 'chain 'Y' and resid 206 through 208' Processing helix chain 'Y' and resid 241 through 249 Processing helix chain 'Y' and resid 254 through 259 Processing helix chain 'Y' and resid 267 through 283 Processing helix chain 'Y' and resid 303 through 312 Processing helix chain 'Y' and resid 340 through 342 No H-bonds generated for 'chain 'Y' and resid 340 through 342' Processing helix chain 'Y' and resid 345 through 349 Processing helix chain 'Y' and resid 361 through 374 Processing helix chain 'Y' and resid 381 through 393 Processing helix chain 'Y' and resid 396 through 413 removed outlier: 3.857A pdb=" N SER Y 404 " --> pdb=" O SER Y 400 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN Y 408 " --> pdb=" O SER Y 404 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG Y 413 " --> pdb=" O ILE Y 409 " (cutoff:3.500A) Processing helix chain 'Y' and resid 420 through 429 Processing helix chain 'Y' and resid 433 through 441 Processing helix chain 'Y' and resid 444 through 446 No H-bonds generated for 'chain 'Y' and resid 444 through 446' Processing sheet with id= A, first strand: chain 'Q' and resid 949 through 954 removed outlier: 6.441A pdb=" N VAL Q1419 " --> pdb=" O ILE Q 950 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N VAL Q 952 " --> pdb=" O VAL Q1419 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG Q1421 " --> pdb=" O VAL Q 952 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N CYS Q 954 " --> pdb=" O ARG Q1421 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU Q1423 " --> pdb=" O CYS Q 954 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'Q' and resid 1082 through 1084 removed outlier: 6.819A pdb=" N THR Q1220 " --> pdb=" O TYR Q1083 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'R' and resid 40 through 44 Processing sheet with id= D, first strand: chain 'R' and resid 67 through 71 Processing sheet with id= E, first strand: chain 'R' and resid 134 through 137 removed outlier: 3.771A pdb=" N THR R 164 " --> pdb=" O ILE R 134 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU R 136 " --> pdb=" O THR R 164 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'R' and resid 700 through 702 removed outlier: 6.877A pdb=" N VAL R 668 " --> pdb=" O ASN R 701 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU R 185 " --> pdb=" O LEU R 669 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N THR R 671 " --> pdb=" O LEU R 185 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILE R 187 " --> pdb=" O THR R 671 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'R' and resid 198 through 200 Processing sheet with id= H, first strand: chain 'R' and resid 275 through 278 Processing sheet with id= I, first strand: chain 'T' and resid 367 through 371 removed outlier: 7.146A pdb=" N ALA T 74 " --> pdb=" O LEU T 368 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N VAL T 370 " --> pdb=" O ALA T 74 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU T 76 " --> pdb=" O VAL T 370 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL T 336 " --> pdb=" O ILE T 75 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU T 77 " --> pdb=" O VAL T 336 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU T 338 " --> pdb=" O LEU T 77 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'T' and resid 301 through 305 Processing sheet with id= K, first strand: chain 'T' and resid 175 through 181 removed outlier: 3.586A pdb=" N GLY T 175 " --> pdb=" O SER T 172 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N HIS T 165 " --> pdb=" O GLU T 150 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU T 146 " --> pdb=" O GLY T 169 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LYS T 171 " --> pdb=" O VAL T 144 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N VAL T 144 " --> pdb=" O LYS T 171 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASP T 198 " --> pdb=" O VAL T 144 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TYR T 201 " --> pdb=" O ARG T 211 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ARG T 211 " --> pdb=" O TYR T 201 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N GLU T 203 " --> pdb=" O VAL T 209 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL T 209 " --> pdb=" O GLU T 203 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'T' and resid 344 through 346 Processing sheet with id= M, first strand: chain 'U' and resid 351 through 355 removed outlier: 6.948A pdb=" N ALA U 70 " --> pdb=" O ILE U 352 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ILE U 354 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU U 72 " --> pdb=" O ILE U 354 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL U 321 " --> pdb=" O VAL U 71 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL U 73 " --> pdb=" O VAL U 321 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N MET U 323 " --> pdb=" O VAL U 73 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'U' and resid 287 through 290 Processing sheet with id= O, first strand: chain 'U' and resid 166 through 171 removed outlier: 4.355A pdb=" N GLY U 156 " --> pdb=" O LEU U 171 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LYS U 161 " --> pdb=" O VAL U 140 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N VAL U 140 " --> pdb=" O LYS U 161 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP U 188 " --> pdb=" O VAL U 140 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N SER U 191 " --> pdb=" O LYS U 201 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N LYS U 201 " --> pdb=" O SER U 191 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ASP U 193 " --> pdb=" O ILE U 199 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ILE U 199 " --> pdb=" O ASP U 193 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'V' and resid 367 through 372 removed outlier: 7.185A pdb=" N ALA V 74 " --> pdb=" O LEU V 368 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N VAL V 370 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU V 76 " --> pdb=" O VAL V 370 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N THR V 372 " --> pdb=" O LEU V 76 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA V 78 " --> pdb=" O THR V 372 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL V 336 " --> pdb=" O ILE V 75 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU V 77 " --> pdb=" O VAL V 336 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU V 338 " --> pdb=" O LEU V 77 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N GLY V 79 " --> pdb=" O LEU V 338 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N SER V 340 " --> pdb=" O GLY V 79 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'V' and resid 301 through 305 Processing sheet with id= R, first strand: chain 'V' and resid 175 through 181 removed outlier: 3.692A pdb=" N GLY V 175 " --> pdb=" O SER V 172 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS V 165 " --> pdb=" O GLU V 150 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU V 146 " --> pdb=" O GLY V 169 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LYS V 171 " --> pdb=" O VAL V 144 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N VAL V 144 " --> pdb=" O LYS V 171 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASP V 198 " --> pdb=" O VAL V 144 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY V 213 " --> pdb=" O VAL V 199 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR V 201 " --> pdb=" O ARG V 211 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ARG V 211 " --> pdb=" O TYR V 201 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLU V 203 " --> pdb=" O VAL V 209 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N VAL V 209 " --> pdb=" O GLU V 203 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'W' and resid 351 through 356 removed outlier: 6.808A pdb=" N ALA W 70 " --> pdb=" O ILE W 352 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ILE W 354 " --> pdb=" O ALA W 70 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU W 72 " --> pdb=" O ILE W 354 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N THR W 356 " --> pdb=" O LEU W 72 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA W 74 " --> pdb=" O THR W 356 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL W 321 " --> pdb=" O VAL W 71 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL W 73 " --> pdb=" O VAL W 321 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N MET W 323 " --> pdb=" O VAL W 73 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N GLY W 75 " --> pdb=" O MET W 323 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N THR W 325 " --> pdb=" O GLY W 75 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'W' and resid 286 through 290 Processing sheet with id= U, first strand: chain 'W' and resid 166 through 171 removed outlier: 3.817A pdb=" N GLY W 156 " --> pdb=" O LEU W 171 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LYS W 161 " --> pdb=" O VAL W 140 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N VAL W 140 " --> pdb=" O LYS W 161 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ASP W 188 " --> pdb=" O VAL W 140 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY W 203 " --> pdb=" O VAL W 189 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER W 191 " --> pdb=" O LYS W 201 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LYS W 201 " --> pdb=" O SER W 191 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ASP W 193 " --> pdb=" O ILE W 199 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE W 199 " --> pdb=" O ASP W 193 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'X' and resid 367 through 372 removed outlier: 7.160A pdb=" N ALA X 74 " --> pdb=" O LEU X 368 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N VAL X 370 " --> pdb=" O ALA X 74 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU X 76 " --> pdb=" O VAL X 370 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N THR X 372 " --> pdb=" O LEU X 76 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA X 78 " --> pdb=" O THR X 372 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL X 336 " --> pdb=" O ILE X 75 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N LEU X 77 " --> pdb=" O VAL X 336 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU X 338 " --> pdb=" O LEU X 77 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N GLY X 79 " --> pdb=" O LEU X 338 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N SER X 340 " --> pdb=" O GLY X 79 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'X' and resid 301 through 305 Processing sheet with id= X, first strand: chain 'X' and resid 199 through 203 removed outlier: 6.446A pdb=" N GLY X 169 " --> pdb=" O THR X 145 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU X 147 " --> pdb=" O ILE X 167 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE X 167 " --> pdb=" O LEU X 147 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N HIS X 165 " --> pdb=" O PRO X 149 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL X 166 " --> pdb=" O LEU X 181 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'X' and resid 344 through 346 Processing sheet with id= Z, first strand: chain 'Y' and resid 352 through 356 removed outlier: 3.505A pdb=" N ILE Y 352 " --> pdb=" O ALA Y 70 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Y' and resid 286 through 290 Processing sheet with id= AB, first strand: chain 'Y' and resid 166 through 171 removed outlier: 3.641A pdb=" N GLY Y 156 " --> pdb=" O LEU Y 171 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU Y 142 " --> pdb=" O THR Y 159 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS Y 161 " --> pdb=" O VAL Y 140 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N VAL Y 140 " --> pdb=" O LYS Y 161 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP Y 188 " --> pdb=" O VAL Y 140 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N SER Y 191 " --> pdb=" O LYS Y 201 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N LYS Y 201 " --> pdb=" O SER Y 191 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ASP Y 193 " --> pdb=" O ILE Y 199 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE Y 199 " --> pdb=" O ASP Y 193 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'Y' and resid 329 through 331 Processing sheet with id= AD, first strand: chain 'Z' and resid 307 through 310 1050 hydrogen bonds defined for protein. 3099 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.86 Time building geometry restraints manager: 12.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9096 1.34 - 1.46: 5669 1.46 - 1.58: 14147 1.58 - 1.71: 20 1.71 - 1.83: 166 Bond restraints: 29098 Sorted by residual: bond pdb=" CB PRO R 27 " pdb=" CG PRO R 27 " ideal model delta sigma weight residual 1.492 1.656 -0.164 5.00e-02 4.00e+02 1.08e+01 bond pdb=" N GLU X 225 " pdb=" CA GLU X 225 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.16e-02 7.43e+03 8.54e+00 bond pdb=" N SER V 340 " pdb=" CA SER V 340 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.29e-02 6.01e+03 7.11e+00 bond pdb=" N ARG V 342 " pdb=" CA ARG V 342 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.21e-02 6.83e+03 6.64e+00 bond pdb=" N GLU R 617 " pdb=" CA GLU R 617 " ideal model delta sigma weight residual 1.459 1.490 -0.032 1.25e-02 6.40e+03 6.35e+00 ... (remaining 29093 not shown) Histogram of bond angle deviations from ideal: 91.80 - 100.69: 26 100.69 - 109.57: 3239 109.57 - 118.46: 20024 118.46 - 127.34: 15865 127.34 - 136.23: 214 Bond angle restraints: 39368 Sorted by residual: angle pdb=" CA PRO R 27 " pdb=" N PRO R 27 " pdb=" CD PRO R 27 " ideal model delta sigma weight residual 112.00 97.75 14.25 1.40e+00 5.10e-01 1.04e+02 angle pdb=" N MET V 344 " pdb=" CA MET V 344 " pdb=" C MET V 344 " ideal model delta sigma weight residual 107.28 91.80 15.48 1.75e+00 3.27e-01 7.83e+01 angle pdb=" N GLY V 343 " pdb=" CA GLY V 343 " pdb=" C GLY V 343 " ideal model delta sigma weight residual 113.18 133.54 -20.36 2.37e+00 1.78e-01 7.38e+01 angle pdb=" N MET V 344 " pdb=" CA MET V 344 " pdb=" CB MET V 344 " ideal model delta sigma weight residual 111.74 125.94 -14.20 1.69e+00 3.50e-01 7.06e+01 angle pdb=" C LEU U 19 " pdb=" N ILE U 20 " pdb=" CA ILE U 20 " ideal model delta sigma weight residual 121.97 133.82 -11.85 1.80e+00 3.09e-01 4.33e+01 ... (remaining 39363 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.07: 17000 33.07 - 66.15: 813 66.15 - 99.22: 53 99.22 - 132.29: 6 132.29 - 165.37: 5 Dihedral angle restraints: 17877 sinusoidal: 7315 harmonic: 10562 Sorted by residual: dihedral pdb=" C5' ADP U 501 " pdb=" O5' ADP U 501 " pdb=" PA ADP U 501 " pdb=" O2A ADP U 501 " ideal model delta sinusoidal sigma weight residual 300.00 134.64 165.37 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" O1B ADP T 501 " pdb=" O3A ADP T 501 " pdb=" PB ADP T 501 " pdb=" PA ADP T 501 " ideal model delta sinusoidal sigma weight residual 300.00 140.64 159.36 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" C5' ADP T 501 " pdb=" O5' ADP T 501 " pdb=" PA ADP T 501 " pdb=" O2A ADP T 501 " ideal model delta sinusoidal sigma weight residual 300.00 150.00 150.00 1 2.00e+01 2.50e-03 4.48e+01 ... (remaining 17874 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3932 0.075 - 0.149: 637 0.149 - 0.224: 44 0.224 - 0.298: 4 0.298 - 0.373: 3 Chirality restraints: 4620 Sorted by residual: chirality pdb=" CG LEU Q 963 " pdb=" CB LEU Q 963 " pdb=" CD1 LEU Q 963 " pdb=" CD2 LEU Q 963 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CB ILE Y 160 " pdb=" CA ILE Y 160 " pdb=" CG1 ILE Y 160 " pdb=" CG2 ILE Y 160 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CB THR U 40 " pdb=" CA THR U 40 " pdb=" OG1 THR U 40 " pdb=" CG2 THR U 40 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 4617 not shown) Planarity restraints: 5039 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR R 58 " -0.089 5.00e-02 4.00e+02 1.31e-01 2.76e+01 pdb=" N PRO R 59 " 0.227 5.00e-02 4.00e+02 pdb=" CA PRO R 59 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO R 59 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG R 599 " -0.067 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO R 600 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO R 600 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO R 600 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU U 182 " -0.020 2.00e-02 2.50e+03 3.94e-02 1.56e+01 pdb=" C GLU U 182 " 0.068 2.00e-02 2.50e+03 pdb=" O GLU U 182 " -0.026 2.00e-02 2.50e+03 pdb=" N LYS U 183 " -0.022 2.00e-02 2.50e+03 ... (remaining 5036 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.13: 5 2.13 - 2.82: 8312 2.82 - 3.51: 36361 3.51 - 4.21: 65551 4.21 - 4.90: 115749 Nonbonded interactions: 225978 Sorted by model distance: nonbonded pdb=" OH TYR W 212 " pdb=" OD1 ASP X 182 " model vdw 1.435 2.440 nonbonded pdb=" CD2 LEU R 614 " pdb=" OE2 GLU R 617 " model vdw 1.666 3.460 nonbonded pdb=" NZ LYS Y 113 " pdb=" OD2 ASP Y 302 " model vdw 1.725 2.520 nonbonded pdb=" NH2 ARG Q1142 " pdb=" CB GLU Y 182 " model vdw 1.888 3.520 nonbonded pdb=" OH TYR W 212 " pdb=" CG ASP X 182 " model vdw 2.070 3.270 ... (remaining 225973 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 'T' and (resid 22 through 463 or resid 501)) selection = (chain 'V' and (resid 22 through 152 or (resid 161 through 163 and (name N or na \ me CA or name C or name O or name CB )) or resid 164 through 463 or resid 501)) selection = (chain 'X' and (resid 22 through 152 or (resid 161 through 163 and (name N or na \ me CA or name C or name O or name CB )) or resid 164 through 463 or resid 501)) } ncs_group { reference = (chain 'U' and (resid 18 through 459 or resid 501)) selection = (chain 'W' and (resid 18 through 181 or (resid 182 and (name N or name CA or nam \ e C or name O or name CB )) or resid 183 through 210 or resid 221 through 459 or \ resid 501)) selection = (chain 'Y' and (resid 18 through 181 or (resid 182 and (name N or name CA or nam \ e C or name O or name CB )) or resid 183 through 210 or resid 221 through 459 or \ resid 501)) } 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: 4.790 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: 0.020 Extract box with map and model: 23.000 Check model and map are aligned: 0.390 Set scattering table: 0.230 Process input model: 75.490 Find NCS groups from input model: 2.330 Set up NCS constraints: 0.160 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:12.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 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 : 0.005 0.164 29098 Z= 0.340 Angle : 0.910 20.362 39368 Z= 0.479 Chirality : 0.054 0.373 4620 Planarity : 0.007 0.131 5039 Dihedral : 18.081 165.365 11057 Min Nonbonded Distance : 1.435 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.09 % Allowed : 28.01 % Favored : 71.90 % Cbeta Deviations : 0.06 % 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: -1.81 (0.12), residues: 3618 helix: -1.54 (0.11), residues: 1493 sheet: 0.58 (0.20), residues: 649 loop : -1.51 (0.14), residues: 1476 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 860 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 857 time to evaluate : 3.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 4 residues processed: 859 average time/residue: 1.6621 time to fit residues: 1632.2954 Evaluate side-chains 821 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 817 time to evaluate : 3.186 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 3 average time/residue: 0.2779 time to fit residues: 6.0772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 304 optimal weight: 0.0010 chunk 273 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 146 optimal weight: 0.1980 chunk 282 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 210 optimal weight: 0.6980 chunk 327 optimal weight: 0.9980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1117 ASN ** R 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 146 GLN R 611 GLN T 29 HIS U 63 ASN U 274 ASN U 310 ASN U 446 GLN V 190 GLN V 205 ASN V 394 GLN X 190 GLN X 256 ASN X 325 ASN Y 173 ASN Y 223 GLN ** Y 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 252 GLN Y 310 ASN Y 441 GLN Y 443 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 29098 Z= 0.221 Angle : 0.568 7.994 39368 Z= 0.285 Chirality : 0.043 0.211 4620 Planarity : 0.004 0.072 5039 Dihedral : 8.313 145.630 4004 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.18 % Allowed : 24.40 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.13), residues: 3618 helix: -0.18 (0.13), residues: 1499 sheet: 0.58 (0.19), residues: 659 loop : -1.19 (0.15), residues: 1460 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1030 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 898 time to evaluate : 3.564 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 132 outliers final: 53 residues processed: 955 average time/residue: 1.5915 time to fit residues: 1749.9262 Evaluate side-chains 917 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 864 time to evaluate : 3.001 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 24 residues processed: 33 average time/residue: 1.0502 time to fit residues: 46.7710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 182 optimal weight: 0.2980 chunk 101 optimal weight: 0.0980 chunk 272 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 90 optimal weight: 0.4980 chunk 328 optimal weight: 0.0670 chunk 354 optimal weight: 0.9990 chunk 292 optimal weight: 0.9990 chunk 325 optimal weight: 0.9990 chunk 111 optimal weight: 0.0070 chunk 263 optimal weight: 2.9990 overall best weight: 0.1936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 146 GLN R 256 ASN R 611 GLN R 723 GLN T 256 ASN T 289 ASN U 63 ASN U 272 GLN U 274 ASN U 310 ASN U 407 GLN U 441 GLN V 205 ASN V 394 GLN X 190 GLN X 256 ASN X 289 ASN X 325 ASN Y 223 GLN ** Y 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 310 ASN Y 441 GLN Y 443 ASN Y 446 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 29098 Z= 0.135 Angle : 0.513 8.737 39368 Z= 0.254 Chirality : 0.041 0.158 4620 Planarity : 0.003 0.055 5039 Dihedral : 7.558 140.606 4004 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.61 % Allowed : 25.25 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 3618 helix: 0.46 (0.14), residues: 1501 sheet: 0.71 (0.19), residues: 653 loop : -1.00 (0.15), residues: 1464 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 992 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 878 time to evaluate : 3.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 114 outliers final: 52 residues processed: 938 average time/residue: 1.6116 time to fit residues: 1746.3068 Evaluate side-chains 909 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 857 time to evaluate : 3.531 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 23 residues processed: 30 average time/residue: 0.9811 time to fit residues: 41.4204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 324 optimal weight: 1.9990 chunk 246 optimal weight: 2.9990 chunk 170 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 chunk 156 optimal weight: 0.6980 chunk 220 optimal weight: 0.9990 chunk 329 optimal weight: 1.9990 chunk 348 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 312 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1117 ASN R 144 GLN R 146 GLN ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 611 GLN T 205 ASN T 256 ASN T 289 ASN U 63 ASN U 272 GLN U 274 ASN U 310 ASN U 407 GLN U 441 GLN U 446 GLN V 205 ASN V 437 ASN X 190 GLN X 256 ASN X 289 ASN X 325 ASN Y 223 GLN ** Y 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 441 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 29098 Z= 0.312 Angle : 0.593 8.850 39368 Z= 0.295 Chirality : 0.045 0.155 4620 Planarity : 0.004 0.057 5039 Dihedral : 7.972 139.029 4004 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.21 % Allowed : 25.54 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.14), residues: 3618 helix: 0.55 (0.14), residues: 1504 sheet: 0.70 (0.19), residues: 674 loop : -0.97 (0.15), residues: 1440 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1016 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 883 time to evaluate : 3.142 Fit side-chains revert: symmetry clash outliers start: 133 outliers final: 68 residues processed: 950 average time/residue: 1.5805 time to fit residues: 1730.2150 Evaluate side-chains 942 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 874 time to evaluate : 3.434 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 36 residues processed: 35 average time/residue: 0.8231 time to fit residues: 41.7642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 290 optimal weight: 1.9990 chunk 198 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 259 optimal weight: 0.9990 chunk 143 optimal weight: 0.7980 chunk 297 optimal weight: 0.8980 chunk 241 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 178 optimal weight: 0.9980 chunk 313 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1207 GLN R 146 GLN R 224 ASN ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 269 ASN R 611 GLN T 205 ASN T 256 ASN U 63 ASN U 272 GLN U 274 ASN U 310 ASN U 407 GLN U 441 GLN U 446 GLN V 205 ASN V 394 GLN X 190 GLN X 256 ASN X 289 ASN X 325 ASN Y 223 GLN ** Y 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 310 ASN Y 441 GLN Y 443 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 29098 Z= 0.268 Angle : 0.576 9.226 39368 Z= 0.286 Chirality : 0.044 0.163 4620 Planarity : 0.004 0.052 5039 Dihedral : 7.926 140.388 4004 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.83 % Allowed : 26.68 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 3618 helix: 0.61 (0.14), residues: 1503 sheet: 0.67 (0.20), residues: 673 loop : -0.94 (0.15), residues: 1442 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1000 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 879 time to evaluate : 3.230 Fit side-chains outliers start: 121 outliers final: 73 residues processed: 937 average time/residue: 1.5921 time to fit residues: 1723.2653 Evaluate side-chains 934 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 861 time to evaluate : 3.092 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 41 residues processed: 35 average time/residue: 0.7538 time to fit residues: 39.4241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 117 optimal weight: 0.7980 chunk 314 optimal weight: 3.9990 chunk 68 optimal weight: 0.0770 chunk 204 optimal weight: 0.0270 chunk 86 optimal weight: 0.6980 chunk 349 optimal weight: 0.9980 chunk 289 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 29 optimal weight: 0.1980 chunk 115 optimal weight: 0.7980 chunk 183 optimal weight: 0.0570 overall best weight: 0.2114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1207 GLN R 146 GLN R 256 ASN R 269 ASN R 611 GLN T 205 ASN T 256 ASN U 63 ASN U 272 GLN U 274 ASN U 310 ASN U 407 GLN U 441 GLN U 446 GLN V 205 ASN X 190 GLN X 256 ASN X 289 ASN X 325 ASN Y 223 GLN Y 310 ASN Y 441 GLN Y 443 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 29098 Z= 0.138 Angle : 0.524 9.903 39368 Z= 0.259 Chirality : 0.042 0.169 4620 Planarity : 0.003 0.061 5039 Dihedral : 7.427 130.812 4004 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.51 % Allowed : 27.44 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.14), residues: 3618 helix: 0.84 (0.14), residues: 1506 sheet: 0.73 (0.20), residues: 683 loop : -0.81 (0.16), residues: 1429 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 989 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 878 time to evaluate : 3.618 Fit side-chains outliers start: 111 outliers final: 68 residues processed: 933 average time/residue: 1.6159 time to fit residues: 1737.6701 Evaluate side-chains 928 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 860 time to evaluate : 3.464 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 42 residues processed: 29 average time/residue: 0.8501 time to fit residues: 36.0435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 336 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 199 optimal weight: 0.9990 chunk 255 optimal weight: 0.9990 chunk 197 optimal weight: 1.9990 chunk 294 optimal weight: 1.9990 chunk 195 optimal weight: 0.0670 chunk 347 optimal weight: 0.8980 chunk 217 optimal weight: 0.9990 chunk 212 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 overall best weight: 0.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1207 GLN R 132 ASN R 146 GLN ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 269 ASN R 611 GLN T 205 ASN T 256 ASN T 289 ASN U 62 GLN U 63 ASN U 272 GLN U 274 ASN U 310 ASN U 407 GLN U 446 GLN V 205 ASN V 314 ASN X 190 GLN X 256 ASN X 289 ASN X 325 ASN Y 23 HIS Y 223 GLN ** Y 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 310 ASN Y 441 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29098 Z= 0.278 Angle : 0.586 9.446 39368 Z= 0.290 Chirality : 0.045 0.166 4620 Planarity : 0.004 0.056 5039 Dihedral : 7.635 131.954 4004 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.70 % Allowed : 27.69 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.14), residues: 3618 helix: 0.77 (0.14), residues: 1506 sheet: 0.75 (0.20), residues: 669 loop : -0.85 (0.16), residues: 1443 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 993 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 876 time to evaluate : 3.255 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 117 outliers final: 77 residues processed: 935 average time/residue: 1.6363 time to fit residues: 1764.7322 Evaluate side-chains 947 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 870 time to evaluate : 3.391 Switching outliers to nearest non-outliers outliers start: 77 outliers final: 46 residues processed: 36 average time/residue: 0.7780 time to fit residues: 41.8911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 215 optimal weight: 0.6980 chunk 138 optimal weight: 0.8980 chunk 207 optimal weight: 0.5980 chunk 104 optimal weight: 0.0270 chunk 68 optimal weight: 0.0370 chunk 67 optimal weight: 5.9990 chunk 221 optimal weight: 1.9990 chunk 237 optimal weight: 0.9980 chunk 172 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 273 optimal weight: 0.9980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1207 GLN R 146 GLN R 224 ASN ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 269 ASN R 611 GLN T 205 ASN T 256 ASN U 63 ASN U 272 GLN U 274 ASN U 310 ASN U 407 GLN U 446 GLN V 205 ASN X 190 GLN X 256 ASN X 289 ASN X 325 ASN Y 23 HIS Y 223 GLN ** Y 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 310 ASN Y 441 GLN Y 443 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29098 Z= 0.185 Angle : 0.551 10.096 39368 Z= 0.272 Chirality : 0.043 0.151 4620 Planarity : 0.003 0.053 5039 Dihedral : 7.518 137.302 4004 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.07 % Allowed : 28.32 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.14), residues: 3618 helix: 0.84 (0.14), residues: 1512 sheet: 0.77 (0.20), residues: 671 loop : -0.82 (0.16), residues: 1435 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 871 time to evaluate : 3.429 Fit side-chains revert: symmetry clash outliers start: 97 outliers final: 61 residues processed: 931 average time/residue: 1.6101 time to fit residues: 1735.1963 Evaluate side-chains 927 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 866 time to evaluate : 3.387 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 42 residues processed: 21 average time/residue: 0.7752 time to fit residues: 26.0166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 316 optimal weight: 2.9990 chunk 333 optimal weight: 2.9990 chunk 304 optimal weight: 0.0670 chunk 324 optimal weight: 1.9990 chunk 195 optimal weight: 0.5980 chunk 141 optimal weight: 2.9990 chunk 254 optimal weight: 0.8980 chunk 99 optimal weight: 0.0570 chunk 292 optimal weight: 0.0020 chunk 306 optimal weight: 0.9990 chunk 323 optimal weight: 0.9980 overall best weight: 0.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1207 GLN R 146 GLN ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 611 GLN S 40 ASN T 205 ASN U 63 ASN U 272 GLN U 274 ASN U 310 ASN U 407 GLN U 446 GLN V 205 ASN W 310 ASN W 443 ASN X 190 GLN X 256 ASN X 289 ASN X 325 ASN Y 47 GLN Y 223 GLN ** Y 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 310 ASN Y 441 GLN Y 443 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29098 Z= 0.163 Angle : 0.544 9.144 39368 Z= 0.269 Chirality : 0.042 0.147 4620 Planarity : 0.003 0.050 5039 Dihedral : 7.328 133.318 4004 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.37 % Allowed : 29.18 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.14), residues: 3618 helix: 0.89 (0.14), residues: 1510 sheet: 0.74 (0.20), residues: 675 loop : -0.80 (0.16), residues: 1433 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 936 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 861 time to evaluate : 3.041 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 62 residues processed: 906 average time/residue: 1.6120 time to fit residues: 1715.6821 Evaluate side-chains 911 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 849 time to evaluate : 3.235 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 42 residues processed: 23 average time/residue: 0.8366 time to fit residues: 29.8103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 212 optimal weight: 1.9990 chunk 342 optimal weight: 0.9980 chunk 209 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 238 optimal weight: 0.5980 chunk 359 optimal weight: 0.8980 chunk 331 optimal weight: 0.9990 chunk 286 optimal weight: 0.9990 chunk 29 optimal weight: 0.2980 chunk 221 optimal weight: 0.6980 chunk 175 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q1204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1207 GLN R 146 GLN ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 611 GLN T 256 ASN T 289 ASN U 62 GLN U 63 ASN U 272 GLN U 274 ASN U 310 ASN U 407 GLN U 446 GLN V 205 ASN X 190 GLN X 256 ASN X 289 ASN X 325 ASN ** Y 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 441 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29098 Z= 0.256 Angle : 0.591 11.434 39368 Z= 0.291 Chirality : 0.044 0.183 4620 Planarity : 0.004 0.068 5039 Dihedral : 7.531 136.198 4004 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.25 % Allowed : 29.49 % Favored : 68.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.14), residues: 3618 helix: 0.77 (0.14), residues: 1511 sheet: 0.74 (0.20), residues: 677 loop : -0.86 (0.16), residues: 1430 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 935 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 864 time to evaluate : 3.047 Fit side-chains outliers start: 71 outliers final: 55 residues processed: 908 average time/residue: 1.6000 time to fit residues: 1681.9427 Evaluate side-chains 913 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 858 time to evaluate : 3.535 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 41 residues processed: 17 average time/residue: 0.5258 time to fit residues: 18.1854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 227 optimal weight: 3.9990 chunk 305 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 264 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 286 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 294 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1097 ASN ** Q1204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1207 GLN R 146 GLN R 177 ASN ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 269 ASN R 611 GLN T 205 ASN T 256 ASN U 63 ASN U 272 GLN U 274 ASN U 310 ASN U 407 GLN U 446 GLN V 205 ASN W 310 ASN X 190 GLN X 256 ASN X 289 ASN X 325 ASN Y 223 GLN ** Y 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 441 GLN Y 443 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.128481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.108335 restraints weight = 39374.454| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.94 r_work: 0.3309 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 29098 Z= 0.396 Angle : 0.665 12.278 39368 Z= 0.329 Chirality : 0.048 0.241 4620 Planarity : 0.004 0.077 5039 Dihedral : 7.936 141.337 4004 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.56 % Allowed : 29.37 % Favored : 68.07 % 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: -0.09 (0.14), residues: 3618 helix: 0.54 (0.14), residues: 1506 sheet: 0.67 (0.20), residues: 669 loop : -0.99 (0.15), residues: 1443 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21282.51 seconds wall clock time: 374 minutes 0.95 seconds (22440.95 seconds total)