Starting phenix.real_space_refine on Thu Dec 14 14:42:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etu_28599/12_2023/8etu_28599_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etu_28599/12_2023/8etu_28599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etu_28599/12_2023/8etu_28599.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etu_28599/12_2023/8etu_28599.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etu_28599/12_2023/8etu_28599_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etu_28599/12_2023/8etu_28599_updated.pdb" } resolution = 2.8 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= 0.020 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 18041 2.51 5 N 4942 2.21 5 O 5580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 192": "OE1" <-> "OE2" Residue "R TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 259": "OE1" <-> "OE2" Residue "R GLU 268": "OE1" <-> "OE2" Residue "R TYR 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 41": "OE1" <-> "OE2" Residue "S ASP 69": "OD1" <-> "OD2" Residue "T GLU 141": "OE1" <-> "OE2" Residue "T ASP 151": "OD1" <-> "OD2" Residue "T TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 351": "OE1" <-> "OE2" Residue "U GLU 33": "OE1" <-> "OE2" Residue "U ASP 95": "OD1" <-> "OD2" Residue "U GLU 110": "OE1" <-> "OE2" Residue "U GLU 134": "OE1" <-> "OE2" Residue "U GLU 226": "OE1" <-> "OE2" Residue "U ASP 261": "OD1" <-> "OD2" Residue "U ASP 271": "OD1" <-> "OD2" Residue "U GLU 279": "OE1" <-> "OE2" Residue "U GLU 282": "OE1" <-> "OE2" Residue "U ASP 315": "OD1" <-> "OD2" Residue "U GLU 316": "OE1" <-> "OE2" Residue "U TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 376": "OE1" <-> "OE2" Residue "U GLU 378": "OE1" <-> "OE2" Residue "U GLU 421": "OE1" <-> "OE2" Residue "U TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 449": "OD1" <-> "OD2" Residue "V GLU 37": "OE1" <-> "OE2" Residue "V GLU 153": "OE1" <-> "OE2" Residue "V ASP 182": "OD1" <-> "OD2" Residue "V GLU 192": "OE1" <-> "OE2" Residue "V TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 228": "OE1" <-> "OE2" Residue "V ASP 253": "OD1" <-> "OD2" Residue "V GLU 302": "OE1" <-> "OE2" Residue "V GLU 441": "OE1" <-> "OE2" Residue "W ASP 218": "OD1" <-> "OD2" Residue "W GLU 226": "OE1" <-> "OE2" Residue "W GLU 228": "OE1" <-> "OE2" Residue "W ASP 302": "OD1" <-> "OD2" Residue "W GLU 374": "OE1" <-> "OE2" Residue "W ASP 382": "OD1" <-> "OD2" Residue "W GLU 393": "OE1" <-> "OE2" Residue "X GLU 37": "OE1" <-> "OE2" Residue "X TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 119": "OE1" <-> "OE2" Residue "X GLU 123": "OE1" <-> "OE2" Residue "X PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 153": "OE1" <-> "OE2" Residue "X TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 227": "OE1" <-> "OE2" Residue "X TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 253": "OD1" <-> "OD2" Residue "X ASP 264": "OD1" <-> "OD2" Residue "X GLU 279": "OE1" <-> "OE2" Residue "X GLU 312": "OE1" <-> "OE2" Residue "X GLU 391": "OE1" <-> "OE2" Residue "Y GLU 33": "OE1" <-> "OE2" Residue "Y GLU 110": "OE1" <-> "OE2" Residue "Y GLU 115": "OE1" <-> "OE2" Residue "Y GLU 182": "OE1" <-> "OE2" Residue "Y ASP 213": "OD1" <-> "OD2" Residue "Y GLU 243": "OE1" <-> "OE2" Residue "Y ASP 261": "OD1" <-> "OD2" Residue "Y GLU 268": "OE1" <-> "OE2" Residue "Y GLU 282": "OE1" <-> "OE2" Residue "Y ASP 302": "OD1" <-> "OD2" Residue "Y PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 346": "OD1" <-> "OD2" Residue "Y GLU 375": "OE1" <-> "OE2" Residue "Y TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 449": "OD1" <-> "OD2" Residue "Q TYR 964": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 1101": "OD1" <-> "OD2" Residue "Q GLU 1173": "OE1" <-> "OE2" Residue "Q TYR 1198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 1222": "OE1" <-> "OE2" Residue "Q GLU 1276": "OE1" <-> "OE2" Residue "Q ASP 1305": "OD1" <-> "OD2" Residue "Q PHE 1322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 1329": "OD1" <-> "OD2" Residue "Q GLU 1333": "OE1" <-> "OE2" Residue "Q ASP 1406": "OD1" <-> "OD2" Residue "Z PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 314": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 28670 Number of models: 1 Model: "" Number of chains: 16 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: 3354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3354 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 425} Chain breaks: 1 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: "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: "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: "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: 14.18, per 1000 atoms: 0.49 Number of scatterers: 28670 At special positions: 0 Unit cell: (132.765, 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 5580 8.00 N 4942 7.00 C 18041 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: 12.00 Conformation dependent library (CDL) restraints added in 5.6 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: 152 helices and 30 sheets defined 38.3% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.34 Creating SS restraints... 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 removed outlier: 4.059A pdb=" N GLU R 156 " --> pdb=" O GLN R 152 " (cutoff:3.500A) 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 263 removed outlier: 3.873A pdb=" N GLU R 262 " --> pdb=" O ASP R 258 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS R 263 " --> pdb=" O GLU R 259 " (cutoff:3.500A) 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 596 Processing helix chain 'R' and resid 608 through 610 No H-bonds generated for 'chain 'R' and resid 608 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: 3.921A 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 628 through 630 No H-bonds generated for 'chain 'R' and resid 628 through 630' Processing helix chain 'R' and resid 638 through 648 Processing helix chain 'R' and resid 659 through 667 removed outlier: 3.544A 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 32 through 39 Processing helix chain 'S' and resid 63 through 82 removed outlier: 4.073A pdb=" N ILE S 67 " --> pdb=" O ALA S 63 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER S 68 " --> pdb=" O ARG S 64 " (cutoff:3.500A) Processing helix chain 'S' and resid 137 through 143 Processing helix chain 'S' and resid 152 through 158 removed outlier: 3.965A pdb=" N LEU S 158 " --> pdb=" O GLU S 154 " (cutoff:3.500A) 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: 3.676A 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: 4.049A pdb=" N ALA T 128 " --> pdb=" O ASN T 124 " (cutoff:3.500A) Processing helix chain 'T' and resid 183 through 192 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 329 removed outlier: 3.763A pdb=" N ASN T 325 " --> pdb=" O PHE T 321 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS T 326 " --> pdb=" O THR T 322 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU T 329 " --> pdb=" O ASN T 325 " (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: 3.755A pdb=" N ASP T 365 " --> pdb=" O PRO T 361 " (cutoff:3.500A) removed outlier: 4.814A 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: 3.569A pdb=" N LEU T 416 " --> pdb=" O LEU T 412 " (cutoff:3.500A) removed outlier: 4.635A 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: 3.938A 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: 3.989A 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 314 removed outlier: 3.582A pdb=" N ARG U 311 " --> pdb=" O SER U 307 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU U 313 " --> pdb=" O ILE U 309 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLU U 314 " --> pdb=" O ASN U 310 " (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 350 removed outlier: 4.096A pdb=" N ARG U 350 " --> pdb=" O ASP U 346 " (cutoff:3.500A) 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 412 removed outlier: 4.583A pdb=" N SER U 404 " --> pdb=" O SER U 400 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL U 405 " --> pdb=" O ASN U 401 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN U 407 " --> pdb=" O ILE U 403 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLN U 408 " --> pdb=" O SER U 404 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE U 409 " --> pdb=" O VAL U 405 " (cutoff:3.500A) Processing helix chain 'U' and resid 420 through 429 Processing helix chain 'U' and resid 433 through 441 Processing helix chain 'V' and resid 52 through 67 Processing helix chain 'V' and resid 86 through 96 Processing helix chain 'V' and resid 107 through 110 removed outlier: 3.877A 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: 3.691A 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 272 removed outlier: 3.548A pdb=" N GLN V 271 " --> pdb=" O SER V 267 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU V 272 " --> pdb=" O MET V 268 " (cutoff:3.500A) 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: 3.727A pdb=" N LYS V 326 " --> pdb=" O THR V 322 " (cutoff:3.500A) removed outlier: 4.325A 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: 3.705A pdb=" N ASP V 365 " --> pdb=" O PRO V 361 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG V 366 " --> pdb=" O ASP V 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 361 through 366' 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 417 Processing helix chain 'V' and resid 419 through 429 removed outlier: 3.705A 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 103 through 105 No H-bonds generated for 'chain 'W' and resid 103 through 105' Processing helix chain 'W' and resid 113 through 124 removed outlier: 4.028A 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: 4.048A pdb=" N PHE W 258 " --> pdb=" O PHE W 254 " (cutoff:3.500A) Processing helix chain 'W' and resid 267 through 283 Processing helix chain 'W' and resid 303 through 314 removed outlier: 3.865A pdb=" N ARG W 311 " --> pdb=" O SER W 307 " (cutoff:3.500A) removed outlier: 4.737A 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: 3.924A pdb=" N ILE W 403 " --> pdb=" O SER W 399 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N SER W 404 " --> pdb=" O SER W 400 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL W 405 " --> pdb=" O ASN W 401 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS W 412 " --> pdb=" O GLN W 408 " (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: 4.011A 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: 3.938A pdb=" N ALA X 128 " --> pdb=" O ASN X 124 " (cutoff:3.500A) Processing helix chain 'X' and resid 183 through 192 removed outlier: 4.186A pdb=" N GLU X 187 " --> pdb=" O THR X 184 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG X 191 " --> pdb=" O SER X 188 " (cutoff:3.500A) removed outlier: 3.799A 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: 4.381A 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: 3.571A pdb=" N ASP X 365 " --> pdb=" O PRO X 361 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG X 366 " --> pdb=" O ASP X 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 361 through 366' 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 50 through 63 Processing helix chain 'Y' and resid 81 through 92 Processing helix chain 'Y' and resid 113 through 124 removed outlier: 4.085A 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 removed outlier: 3.560A pdb=" N SER Y 249 " --> pdb=" O ASP Y 245 " (cutoff:3.500A) 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 311 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: 3.835A pdb=" N SER Y 404 " --> pdb=" O SER Y 400 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN Y 408 " --> pdb=" O SER Y 404 " (cutoff:3.500A) Processing helix chain 'Y' and resid 420 through 429 Processing helix chain 'Y' and resid 433 through 446 removed outlier: 3.701A pdb=" N ASN Y 443 " --> pdb=" O TYR Y 439 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N SER Y 445 " --> pdb=" O GLN Y 441 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N GLN Y 446 " --> pdb=" O GLU Y 442 " (cutoff:3.500A) Processing helix chain 'Q' and resid 958 through 970 Processing helix chain 'Q' and resid 975 through 984 Processing helix chain 'Q' and resid 1000 through 1012 removed outlier: 3.780A pdb=" N GLN Q1006 " --> pdb=" O ASN Q1002 " (cutoff:3.500A) removed outlier: 3.634A 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 1143 Processing helix chain 'Q' and resid 1148 through 1153 Processing helix chain 'Q' and resid 1170 through 1175 Processing helix chain 'Q' and resid 1177 through 1179 No H-bonds generated for 'chain 'Q' and resid 1177 through 1179' 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 1281 through 1283 No H-bonds generated for 'chain 'Q' and resid 1281 through 1283' Processing helix chain 'Q' and resid 1293 through 1297 Processing helix chain 'Q' and resid 1299 through 1314 removed outlier: 4.362A pdb=" N VAL Q1309 " --> pdb=" O ASP Q1305 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LYS Q1310 " --> pdb=" O GLU Q1306 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU Q1311 " --> pdb=" O LEU Q1307 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1326 through 1337 Processing helix chain 'Q' and resid 1357 through 1363 Processing helix chain 'Q' and resid 1398 through 1407 Processing helix chain 'Q' and resid 1428 through 1431 No H-bonds generated for 'chain 'Q' and resid 1428 through 1431' Processing sheet with id= A, first strand: chain 'R' and resid 14 through 16 removed outlier: 3.535A pdb=" N VAL R 14 " --> pdb=" O VAL R 276 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'R' and resid 40 through 44 Processing sheet with id= C, first strand: chain 'R' and resid 67 through 71 Processing sheet with id= D, first strand: chain 'R' and resid 700 through 702 removed outlier: 6.850A pdb=" N VAL R 668 " --> pdb=" O ASN R 701 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU R 185 " --> pdb=" O LEU R 669 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N THR R 671 " --> pdb=" O LEU R 185 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE R 187 " --> pdb=" O THR R 671 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'T' and resid 367 through 372 removed outlier: 7.284A pdb=" N ALA T 74 " --> pdb=" O LEU T 368 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N VAL T 370 " --> pdb=" O ALA T 74 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU T 76 " --> pdb=" O VAL T 370 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N THR T 372 " --> pdb=" O LEU T 76 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA T 78 " --> pdb=" O THR T 372 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL T 336 " --> pdb=" O ILE T 75 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LEU T 77 " --> pdb=" O VAL T 336 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU T 338 " --> pdb=" O LEU T 77 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N GLY T 79 " --> pdb=" O LEU T 338 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N SER T 340 " --> pdb=" O GLY T 79 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'T' and resid 301 through 305 Processing sheet with id= G, first strand: chain 'T' and resid 175 through 181 removed outlier: 3.667A pdb=" N GLY T 175 " --> pdb=" O SER T 172 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N HIS T 165 " --> pdb=" O GLU T 150 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU T 150 " --> pdb=" O HIS T 165 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE T 167 " --> pdb=" O THR T 148 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU T 146 " --> pdb=" O GLY T 169 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LYS T 171 " --> pdb=" O VAL T 144 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N VAL T 144 " --> pdb=" O LYS T 171 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASP T 198 " --> pdb=" O VAL T 144 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N TYR T 201 " --> pdb=" O ARG T 211 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ARG T 211 " --> pdb=" O TYR T 201 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLU T 203 " --> pdb=" O VAL T 209 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL T 209 " --> pdb=" O GLU T 203 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'T' and resid 344 through 346 Processing sheet with id= I, first strand: chain 'U' and resid 351 through 356 removed outlier: 7.054A pdb=" N ALA U 70 " --> pdb=" O ILE U 352 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N ILE U 354 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU U 72 " --> pdb=" O ILE U 354 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N THR U 356 " --> pdb=" O LEU U 72 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA U 74 " --> pdb=" O THR U 356 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL U 321 " --> pdb=" O VAL U 71 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL U 73 " --> pdb=" O VAL U 321 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N MET U 323 " --> pdb=" O VAL U 73 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N GLY U 75 " --> pdb=" O MET U 323 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N THR U 325 " --> pdb=" O GLY U 75 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'U' and resid 287 through 290 Processing sheet with id= K, first strand: chain 'U' and resid 166 through 171 removed outlier: 4.139A pdb=" N GLY U 156 " --> pdb=" O LEU U 171 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LYS U 161 " --> pdb=" O VAL U 140 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N VAL U 140 " --> pdb=" O LYS U 161 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP U 188 " --> pdb=" O VAL U 140 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N SER U 191 " --> pdb=" O LYS U 201 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N LYS U 201 " --> pdb=" O SER U 191 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ASP U 193 " --> pdb=" O ILE U 199 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ILE U 199 " --> pdb=" O ASP U 193 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'U' and resid 329 through 331 Processing sheet with id= M, first strand: chain 'V' and resid 368 through 371 removed outlier: 6.477A pdb=" N VAL V 336 " --> pdb=" O ILE V 75 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LEU V 77 " --> pdb=" O VAL V 336 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU V 338 " --> pdb=" O LEU V 77 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'V' and resid 301 through 305 Processing sheet with id= O, first strand: chain 'V' and resid 175 through 181 removed outlier: 3.700A pdb=" N GLY V 175 " --> pdb=" O SER V 172 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N HIS V 165 " --> pdb=" O GLU V 150 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU V 146 " --> pdb=" O GLY V 169 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LYS V 171 " --> pdb=" O VAL V 144 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N VAL V 144 " --> pdb=" O LYS V 171 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASP V 198 " --> pdb=" O VAL V 144 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TYR V 201 " --> pdb=" O ARG V 211 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ARG V 211 " --> pdb=" O TYR V 201 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N GLU V 203 " --> pdb=" O VAL V 209 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N VAL V 209 " --> pdb=" O GLU V 203 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'V' and resid 344 through 346 Processing sheet with id= Q, first strand: chain 'W' and resid 351 through 356 removed outlier: 6.897A pdb=" N ALA W 70 " --> pdb=" O ILE W 352 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ILE W 354 " --> pdb=" O ALA W 70 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU W 72 " --> pdb=" O ILE W 354 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N THR W 356 " --> pdb=" O LEU W 72 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA W 74 " --> pdb=" O THR W 356 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL W 321 " --> pdb=" O VAL W 71 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N VAL W 73 " --> pdb=" O VAL W 321 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N MET W 323 " --> pdb=" O VAL W 73 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N GLY W 75 " --> pdb=" O MET W 323 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N THR W 325 " --> pdb=" O GLY W 75 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'W' and resid 286 through 290 Processing sheet with id= S, first strand: chain 'W' and resid 166 through 171 removed outlier: 3.831A pdb=" N GLY W 156 " --> pdb=" O LEU W 171 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU W 142 " --> pdb=" O THR W 159 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS W 161 " --> pdb=" O VAL W 140 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N VAL W 140 " --> pdb=" O LYS W 161 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE W 190 " --> pdb=" O GLY W 138 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ASP W 188 " --> pdb=" O VAL W 140 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY W 203 " --> pdb=" O VAL W 189 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N SER W 191 " --> pdb=" O LYS W 201 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N LYS W 201 " --> pdb=" O SER W 191 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ASP W 193 " --> pdb=" O ILE W 199 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ILE W 199 " --> pdb=" O ASP W 193 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'X' and resid 367 through 371 removed outlier: 7.049A pdb=" N ALA X 74 " --> pdb=" O LEU X 368 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N VAL X 370 " --> pdb=" O ALA X 74 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU X 76 " --> pdb=" O VAL X 370 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL X 336 " --> pdb=" O ILE X 75 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N LEU X 77 " --> pdb=" O VAL X 336 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU X 338 " --> pdb=" O LEU X 77 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'X' and resid 301 through 305 removed outlier: 3.536A pdb=" N VAL X 139 " --> pdb=" O LYS X 239 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS X 239 " --> pdb=" O VAL X 139 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'X' and resid 175 through 181 removed outlier: 3.556A pdb=" N GLY X 175 " --> pdb=" O SER X 172 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL X 166 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS X 165 " --> pdb=" O GLU X 150 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU X 146 " --> pdb=" O GLY X 169 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LYS X 171 " --> pdb=" O VAL X 144 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VAL X 144 " --> pdb=" O LYS X 171 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY X 142 " --> pdb=" O ILE X 200 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ASP X 198 " --> pdb=" O VAL X 144 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TYR X 201 " --> pdb=" O ARG X 211 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ARG X 211 " --> pdb=" O TYR X 201 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'X' and resid 344 through 346 Processing sheet with id= X, first strand: chain 'Y' and resid 352 through 355 removed outlier: 3.682A pdb=" N ILE Y 352 " --> pdb=" O ALA Y 70 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'Y' and resid 287 through 290 removed outlier: 3.640A pdb=" N GLU Y 287 " --> pdb=" O LYS Y 128 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'Y' and resid 166 through 171 removed outlier: 3.604A pdb=" N LEU Y 171 " --> pdb=" O GLY Y 156 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY Y 156 " --> pdb=" O LEU Y 171 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU Y 142 " --> pdb=" O THR Y 159 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LYS Y 161 " --> pdb=" O VAL Y 140 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N VAL Y 140 " --> pdb=" O LYS Y 161 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASP Y 188 " --> pdb=" O VAL Y 140 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N SER Y 191 " --> pdb=" O LYS Y 201 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LYS Y 201 " --> pdb=" O SER Y 191 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ASP Y 193 " --> pdb=" O ILE Y 199 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE Y 199 " --> pdb=" O ASP Y 193 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Y' and resid 329 through 331 Processing sheet with id= AB, first strand: chain 'Q' and resid 949 through 954 removed outlier: 6.312A pdb=" N VAL Q1419 " --> pdb=" O ILE Q 950 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL Q 952 " --> pdb=" O VAL Q1419 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ARG Q1421 " --> pdb=" O VAL Q 952 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N CYS Q 954 " --> pdb=" O ARG Q1421 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU Q1423 " --> pdb=" O CYS Q 954 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'Q' and resid 1026 through 1028 Processing sheet with id= AD, first strand: chain 'Q' and resid 1082 through 1084 removed outlier: 6.760A pdb=" N THR Q1220 " --> pdb=" O TYR Q1083 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD 1043 hydrogen bonds defined for protein. 3090 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: 10.13 Time building geometry restraints manager: 12.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9541 1.34 - 1.46: 5841 1.46 - 1.59: 13536 1.59 - 1.71: 18 1.71 - 1.83: 166 Bond restraints: 29102 Sorted by residual: bond pdb=" N TYR Y 212 " pdb=" CA TYR Y 212 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.28e-02 6.10e+03 9.33e+00 bond pdb=" N LEU X 224 " pdb=" CA LEU X 224 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.21e-02 6.83e+03 8.24e+00 bond pdb=" N GLU X 225 " pdb=" CA GLU X 225 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.23e-02 6.61e+03 8.11e+00 bond pdb=" N LEU Q1383 " pdb=" CA LEU Q1383 " ideal model delta sigma weight residual 1.454 1.487 -0.034 1.23e-02 6.61e+03 7.52e+00 bond pdb=" N VAL X 230 " pdb=" CA VAL X 230 " ideal model delta sigma weight residual 1.461 1.491 -0.030 1.23e-02 6.61e+03 5.93e+00 ... (remaining 29097 not shown) Histogram of bond angle deviations from ideal: 88.05 - 97.66: 4 97.66 - 107.28: 914 107.28 - 116.89: 20033 116.89 - 126.51: 18135 126.51 - 136.13: 287 Bond angle restraints: 39373 Sorted by residual: angle pdb=" N ALA Q1386 " pdb=" CA ALA Q1386 " pdb=" C ALA Q1386 " ideal model delta sigma weight residual 108.32 88.05 20.27 1.64e+00 3.72e-01 1.53e+02 angle pdb=" N ALA Q1385 " pdb=" CA ALA Q1385 " pdb=" C ALA Q1385 " ideal model delta sigma weight residual 108.63 89.86 18.77 1.60e+00 3.91e-01 1.38e+02 angle pdb=" N ALA Q1386 " pdb=" CA ALA Q1386 " pdb=" CB ALA Q1386 " ideal model delta sigma weight residual 110.57 128.70 -18.13 1.69e+00 3.50e-01 1.15e+02 angle pdb=" N TYR T 462 " pdb=" CA TYR T 462 " pdb=" C TYR T 462 " ideal model delta sigma weight residual 111.39 124.25 -12.86 1.38e+00 5.25e-01 8.69e+01 angle pdb=" CA MET R 714 " pdb=" CB MET R 714 " pdb=" CG MET R 714 " ideal model delta sigma weight residual 114.10 125.57 -11.47 2.00e+00 2.50e-01 3.29e+01 ... (remaining 39368 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 17190 35.78 - 71.56: 636 71.56 - 107.33: 47 107.33 - 143.11: 3 143.11 - 178.89: 4 Dihedral angle restraints: 17880 sinusoidal: 7318 harmonic: 10562 Sorted by residual: 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 -60.00 118.89 -178.89 1 2.00e+01 2.50e-03 4.80e+01 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 300.00 137.99 162.01 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" O2A ADP T 501 " pdb=" O3A ADP T 501 " pdb=" PA ADP T 501 " pdb=" PB ADP T 501 " ideal model delta sinusoidal sigma weight residual -60.00 93.12 -153.12 1 2.00e+01 2.50e-03 4.54e+01 ... (remaining 17877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 4478 0.117 - 0.234: 138 0.234 - 0.351: 2 0.351 - 0.469: 0 0.469 - 0.586: 2 Chirality restraints: 4620 Sorted by residual: chirality pdb=" CA ALA Q1385 " pdb=" N ALA Q1385 " pdb=" C ALA Q1385 " pdb=" CB ALA Q1385 " both_signs ideal model delta sigma weight residual False 2.48 3.07 -0.59 2.00e-01 2.50e+01 8.58e+00 chirality pdb=" CA TYR T 462 " pdb=" N TYR T 462 " pdb=" C TYR T 462 " pdb=" CB TYR T 462 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.99e+00 chirality pdb=" CB VAL Q1152 " pdb=" CA VAL Q1152 " pdb=" CG1 VAL Q1152 " pdb=" CG2 VAL Q1152 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 4617 not shown) Planarity restraints: 5040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE X 222 " 0.025 2.00e-02 2.50e+03 5.05e-02 2.55e+01 pdb=" C PHE X 222 " -0.087 2.00e-02 2.50e+03 pdb=" O PHE X 222 " 0.033 2.00e-02 2.50e+03 pdb=" N ASP X 223 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA S 148 " -0.069 5.00e-02 4.00e+02 1.05e-01 1.75e+01 pdb=" N PRO S 149 " 0.181 5.00e-02 4.00e+02 pdb=" CA PRO S 149 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO S 149 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP S 69 " -0.015 2.00e-02 2.50e+03 3.13e-02 9.77e+00 pdb=" CG ASP S 69 " 0.054 2.00e-02 2.50e+03 pdb=" OD1 ASP S 69 " -0.020 2.00e-02 2.50e+03 pdb=" OD2 ASP S 69 " -0.019 2.00e-02 2.50e+03 ... (remaining 5037 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.24: 9 2.24 - 2.91: 11150 2.91 - 3.57: 39187 3.57 - 4.24: 64764 4.24 - 4.90: 111970 Nonbonded interactions: 227080 Sorted by model distance: nonbonded pdb=" CE1 TYR W 212 " pdb=" NH2 ARG X 180 " model vdw 1.580 3.420 nonbonded pdb=" CH2 TRP Q1361 " pdb=" O ALA Q1385 " model vdw 1.735 3.340 nonbonded pdb=" O ARG V 413 " pdb=" OE1 GLN V 417 " model vdw 1.834 3.040 nonbonded pdb=" CZ2 TRP Q1361 " pdb=" O ALA Q1385 " model vdw 1.856 3.340 nonbonded pdb=" CD1 ILE W 303 " pdb=" CG2 THR W 335 " model vdw 2.152 3.880 ... (remaining 227075 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 210 or resid 221 through 459 or resid 501)) selection = (chain 'Y' and (resid 18 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: 6.790 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: 0.040 Extract box with map and model: 23.260 Check model and map are aligned: 0.440 Set scattering table: 0.280 Process input model: 74.990 Find NCS groups from input model: 2.450 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:14.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 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 0.062 29102 Z= 0.321 Angle : 0.921 20.273 39373 Z= 0.481 Chirality : 0.052 0.586 4620 Planarity : 0.006 0.105 5040 Dihedral : 17.824 178.892 11060 Min Nonbonded Distance : 1.580 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.06 % Allowed : 26.13 % Favored : 73.81 % 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: -1.69 (0.12), residues: 3618 helix: -1.44 (0.11), residues: 1475 sheet: 0.58 (0.20), residues: 672 loop : -1.46 (0.15), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP Q1361 HIS 0.022 0.001 HIS U 153 PHE 0.035 0.002 PHE S 32 TYR 0.022 0.002 TYR V 462 ARG 0.010 0.001 ARG Q1431 *********************** 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 943 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 941 time to evaluate : 3.529 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 outliers start: 2 outliers final: 1 residues processed: 941 average time/residue: 1.6447 time to fit residues: 1769.3476 Evaluate side-chains 802 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 801 time to evaluate : 3.281 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 4.5187 ------------------------------------------------------------------------------- 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: 0.0870 chunk 273 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 282 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 210 optimal weight: 0.2980 chunk 327 optimal weight: 1.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 146 GLN ** R 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 633 GLN R 697 ASN S 162 ASN T 29 HIS T 205 ASN U 36 GLN U 144 GLN U 237 HIS U 272 GLN U 441 GLN U 446 GLN U 455 GLN V 51 GLN V 263 GLN V 331 ASN V 394 GLN V 417 GLN W 144 GLN W 155 GLN W 173 ASN X 51 GLN X 271 GLN X 314 ASN X 325 ASN Y 230 GLN Y 248 ASN Y 310 ASN Q1211 HIS Q1244 GLN Q1316 HIS Q1403 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29102 Z= 0.269 Angle : 0.623 8.354 39373 Z= 0.310 Chirality : 0.045 0.171 4620 Planarity : 0.004 0.071 5040 Dihedral : 7.595 139.352 4004 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.80 % Allowed : 26.76 % Favored : 69.44 % 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: -0.60 (0.13), residues: 3618 helix: -0.03 (0.13), residues: 1486 sheet: 0.57 (0.20), residues: 659 loop : -1.16 (0.15), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP Q1361 HIS 0.006 0.001 HIS Q1211 PHE 0.023 0.001 PHE R 691 TYR 0.024 0.002 TYR R 724 ARG 0.010 0.001 ARG V 371 *********************** 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 931 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 811 time to evaluate : 3.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 120 outliers final: 34 residues processed: 866 average time/residue: 1.7105 time to fit residues: 1693.9312 Evaluate side-chains 827 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 793 time to evaluate : 3.405 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 19 residues processed: 16 average time/residue: 0.6402 time to fit residues: 18.6030 ------------------------------------------------------------------------------- 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: 0.8980 chunk 101 optimal weight: 2.9990 chunk 272 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 90 optimal weight: 0.0980 chunk 328 optimal weight: 0.9980 chunk 354 optimal weight: 0.0770 chunk 292 optimal weight: 0.7980 chunk 325 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 263 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 611 GLN ** R 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 633 GLN R 697 ASN R 749 ASN T 205 ASN T 331 ASN U 144 GLN U 237 HIS V 263 GLN V 394 GLN V 417 GLN W 173 ASN W 360 ASN ** W 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 271 GLN X 289 ASN X 325 ASN Y 49 GLN Y 230 GLN Y 310 ASN Y 373 GLN Q1244 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29102 Z= 0.209 Angle : 0.584 11.502 39373 Z= 0.287 Chirality : 0.043 0.153 4620 Planarity : 0.004 0.057 5040 Dihedral : 7.074 137.176 4004 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.11 % Allowed : 27.78 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.14), residues: 3618 helix: 0.54 (0.14), residues: 1486 sheet: 0.52 (0.20), residues: 653 loop : -1.01 (0.15), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q1361 HIS 0.008 0.001 HIS T 165 PHE 0.022 0.001 PHE R 691 TYR 0.019 0.001 TYR X 323 ARG 0.010 0.000 ARG T 431 *********************** 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 935 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 805 time to evaluate : 3.367 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 outliers start: 130 outliers final: 56 residues processed: 865 average time/residue: 1.6865 time to fit residues: 1667.3221 Evaluate side-chains 842 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 786 time to evaluate : 3.485 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 28 residues processed: 31 average time/residue: 0.7214 time to fit residues: 34.8950 ------------------------------------------------------------------------------- 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: 0.3980 chunk 246 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 220 optimal weight: 0.6980 chunk 329 optimal weight: 0.0980 chunk 348 optimal weight: 4.9990 chunk 172 optimal weight: 0.3980 chunk 312 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 107 ASN R 146 GLN ** R 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 633 GLN R 697 ASN S 141 GLN T 205 ASN U 144 GLN U 237 HIS V 263 GLN ** V 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 417 GLN W 47 GLN W 173 ASN ** W 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 271 GLN X 289 ASN X 325 ASN Y 49 GLN Y 310 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29102 Z= 0.191 Angle : 0.572 11.195 39373 Z= 0.279 Chirality : 0.042 0.149 4620 Planarity : 0.003 0.057 5040 Dihedral : 6.767 135.025 4004 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.83 % Allowed : 28.95 % Favored : 67.23 % 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: 0.05 (0.14), residues: 3618 helix: 0.80 (0.14), residues: 1494 sheet: 0.49 (0.20), residues: 659 loop : -0.92 (0.16), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Y 280 HIS 0.005 0.001 HIS V 165 PHE 0.021 0.001 PHE R 691 TYR 0.028 0.001 TYR R 724 ARG 0.007 0.000 ARG W 204 *********************** 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 916 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 795 time to evaluate : 3.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 121 outliers final: 55 residues processed: 859 average time/residue: 1.7090 time to fit residues: 1688.4344 Evaluate side-chains 838 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 783 time to evaluate : 3.324 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 31 residues processed: 29 average time/residue: 0.8335 time to fit residues: 35.6817 ------------------------------------------------------------------------------- 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: 2.9990 chunk 198 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 259 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 297 optimal weight: 1.9990 chunk 241 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 178 optimal weight: 1.9990 chunk 313 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 633 GLN R 697 ASN T 205 ASN ** T 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 144 GLN V 263 GLN V 314 ASN ** V 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 417 GLN W 173 ASN X 271 GLN X 289 ASN X 325 ASN Y 49 GLN Y 310 ASN Y 373 GLN Q1244 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 29102 Z= 0.338 Angle : 0.629 11.134 39373 Z= 0.310 Chirality : 0.045 0.193 4620 Planarity : 0.004 0.056 5040 Dihedral : 6.876 133.495 4004 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.08 % Allowed : 28.76 % Favored : 67.16 % 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: -0.02 (0.14), residues: 3618 helix: 0.73 (0.14), residues: 1508 sheet: 0.50 (0.20), residues: 662 loop : -0.99 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP Y 280 HIS 0.005 0.001 HIS V 165 PHE 0.022 0.002 PHE R 691 TYR 0.021 0.002 TYR R 724 ARG 0.007 0.000 ARG W 204 *********************** 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 934 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 805 time to evaluate : 3.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 129 outliers final: 69 residues processed: 865 average time/residue: 1.6983 time to fit residues: 1688.4869 Evaluate side-chains 860 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 791 time to evaluate : 3.360 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 38 residues processed: 35 average time/residue: 0.8127 time to fit residues: 42.1873 ------------------------------------------------------------------------------- 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: 2.9990 chunk 314 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 349 optimal weight: 4.9990 chunk 289 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 115 optimal weight: 0.5980 chunk 183 optimal weight: 0.6980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 65 ASN ** R 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 610 HIS R 633 GLN R 697 ASN S 141 GLN T 205 ASN ** T 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 144 GLN U 310 ASN V 51 GLN V 263 GLN V 394 GLN V 417 GLN W 173 ASN X 256 ASN X 271 GLN X 289 ASN X 325 ASN Y 310 ASN Y 373 GLN Q1244 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 29102 Z= 0.377 Angle : 0.651 10.210 39373 Z= 0.322 Chirality : 0.047 0.244 4620 Planarity : 0.004 0.057 5040 Dihedral : 6.937 131.569 4004 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.99 % Allowed : 29.55 % Favored : 66.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.14), residues: 3618 helix: 0.66 (0.14), residues: 1507 sheet: 0.52 (0.19), residues: 666 loop : -1.04 (0.16), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP Y 280 HIS 0.006 0.001 HIS T 250 PHE 0.023 0.002 PHE R 691 TYR 0.023 0.002 TYR V 462 ARG 0.007 0.000 ARG T 371 *********************** 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 934 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 808 time to evaluate : 3.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 126 outliers final: 72 residues processed: 875 average time/residue: 1.7005 time to fit residues: 1702.4711 Evaluate side-chains 865 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 793 time to evaluate : 3.682 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 46 residues processed: 29 average time/residue: 0.7399 time to fit residues: 33.0880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.737 > 50: distance: 107 - 111: 9.334 distance: 111 - 112: 6.326 distance: 112 - 113: 14.085 distance: 112 - 115: 4.477 distance: 113 - 114: 8.520 distance: 113 - 122: 13.785 distance: 115 - 116: 9.020 distance: 116 - 117: 7.388 distance: 116 - 118: 8.226 distance: 117 - 119: 6.782 distance: 118 - 120: 3.518 distance: 119 - 121: 4.543 distance: 120 - 121: 5.074 distance: 122 - 123: 24.725 distance: 123 - 124: 6.571 distance: 123 - 126: 26.828 distance: 124 - 125: 37.759 distance: 124 - 128: 18.379 distance: 126 - 127: 15.544 distance: 128 - 129: 14.431 distance: 129 - 130: 26.689 distance: 129 - 132: 19.718 distance: 130 - 131: 33.781 distance: 130 - 134: 15.191 distance: 132 - 133: 15.906 distance: 134 - 135: 25.343 distance: 135 - 136: 20.522 distance: 135 - 138: 22.748 distance: 136 - 137: 24.104 distance: 136 - 142: 19.644 distance: 138 - 139: 11.168 distance: 139 - 140: 13.549 distance: 139 - 141: 8.669 distance: 142 - 143: 22.523 distance: 143 - 144: 24.553 distance: 143 - 146: 7.275 distance: 144 - 145: 28.526 distance: 144 - 150: 29.024 distance: 146 - 147: 7.327 distance: 146 - 148: 6.200 distance: 147 - 149: 5.489 distance: 150 - 151: 15.689 distance: 151 - 152: 28.605 distance: 151 - 154: 8.853 distance: 152 - 153: 26.241 distance: 152 - 156: 3.915 distance: 154 - 155: 8.719 distance: 156 - 157: 9.545 distance: 157 - 158: 31.656 distance: 157 - 160: 39.157 distance: 158 - 159: 42.798 distance: 158 - 164: 46.252 distance: 160 - 161: 16.733 distance: 161 - 162: 15.438 distance: 162 - 163: 4.289 distance: 164 - 165: 37.960 distance: 164 - 170: 35.847 distance: 165 - 166: 34.685 distance: 165 - 168: 37.358 distance: 166 - 167: 23.224 distance: 166 - 171: 13.489 distance: 168 - 169: 17.686 distance: 169 - 170: 50.899 distance: 171 - 172: 7.888 distance: 172 - 173: 14.548 distance: 172 - 175: 13.939 distance: 173 - 174: 36.458 distance: 173 - 177: 19.386 distance: 175 - 176: 9.180 distance: 177 - 178: 11.570 distance: 178 - 179: 12.102 distance: 178 - 181: 17.081 distance: 179 - 180: 32.849 distance: 179 - 185: 10.163 distance: 181 - 182: 28.090 distance: 182 - 183: 7.469 distance: 183 - 184: 3.962