Starting phenix.real_space_refine on Sat Mar 16 10:34:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evb_28625/03_2024/8evb_28625_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evb_28625/03_2024/8evb_28625.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evb_28625/03_2024/8evb_28625_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evb_28625/03_2024/8evb_28625_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evb_28625/03_2024/8evb_28625_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evb_28625/03_2024/8evb_28625.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evb_28625/03_2024/8evb_28625.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evb_28625/03_2024/8evb_28625_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evb_28625/03_2024/8evb_28625_neut_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 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 4 5.49 5 S 65 5.16 5 C 9427 2.51 5 N 2354 2.21 5 O 2606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 170": "NH1" <-> "NH2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ASP 193": "OD1" <-> "OD2" Residue "A ARG 221": "NH1" <-> "NH2" Residue "A PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 410": "NH1" <-> "NH2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 432": "OD1" <-> "OD2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A GLU 455": "OE1" <-> "OE2" Residue "A ARG 481": "NH1" <-> "NH2" Residue "A GLU 487": "OE1" <-> "OE2" Residue "A ARG 499": "NH1" <-> "NH2" Residue "A PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 549": "OE1" <-> "OE2" Residue "A ARG 563": "NH1" <-> "NH2" Residue "A ASP 575": "OD1" <-> "OD2" Residue "A TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 600": "OE1" <-> "OE2" Residue "B TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 170": "NH1" <-> "NH2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 211": "OD1" <-> "OD2" Residue "B ARG 221": "NH1" <-> "NH2" Residue "B GLU 228": "OE1" <-> "OE2" Residue "B ARG 238": "NH1" <-> "NH2" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 347": "NH1" <-> "NH2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 410": "NH1" <-> "NH2" Residue "B GLU 412": "OE1" <-> "OE2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 439": "NH1" <-> "NH2" Residue "B ASP 475": "OD1" <-> "OD2" Residue "B ARG 499": "NH1" <-> "NH2" Residue "B ASP 533": "OD1" <-> "OD2" Residue "B TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 569": "NH1" <-> "NH2" Residue "B TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 582": "OD1" <-> "OD2" Residue "B ASP 583": "OD1" <-> "OD2" Residue "B GLU 586": "OE1" <-> "OE2" Residue "B GLU 599": "OE1" <-> "OE2" Residue "B ARG 603": "NH1" <-> "NH2" Residue "C ASP 162": "OD1" <-> "OD2" Residue "C TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 198": "OE1" <-> "OE2" Residue "C ASP 207": "OD1" <-> "OD2" Residue "C ASP 211": "OD1" <-> "OD2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "C PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 228": "OE1" <-> "OE2" Residue "C ASP 235": "OD1" <-> "OD2" Residue "C ARG 238": "NH1" <-> "NH2" Residue "C PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 347": "NH1" <-> "NH2" Residue "C GLU 377": "OE1" <-> "OE2" Residue "C PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 439": "NH1" <-> "NH2" Residue "C ASP 462": "OD1" <-> "OD2" Residue "C ASP 475": "OD1" <-> "OD2" Residue "C GLU 493": "OE1" <-> "OE2" Residue "C ARG 499": "NH1" <-> "NH2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 514": "OD1" <-> "OD2" Residue "C PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 563": "NH1" <-> "NH2" Residue "C TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 582": "OD1" <-> "OD2" Residue "C GLU 600": "OE1" <-> "OE2" Residue "C ARG 603": "NH1" <-> "NH2" Residue "D TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 215": "OD1" <-> "OD2" Residue "D TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "D ARG 279": "NH1" <-> "NH2" Residue "D ASP 282": "OD1" <-> "OD2" Residue "D ARG 291": "NH1" <-> "NH2" Residue "D ARG 295": "NH1" <-> "NH2" Residue "D PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 324": "NH1" <-> "NH2" Residue "D GLU 336": "OE1" <-> "OE2" Residue "D PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 352": "NH1" <-> "NH2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "D PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 384": "NH1" <-> "NH2" Residue "D ARG 396": "NH1" <-> "NH2" Residue "D ARG 403": "NH1" <-> "NH2" Residue "D GLU 413": "OE1" <-> "OE2" Residue "D PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 460": "OD1" <-> "OD2" Residue "D TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 480": "NH1" <-> "NH2" Residue "D ARG 491": "NH1" <-> "NH2" Residue "D ASP 494": "OD1" <-> "OD2" Residue "D GLU 495": "OE1" <-> "OE2" Residue "D ASP 513": "OD1" <-> "OD2" Residue "D PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 523": "OD1" <-> "OD2" Residue "D ARG 539": "NH1" <-> "NH2" Residue "D GLU 556": "OE1" <-> "OE2" Residue "D GLU 560": "OE1" <-> "OE2" Residue "D ASP 576": "OD1" <-> "OD2" Residue "D PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 643": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14456 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3629 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 444, 3618 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 13, 'TRANS': 430} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 444, 3618 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 13, 'TRANS': 430} Chain breaks: 1 bond proxies already assigned to first conformer: 3686 Chain: "B" Number of atoms: 3532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3532 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 13, 'TRANS': 418} Chain breaks: 3 Chain: "C" Number of atoms: 3576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3576 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 14, 'TRANS': 423} Chain breaks: 1 Chain: "D" Number of atoms: 3585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3585 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 13, 'TRANS': 423} Chain breaks: 1 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE A 392 " occ=0.60 ... (20 atoms not shown) pdb=" CZ BPHE A 392 " occ=0.40 Time building chain proxies: 9.27, per 1000 atoms: 0.64 Number of scatterers: 14456 At special positions: 0 Unit cell: (103.75, 110.39, 125.33, 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 65 16.00 P 4 15.00 O 2606 8.00 N 2354 7.00 C 9427 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 801 " - " ASN A 339 " " NAG B 801 " - " ASN B 339 " " NAG C 801 " - " ASN C 339 " Time building additional restraints: 4.71 Conformation dependent library (CDL) restraints added in 3.2 seconds 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3322 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 70 helices and 9 sheets defined 57.7% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.72 Creating SS restraints... Processing helix chain 'A' and resid 166 through 191 Proline residue: A 178 - end of helix removed outlier: 5.431A pdb=" N ILE A 187 " --> pdb=" O TRP A 183 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N CYS A 188 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 Processing helix chain 'A' and resid 201 through 221 Processing helix chain 'A' and resid 236 through 244 Processing helix chain 'A' and resid 247 through 255 Processing helix chain 'A' and resid 274 through 278 removed outlier: 3.773A pdb=" N ARG A 277 " --> pdb=" O ARG A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 294 Processing helix chain 'A' and resid 298 through 328 Processing helix chain 'A' and resid 348 through 363 Processing helix chain 'A' and resid 375 through 405 Processing helix chain 'A' and resid 410 through 427 Processing helix chain 'A' and resid 431 through 446 Processing helix chain 'A' and resid 453 through 456 No H-bonds generated for 'chain 'A' and resid 453 through 456' Processing helix chain 'A' and resid 462 through 472 Processing helix chain 'A' and resid 474 through 477 No H-bonds generated for 'chain 'A' and resid 474 through 477' Processing helix chain 'A' and resid 488 through 496 Processing helix chain 'A' and resid 549 through 552 No H-bonds generated for 'chain 'A' and resid 549 through 552' Processing helix chain 'A' and resid 581 through 587 Processing helix chain 'A' and resid 593 through 608 Processing helix chain 'B' and resid 166 through 192 Proline residue: B 178 - end of helix Processing helix chain 'B' and resid 195 through 198 No H-bonds generated for 'chain 'B' and resid 195 through 198' Processing helix chain 'B' and resid 200 through 222 Processing helix chain 'B' and resid 236 through 244 Processing helix chain 'B' and resid 247 through 255 Processing helix chain 'B' and resid 271 through 278 removed outlier: 4.129A pdb=" N LEU B 278 " --> pdb=" O ARG B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 294 Processing helix chain 'B' and resid 298 through 328 Processing helix chain 'B' and resid 344 through 346 No H-bonds generated for 'chain 'B' and resid 344 through 346' Processing helix chain 'B' and resid 348 through 363 Processing helix chain 'B' and resid 375 through 404 removed outlier: 3.577A pdb=" N VAL B 399 " --> pdb=" O ILE B 395 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLY B 400 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 427 Processing helix chain 'B' and resid 431 through 446 Processing helix chain 'B' and resid 453 through 456 No H-bonds generated for 'chain 'B' and resid 453 through 456' Processing helix chain 'B' and resid 462 through 476 Processing helix chain 'B' and resid 581 through 586 Processing helix chain 'B' and resid 592 through 609 Processing helix chain 'C' and resid 166 through 192 removed outlier: 3.896A pdb=" N LEU C 177 " --> pdb=" O THR C 173 " (cutoff:3.500A) Proline residue: C 178 - end of helix removed outlier: 3.818A pdb=" N CYS C 191 " --> pdb=" O ILE C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 221 Processing helix chain 'C' and resid 236 through 245 Processing helix chain 'C' and resid 247 through 254 Processing helix chain 'C' and resid 272 through 277 Processing helix chain 'C' and resid 282 through 294 Processing helix chain 'C' and resid 298 through 328 Processing helix chain 'C' and resid 348 through 363 Processing helix chain 'C' and resid 375 through 406 Processing helix chain 'C' and resid 408 through 427 Processing helix chain 'C' and resid 431 through 446 Processing helix chain 'C' and resid 454 through 457 No H-bonds generated for 'chain 'C' and resid 454 through 457' Processing helix chain 'C' and resid 462 through 477 removed outlier: 4.595A pdb=" N ASN C 471 " --> pdb=" O GLU C 467 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N VAL C 472 " --> pdb=" O ILE C 468 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N HIS C 473 " --> pdb=" O ALA C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 495 Processing helix chain 'C' and resid 581 through 586 Processing helix chain 'C' and resid 593 through 606 Processing helix chain 'D' and resid 216 through 241 removed outlier: 4.069A pdb=" N ASN D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Proline residue: D 237 - end of helix Processing helix chain 'D' and resid 250 through 270 Processing helix chain 'D' and resid 272 through 274 No H-bonds generated for 'chain 'D' and resid 272 through 274' Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 299 through 306 Processing helix chain 'D' and resid 311 through 314 No H-bonds generated for 'chain 'D' and resid 311 through 314' Processing helix chain 'D' and resid 321 through 324 No H-bonds generated for 'chain 'D' and resid 321 through 324' Processing helix chain 'D' and resid 331 through 344 Processing helix chain 'D' and resid 349 through 378 removed outlier: 3.625A pdb=" N VAL D 353 " --> pdb=" O TYR D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 405 Processing helix chain 'D' and resid 417 through 448 removed outlier: 3.756A pdb=" N GLY D 439 " --> pdb=" O SER D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 468 Processing helix chain 'D' and resid 473 through 490 Processing helix chain 'D' and resid 496 through 499 No H-bonds generated for 'chain 'D' and resid 496 through 499' Processing helix chain 'D' and resid 504 through 521 removed outlier: 3.507A pdb=" N SER D 517 " --> pdb=" O ASP D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 538 Processing helix chain 'D' and resid 621 through 628 Processing helix chain 'D' and resid 632 through 644 Processing sheet with id= A, first strand: chain 'A' and resid 499 through 503 removed outlier: 3.530A pdb=" N ARG A 499 " --> pdb=" O CYS A 578 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 574 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 521 " --> pdb=" O PHE A 577 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 527 through 530 removed outlier: 3.524A pdb=" N LEU A 527 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL A 539 " --> pdb=" O VAL A 529 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 499 through 503 removed outlier: 4.153A pdb=" N ASP B 575 " --> pdb=" O ASN B 523 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN B 523 " --> pdb=" O ASP B 575 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 528 through 530 removed outlier: 3.824A pdb=" N ALA B 528 " --> pdb=" O ARG B 569 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG B 569 " --> pdb=" O ALA B 528 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN B 567 " --> pdb=" O VAL B 530 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 501 through 503 Processing sheet with id= F, first strand: chain 'C' and resid 567 through 570 removed outlier: 3.996A pdb=" N ASN C 567 " --> pdb=" O VAL C 530 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL C 539 " --> pdb=" O VAL C 529 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 277 through 279 removed outlier: 4.117A pdb=" N PHE D 277 " --> pdb=" O ILE D 284 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 541 through 545 removed outlier: 3.810A pdb=" N LYS D 541 " --> pdb=" O THR D 618 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 569 through 572 759 hydrogen bonds defined for protein. 2248 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: 4.05 Time building geometry restraints manager: 5.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2294 1.32 - 1.44: 4170 1.44 - 1.57: 8234 1.57 - 1.70: 0 1.70 - 1.83: 104 Bond restraints: 14802 Sorted by residual: bond pdb=" C2' PCG A 802 " pdb=" C3' PCG A 802 " ideal model delta sigma weight residual 1.200 1.569 -0.369 2.00e-02 2.50e+03 3.40e+02 bond pdb=" C2' PCG B 802 " pdb=" C3' PCG B 802 " ideal model delta sigma weight residual 1.200 1.569 -0.369 2.00e-02 2.50e+03 3.40e+02 bond pdb=" C2' PCG D 901 " pdb=" C3' PCG D 901 " ideal model delta sigma weight residual 1.200 1.568 -0.368 2.00e-02 2.50e+03 3.39e+02 bond pdb=" C2' PCG C 802 " pdb=" C3' PCG C 802 " ideal model delta sigma weight residual 1.200 1.568 -0.368 2.00e-02 2.50e+03 3.38e+02 bond pdb=" C3' PCG B 802 " pdb=" C4' PCG B 802 " ideal model delta sigma weight residual 1.808 1.532 0.276 2.00e-02 2.50e+03 1.91e+02 ... (remaining 14797 not shown) Histogram of bond angle deviations from ideal: 97.94 - 105.94: 304 105.94 - 113.94: 8260 113.94 - 121.93: 8832 121.93 - 129.93: 2591 129.93 - 137.93: 101 Bond angle restraints: 20088 Sorted by residual: angle pdb=" C GLN D 272 " pdb=" N PRO D 273 " pdb=" CA PRO D 273 " ideal model delta sigma weight residual 121.65 114.66 6.99 1.01e+00 9.80e-01 4.79e+01 angle pdb=" N MET B 300 " pdb=" CA MET B 300 " pdb=" C MET B 300 " ideal model delta sigma weight residual 111.07 105.04 6.03 1.07e+00 8.73e-01 3.18e+01 angle pdb=" C3' PCG D 901 " pdb=" C4' PCG D 901 " pdb=" C5' PCG D 901 " ideal model delta sigma weight residual 112.23 128.17 -15.94 3.00e+00 1.11e-01 2.82e+01 angle pdb=" C3' PCG C 802 " pdb=" C4' PCG C 802 " pdb=" C5' PCG C 802 " ideal model delta sigma weight residual 112.23 128.11 -15.88 3.00e+00 1.11e-01 2.80e+01 angle pdb=" C3' PCG A 802 " pdb=" C4' PCG A 802 " pdb=" C5' PCG A 802 " ideal model delta sigma weight residual 112.23 128.10 -15.87 3.00e+00 1.11e-01 2.80e+01 ... (remaining 20083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 7580 17.37 - 34.73: 962 34.73 - 52.10: 195 52.10 - 69.46: 23 69.46 - 86.83: 11 Dihedral angle restraints: 8771 sinusoidal: 3605 harmonic: 5166 Sorted by residual: dihedral pdb=" CA VAL C 480 " pdb=" C VAL C 480 " pdb=" N ARG C 481 " pdb=" CA ARG C 481 " ideal model delta harmonic sigma weight residual 180.00 -152.41 -27.59 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA GLY B 544 " pdb=" C GLY B 544 " pdb=" N SER B 545 " pdb=" CA SER B 545 " ideal model delta harmonic sigma weight residual -180.00 -155.57 -24.43 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA ALA A 469 " pdb=" C ALA A 469 " pdb=" N ILE A 470 " pdb=" CA ILE A 470 " ideal model delta harmonic sigma weight residual 180.00 156.66 23.34 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 8768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.336: 2270 0.336 - 0.673: 9 0.673 - 1.009: 0 1.009 - 1.345: 0 1.345 - 1.681: 4 Chirality restraints: 2283 Sorted by residual: chirality pdb=" C4' PCG A 802 " pdb=" C3' PCG A 802 " pdb=" C5' PCG A 802 " pdb=" O4' PCG A 802 " both_signs ideal model delta sigma weight residual False -2.40 -0.72 -1.68 2.00e-01 2.50e+01 7.07e+01 chirality pdb=" C4' PCG C 802 " pdb=" C3' PCG C 802 " pdb=" C5' PCG C 802 " pdb=" O4' PCG C 802 " both_signs ideal model delta sigma weight residual False -2.40 -0.72 -1.68 2.00e-01 2.50e+01 7.06e+01 chirality pdb=" C4' PCG D 901 " pdb=" C3' PCG D 901 " pdb=" C5' PCG D 901 " pdb=" O4' PCG D 901 " both_signs ideal model delta sigma weight residual False -2.40 -0.72 -1.68 2.00e-01 2.50e+01 7.05e+01 ... (remaining 2280 not shown) Planarity restraints: 2468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D 406 " 0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C ILE D 406 " -0.060 2.00e-02 2.50e+03 pdb=" O ILE D 406 " 0.023 2.00e-02 2.50e+03 pdb=" N THR D 407 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 609 " 0.016 2.00e-02 2.50e+03 3.29e-02 1.09e+01 pdb=" CG ASP A 609 " -0.057 2.00e-02 2.50e+03 pdb=" OD1 ASP A 609 " 0.020 2.00e-02 2.50e+03 pdb=" OD2 ASP A 609 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 182 " -0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C ASN C 182 " 0.056 2.00e-02 2.50e+03 pdb=" O ASN C 182 " -0.021 2.00e-02 2.50e+03 pdb=" N TRP C 183 " -0.019 2.00e-02 2.50e+03 ... (remaining 2465 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 290 2.67 - 3.23: 12989 3.23 - 3.79: 23869 3.79 - 4.34: 29372 4.34 - 4.90: 47899 Nonbonded interactions: 114419 Sorted by model distance: nonbonded pdb=" O LEU C 278 " pdb=" CD1 LEU C 278 " model vdw 2.116 3.460 nonbonded pdb=" OD1 ASN B 299 " pdb=" CE MET B 402 " model vdw 2.199 3.460 nonbonded pdb=" O ASN C 182 " pdb=" CB LEU C 186 " model vdw 2.261 2.752 nonbonded pdb=" O GLY D 591 " pdb=" O2A PCG D 901 " model vdw 2.304 3.040 nonbonded pdb=" OG SER C 558 " pdb=" O ILE C 605 " model vdw 2.308 2.440 ... (remaining 114414 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 159 through 257 or resid 270 through 391 or resid 393 thro \ ugh 483 or resid 489 through 552 or resid 557 through 607 or resid 801 through 8 \ 02)) selection = (chain 'B' and (resid 159 through 257 or resid 270 through 391 or resid 393 thro \ ugh 607 or resid 801 through 802)) selection = (chain 'C' and (resid 159 through 257 or resid 270 through 391 or resid 393 thro \ ugh 483 or resid 489 through 552 or resid 557 through 607 or resid 801 through 8 \ 02)) } 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 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: 0.010 Extract box with map and model: 7.030 Check model and map are aligned: 0.220 Set scattering table: 0.120 Process input model: 40.830 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.070 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 : 0.014 0.369 14802 Z= 0.912 Angle : 1.294 15.940 20088 Z= 0.662 Chirality : 0.105 1.681 2283 Planarity : 0.010 0.076 2465 Dihedral : 15.304 86.830 5449 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.63 % Allowed : 12.25 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.11 (0.13), residues: 1734 helix: -3.41 (0.08), residues: 1111 sheet: -2.06 (0.55), residues: 53 loop : -3.02 (0.21), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP D 221 HIS 0.005 0.002 HIS C 242 PHE 0.028 0.003 PHE A 301 TYR 0.037 0.003 TYR B 199 ARG 0.014 0.001 ARG D 324 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 279 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 GLN cc_start: 0.7890 (tp-100) cc_final: 0.7613 (tp-100) REVERT: A 467 GLU cc_start: 0.7997 (tp30) cc_final: 0.7754 (tp30) REVERT: B 229 GLN cc_start: 0.7969 (tt0) cc_final: 0.7162 (tt0) REVERT: B 417 ILE cc_start: 0.9083 (mt) cc_final: 0.8075 (mt) REVERT: B 422 GLN cc_start: 0.8959 (tm-30) cc_final: 0.8709 (tm-30) REVERT: B 607 MET cc_start: 0.6931 (mmp) cc_final: 0.6605 (ttm) REVERT: C 188 CYS cc_start: 0.8204 (t) cc_final: 0.7685 (t) REVERT: C 228 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7270 (tp30) REVERT: C 229 GLN cc_start: 0.7560 (mt0) cc_final: 0.7234 (pt0) REVERT: C 276 ASN cc_start: 0.6253 (m-40) cc_final: 0.6035 (m-40) REVERT: C 299 ASN cc_start: 0.7670 (m110) cc_final: 0.7030 (p0) REVERT: C 422 GLN cc_start: 0.9167 (tm-30) cc_final: 0.8796 (tm-30) REVERT: C 573 TYR cc_start: 0.8805 (m-80) cc_final: 0.8362 (m-80) REVERT: C 585 MET cc_start: 0.8930 (mmp) cc_final: 0.8539 (mmp) outliers start: 9 outliers final: 5 residues processed: 284 average time/residue: 0.2507 time to fit residues: 106.0925 Evaluate side-chains 192 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 187 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 537 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 88 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 ASN ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 ASN ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 345 HIS C 241 GLN C 276 ASN C 345 HIS D 367 ASN D 426 ASN ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14802 Z= 0.182 Angle : 0.621 12.834 20088 Z= 0.314 Chirality : 0.040 0.283 2283 Planarity : 0.005 0.054 2465 Dihedral : 5.980 65.798 2047 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.79 % Allowed : 17.64 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.17), residues: 1734 helix: -0.94 (0.13), residues: 1123 sheet: -1.50 (0.59), residues: 56 loop : -2.49 (0.23), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 221 HIS 0.011 0.001 HIS C 242 PHE 0.045 0.001 PHE B 413 TYR 0.018 0.001 TYR C 546 ARG 0.004 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 220 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 MET cc_start: 0.6890 (ppp) cc_final: 0.6174 (ppp) REVERT: A 467 GLU cc_start: 0.8010 (tp30) cc_final: 0.7809 (tp30) REVERT: B 416 LYS cc_start: 0.8689 (mtpt) cc_final: 0.8455 (mtmm) REVERT: B 422 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8713 (tm-30) REVERT: B 607 MET cc_start: 0.6900 (mmp) cc_final: 0.6559 (ttm) REVERT: C 175 ILE cc_start: 0.8860 (tp) cc_final: 0.8530 (tp) REVERT: C 188 CYS cc_start: 0.8194 (t) cc_final: 0.7780 (t) REVERT: C 299 ASN cc_start: 0.7703 (m110) cc_final: 0.7074 (p0) REVERT: C 422 GLN cc_start: 0.9194 (tm-30) cc_final: 0.8985 (tm-30) REVERT: C 573 TYR cc_start: 0.8811 (m-80) cc_final: 0.8359 (m-80) REVERT: C 585 MET cc_start: 0.8966 (mmp) cc_final: 0.8621 (mmp) REVERT: D 405 LEU cc_start: 0.9134 (tp) cc_final: 0.8699 (mp) REVERT: D 426 ASN cc_start: 0.8701 (OUTLIER) cc_final: 0.8275 (t0) outliers start: 43 outliers final: 19 residues processed: 249 average time/residue: 0.2300 time to fit residues: 87.1311 Evaluate side-chains 205 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 185 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 382 THR Chi-restraints excluded: chain D residue 426 ASN Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 515 ASN Chi-restraints excluded: chain D residue 626 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 157 optimal weight: 0.8980 chunk 170 optimal weight: 7.9990 chunk 140 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 126 optimal weight: 20.0000 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN B 276 ASN B 407 ASN ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14802 Z= 0.162 Angle : 0.584 13.705 20088 Z= 0.289 Chirality : 0.040 0.160 2283 Planarity : 0.004 0.040 2465 Dihedral : 5.168 49.500 2037 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.66 % Allowed : 19.29 % Favored : 78.05 % 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: -1.06 (0.19), residues: 1734 helix: 0.06 (0.15), residues: 1127 sheet: -1.31 (0.61), residues: 56 loop : -2.12 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 221 HIS 0.006 0.001 HIS C 242 PHE 0.031 0.001 PHE B 413 TYR 0.022 0.001 TYR B 184 ARG 0.003 0.000 ARG D 636 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 202 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 MET cc_start: 0.6798 (ppp) cc_final: 0.6184 (ppp) REVERT: B 276 ASN cc_start: 0.7886 (OUTLIER) cc_final: 0.7537 (t0) REVERT: B 407 ASN cc_start: 0.8035 (OUTLIER) cc_final: 0.7723 (p0) REVERT: B 434 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8493 (mm-30) REVERT: B 607 MET cc_start: 0.6901 (mmp) cc_final: 0.6544 (ttm) REVERT: C 175 ILE cc_start: 0.8830 (tp) cc_final: 0.8508 (tp) REVERT: C 188 CYS cc_start: 0.8280 (t) cc_final: 0.7780 (t) REVERT: C 299 ASN cc_start: 0.7574 (m110) cc_final: 0.7017 (p0) REVERT: C 422 GLN cc_start: 0.9186 (tm-30) cc_final: 0.8965 (tm-30) REVERT: C 573 TYR cc_start: 0.8782 (m-80) cc_final: 0.8340 (m-80) REVERT: C 585 MET cc_start: 0.8960 (mmp) cc_final: 0.8552 (mmp) REVERT: D 330 LYS cc_start: 0.8672 (mmmm) cc_final: 0.8041 (mmmt) outliers start: 41 outliers final: 27 residues processed: 229 average time/residue: 0.2081 time to fit residues: 74.7722 Evaluate side-chains 207 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 178 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 568 ILE Chi-restraints excluded: chain D residue 260 CYS Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 369 CYS Chi-restraints excluded: chain D residue 515 ASN Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 626 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 155 optimal weight: 1.9990 chunk 118 optimal weight: 0.0470 chunk 81 optimal weight: 10.0000 chunk 17 optimal weight: 0.2980 chunk 75 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 167 optimal weight: 20.0000 chunk 82 optimal weight: 8.9990 chunk 149 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 ASN ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN B 407 ASN D 272 GLN D 301 GLN D 367 ASN D 426 ASN ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 14802 Z= 0.144 Angle : 0.557 14.750 20088 Z= 0.274 Chirality : 0.039 0.235 2283 Planarity : 0.004 0.044 2465 Dihedral : 4.758 44.684 2035 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.98 % Allowed : 19.54 % Favored : 77.47 % 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: -0.40 (0.20), residues: 1734 helix: 0.65 (0.15), residues: 1121 sheet: -1.11 (0.62), residues: 56 loop : -2.04 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 221 HIS 0.005 0.001 HIS C 242 PHE 0.022 0.001 PHE B 413 TYR 0.014 0.001 TYR A 423 ARG 0.009 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 196 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 MET cc_start: 0.6785 (ppp) cc_final: 0.6223 (ppp) REVERT: A 537 GLN cc_start: 0.8946 (mp10) cc_final: 0.8638 (mm-40) REVERT: B 276 ASN cc_start: 0.7847 (OUTLIER) cc_final: 0.7414 (t0) REVERT: B 434 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8449 (mm-30) REVERT: B 607 MET cc_start: 0.6885 (mmp) cc_final: 0.6477 (ttm) REVERT: C 175 ILE cc_start: 0.8752 (tp) cc_final: 0.8457 (tp) REVERT: C 188 CYS cc_start: 0.8282 (t) cc_final: 0.7811 (t) REVERT: C 299 ASN cc_start: 0.7456 (m110) cc_final: 0.7096 (p0) REVERT: C 410 ARG cc_start: 0.8497 (mtt90) cc_final: 0.8235 (mtp85) REVERT: C 422 GLN cc_start: 0.9174 (tm-30) cc_final: 0.8952 (tm-30) REVERT: C 573 TYR cc_start: 0.8748 (m-80) cc_final: 0.8328 (m-80) REVERT: C 585 MET cc_start: 0.8944 (mmp) cc_final: 0.8514 (mmp) REVERT: D 330 LYS cc_start: 0.8658 (mmmm) cc_final: 0.8048 (mmmt) REVERT: D 426 ASN cc_start: 0.8636 (OUTLIER) cc_final: 0.8354 (t0) REVERT: D 454 TYR cc_start: 0.8275 (t80) cc_final: 0.8052 (t80) REVERT: D 459 MET cc_start: 0.8179 (ttp) cc_final: 0.7949 (ttp) REVERT: D 493 LEU cc_start: 0.8705 (tt) cc_final: 0.8486 (tt) REVERT: D 630 HIS cc_start: 0.7164 (m-70) cc_final: 0.6943 (m-70) outliers start: 46 outliers final: 25 residues processed: 230 average time/residue: 0.2165 time to fit residues: 78.4744 Evaluate side-chains 209 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 182 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 421 LYS Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 568 ILE Chi-restraints excluded: chain D residue 260 CYS Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 369 CYS Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 426 ASN Chi-restraints excluded: chain D residue 515 ASN Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 626 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 139 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 chunk 68 optimal weight: 0.8980 chunk 142 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 chunk 150 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN D 272 GLN D 367 ASN D 426 ASN ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14802 Z= 0.162 Angle : 0.568 15.001 20088 Z= 0.277 Chirality : 0.039 0.271 2283 Planarity : 0.003 0.036 2465 Dihedral : 4.550 37.721 2035 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.66 % Allowed : 20.69 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.20), residues: 1734 helix: 0.97 (0.16), residues: 1115 sheet: -0.86 (0.64), residues: 56 loop : -1.92 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 221 HIS 0.005 0.001 HIS C 242 PHE 0.021 0.001 PHE B 413 TYR 0.012 0.001 TYR D 266 ARG 0.003 0.000 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 188 time to evaluate : 1.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 MET cc_start: 0.6760 (ppp) cc_final: 0.6262 (ppp) REVERT: A 537 GLN cc_start: 0.8949 (mp10) cc_final: 0.8669 (mm-40) REVERT: B 276 ASN cc_start: 0.7862 (OUTLIER) cc_final: 0.7482 (t0) REVERT: B 434 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8454 (mm-30) REVERT: B 607 MET cc_start: 0.6931 (mmp) cc_final: 0.6429 (ttm) REVERT: C 175 ILE cc_start: 0.8767 (tp) cc_final: 0.8466 (tp) REVERT: C 188 CYS cc_start: 0.8278 (t) cc_final: 0.7771 (t) REVERT: C 299 ASN cc_start: 0.7603 (m110) cc_final: 0.7066 (p0) REVERT: C 410 ARG cc_start: 0.8496 (mtt90) cc_final: 0.8235 (mtp85) REVERT: C 422 GLN cc_start: 0.9163 (tm-30) cc_final: 0.8943 (tm-30) REVERT: C 573 TYR cc_start: 0.8736 (m-80) cc_final: 0.8346 (m-80) REVERT: C 585 MET cc_start: 0.8962 (mmp) cc_final: 0.8568 (mmp) REVERT: D 330 LYS cc_start: 0.8674 (mmmm) cc_final: 0.8127 (mmmt) REVERT: D 426 ASN cc_start: 0.8669 (OUTLIER) cc_final: 0.8332 (t0) REVERT: D 459 MET cc_start: 0.8227 (ttp) cc_final: 0.7973 (ttp) REVERT: D 561 MET cc_start: 0.7606 (ttm) cc_final: 0.7359 (ttm) outliers start: 41 outliers final: 27 residues processed: 220 average time/residue: 0.2224 time to fit residues: 76.6597 Evaluate side-chains 207 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 178 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 421 LYS Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 369 CYS Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 426 ASN Chi-restraints excluded: chain D residue 515 ASN Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 626 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 56 optimal weight: 7.9990 chunk 150 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 167 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN ** C 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 GLN D 367 ASN D 426 ASN ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14802 Z= 0.223 Angle : 0.594 14.249 20088 Z= 0.290 Chirality : 0.041 0.272 2283 Planarity : 0.003 0.035 2465 Dihedral : 4.463 34.926 2035 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.06 % Allowed : 20.11 % Favored : 75.82 % 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: 0.11 (0.20), residues: 1734 helix: 1.03 (0.15), residues: 1128 sheet: -0.76 (0.64), residues: 56 loop : -1.83 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 221 HIS 0.005 0.001 HIS C 242 PHE 0.017 0.001 PHE B 301 TYR 0.015 0.001 TYR A 423 ARG 0.004 0.000 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 187 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 MET cc_start: 0.6811 (ppp) cc_final: 0.6353 (ppp) REVERT: A 537 GLN cc_start: 0.9000 (mp10) cc_final: 0.8731 (mm-40) REVERT: B 276 ASN cc_start: 0.7881 (OUTLIER) cc_final: 0.7457 (t0) REVERT: B 434 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8392 (mm-30) REVERT: B 584 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7754 (pp) REVERT: C 175 ILE cc_start: 0.8856 (tp) cc_final: 0.8568 (tp) REVERT: C 188 CYS cc_start: 0.8325 (t) cc_final: 0.7928 (t) REVERT: C 299 ASN cc_start: 0.7622 (m110) cc_final: 0.7113 (p0) REVERT: C 410 ARG cc_start: 0.8526 (mtt90) cc_final: 0.8261 (mtp85) REVERT: C 422 GLN cc_start: 0.9186 (tm-30) cc_final: 0.8952 (tm-30) REVERT: C 573 TYR cc_start: 0.8772 (m-80) cc_final: 0.8380 (m-80) REVERT: C 585 MET cc_start: 0.8998 (mmp) cc_final: 0.8660 (mmp) REVERT: D 239 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8083 (mtm180) REVERT: D 330 LYS cc_start: 0.8746 (mmmm) cc_final: 0.8237 (mmmt) REVERT: D 426 ASN cc_start: 0.8653 (OUTLIER) cc_final: 0.8401 (t0) REVERT: D 459 MET cc_start: 0.8232 (ttp) cc_final: 0.7994 (ttp) REVERT: D 557 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8684 (tt) REVERT: D 561 MET cc_start: 0.7676 (ttm) cc_final: 0.7462 (ttm) REVERT: D 630 HIS cc_start: 0.7223 (m-70) cc_final: 0.6983 (m-70) outliers start: 63 outliers final: 40 residues processed: 234 average time/residue: 0.2091 time to fit residues: 77.0527 Evaluate side-chains 218 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 173 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 421 LYS Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 369 CYS Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 426 ASN Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 515 ASN Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 626 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 161 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 94 optimal weight: 0.8980 chunk 140 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 166 optimal weight: 9.9990 chunk 104 optimal weight: 8.9990 chunk 101 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN D 272 GLN D 367 ASN D 426 ASN ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14802 Z= 0.167 Angle : 0.587 15.568 20088 Z= 0.282 Chirality : 0.040 0.282 2283 Planarity : 0.003 0.034 2465 Dihedral : 4.340 32.508 2035 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.05 % Allowed : 21.19 % Favored : 75.76 % 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: 0.29 (0.21), residues: 1734 helix: 1.18 (0.16), residues: 1125 sheet: -0.78 (0.61), residues: 56 loop : -1.78 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 221 HIS 0.005 0.001 HIS C 242 PHE 0.019 0.001 PHE B 413 TYR 0.011 0.001 TYR B 354 ARG 0.004 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 188 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 MET cc_start: 0.6731 (ppp) cc_final: 0.6372 (ppp) REVERT: A 207 ASP cc_start: 0.7846 (t0) cc_final: 0.7470 (t0) REVERT: A 537 GLN cc_start: 0.8987 (mp10) cc_final: 0.8723 (mm-40) REVERT: B 276 ASN cc_start: 0.7974 (OUTLIER) cc_final: 0.7680 (t0) REVERT: B 434 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8488 (mm-30) REVERT: B 519 MET cc_start: 0.7208 (tpp) cc_final: 0.6976 (mmt) REVERT: B 607 MET cc_start: 0.6937 (mmp) cc_final: 0.6541 (ptp) REVERT: C 175 ILE cc_start: 0.8766 (tp) cc_final: 0.8508 (tp) REVERT: C 188 CYS cc_start: 0.8234 (t) cc_final: 0.7801 (t) REVERT: C 299 ASN cc_start: 0.7548 (m110) cc_final: 0.7052 (p0) REVERT: C 410 ARG cc_start: 0.8473 (mtt90) cc_final: 0.8252 (mtp85) REVERT: C 422 GLN cc_start: 0.9168 (tm-30) cc_final: 0.8928 (tm-30) REVERT: C 573 TYR cc_start: 0.8748 (m-80) cc_final: 0.8369 (m-80) REVERT: C 585 MET cc_start: 0.8985 (mmp) cc_final: 0.8623 (mmp) REVERT: D 330 LYS cc_start: 0.8697 (mmmm) cc_final: 0.8249 (mmmt) REVERT: D 426 ASN cc_start: 0.8636 (OUTLIER) cc_final: 0.8345 (t0) REVERT: D 561 MET cc_start: 0.7669 (ttm) cc_final: 0.7425 (ttm) REVERT: D 630 HIS cc_start: 0.7244 (m-70) cc_final: 0.7010 (m-70) outliers start: 47 outliers final: 32 residues processed: 226 average time/residue: 0.2268 time to fit residues: 81.6075 Evaluate side-chains 209 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 175 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 421 LYS Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 369 CYS Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 426 ASN Chi-restraints excluded: chain D residue 515 ASN Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 626 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 103 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 32 optimal weight: 0.0670 chunk 106 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 82 optimal weight: 0.0870 chunk 15 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 overall best weight: 0.7898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN B 305 ASN C 562 ASN D 272 GLN D 367 ASN D 426 ASN ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 14802 Z= 0.158 Angle : 0.586 14.777 20088 Z= 0.280 Chirality : 0.040 0.270 2283 Planarity : 0.003 0.034 2465 Dihedral : 4.243 31.259 2035 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.66 % Allowed : 21.64 % Favored : 75.70 % 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: 0.39 (0.21), residues: 1734 helix: 1.31 (0.16), residues: 1118 sheet: -0.84 (0.60), residues: 56 loop : -1.81 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 221 HIS 0.005 0.001 HIS C 242 PHE 0.024 0.001 PHE D 516 TYR 0.014 0.001 TYR A 423 ARG 0.002 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 185 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 MET cc_start: 0.6721 (ppp) cc_final: 0.6393 (ppp) REVERT: A 207 ASP cc_start: 0.7861 (t0) cc_final: 0.7446 (t0) REVERT: A 537 GLN cc_start: 0.8982 (mp10) cc_final: 0.8724 (mm-40) REVERT: B 276 ASN cc_start: 0.7949 (OUTLIER) cc_final: 0.7595 (t0) REVERT: B 434 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8514 (mm-30) REVERT: B 519 MET cc_start: 0.7239 (tpp) cc_final: 0.7025 (mmt) REVERT: B 607 MET cc_start: 0.6944 (mmp) cc_final: 0.6486 (ptm) REVERT: C 175 ILE cc_start: 0.8744 (tp) cc_final: 0.8499 (tp) REVERT: C 188 CYS cc_start: 0.8255 (t) cc_final: 0.7790 (t) REVERT: C 299 ASN cc_start: 0.7509 (m110) cc_final: 0.6996 (p0) REVERT: C 410 ARG cc_start: 0.8483 (mtt90) cc_final: 0.8260 (mtp85) REVERT: C 422 GLN cc_start: 0.9152 (tm-30) cc_final: 0.8919 (tm-30) REVERT: C 573 TYR cc_start: 0.8727 (m-80) cc_final: 0.8339 (m-80) REVERT: C 585 MET cc_start: 0.8978 (mmp) cc_final: 0.8606 (mmp) REVERT: D 330 LYS cc_start: 0.8688 (mmmm) cc_final: 0.8283 (mmmt) REVERT: D 426 ASN cc_start: 0.8607 (OUTLIER) cc_final: 0.8374 (t0) REVERT: D 537 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8202 (tp) outliers start: 41 outliers final: 33 residues processed: 215 average time/residue: 0.2421 time to fit residues: 82.6692 Evaluate side-chains 212 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 176 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 421 LYS Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 471 ASN Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 369 CYS Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 426 ASN Chi-restraints excluded: chain D residue 515 ASN Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 626 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 159 optimal weight: 9.9990 chunk 145 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 67 optimal weight: 0.2980 chunk 122 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 140 optimal weight: 4.9990 chunk 146 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN D 272 GLN D 367 ASN D 426 ASN ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14802 Z= 0.154 Angle : 0.577 14.175 20088 Z= 0.277 Chirality : 0.040 0.269 2283 Planarity : 0.003 0.033 2465 Dihedral : 4.193 30.478 2035 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.92 % Allowed : 21.51 % Favored : 75.57 % 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: 0.47 (0.21), residues: 1734 helix: 1.37 (0.16), residues: 1117 sheet: -0.85 (0.58), residues: 56 loop : -1.78 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP D 221 HIS 0.005 0.001 HIS C 242 PHE 0.017 0.001 PHE B 413 TYR 0.011 0.001 TYR D 266 ARG 0.003 0.000 ARG D 274 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 181 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 MET cc_start: 0.6658 (ppp) cc_final: 0.6310 (ppp) REVERT: A 207 ASP cc_start: 0.7890 (t0) cc_final: 0.7453 (t0) REVERT: A 537 GLN cc_start: 0.8977 (mp10) cc_final: 0.8728 (mm-40) REVERT: B 276 ASN cc_start: 0.7975 (OUTLIER) cc_final: 0.7626 (t0) REVERT: B 434 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8513 (mm-30) REVERT: B 519 MET cc_start: 0.7222 (tpp) cc_final: 0.7020 (mmt) REVERT: B 607 MET cc_start: 0.6920 (mmp) cc_final: 0.6469 (ptm) REVERT: C 175 ILE cc_start: 0.8714 (tp) cc_final: 0.8484 (tp) REVERT: C 188 CYS cc_start: 0.8262 (t) cc_final: 0.7773 (t) REVERT: C 299 ASN cc_start: 0.7492 (m110) cc_final: 0.6986 (p0) REVERT: C 422 GLN cc_start: 0.9158 (tm-30) cc_final: 0.8940 (tm-30) REVERT: C 573 TYR cc_start: 0.8703 (m-80) cc_final: 0.8312 (m-80) REVERT: C 585 MET cc_start: 0.8975 (mmp) cc_final: 0.8592 (mmp) REVERT: D 330 LYS cc_start: 0.8685 (mmmm) cc_final: 0.8311 (mmmt) REVERT: D 426 ASN cc_start: 0.8604 (OUTLIER) cc_final: 0.8372 (t0) REVERT: D 483 TYR cc_start: 0.8634 (m-80) cc_final: 0.8383 (m-80) REVERT: D 537 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8131 (tp) REVERT: D 630 HIS cc_start: 0.7277 (m-70) cc_final: 0.7049 (m-70) outliers start: 45 outliers final: 35 residues processed: 214 average time/residue: 0.2091 time to fit residues: 71.1011 Evaluate side-chains 213 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 175 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 421 LYS Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 471 ASN Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain D residue 233 CYS Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 369 CYS Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 426 ASN Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 626 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 164 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 158 optimal weight: 0.9980 chunk 137 optimal weight: 0.0770 chunk 14 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN D 367 ASN D 426 ASN ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 14802 Z= 0.155 Angle : 0.585 14.323 20088 Z= 0.279 Chirality : 0.040 0.260 2283 Planarity : 0.003 0.032 2465 Dihedral : 4.144 29.931 2035 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.86 % Allowed : 21.76 % Favored : 75.38 % 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: 0.53 (0.21), residues: 1734 helix: 1.41 (0.16), residues: 1118 sheet: -0.76 (0.55), residues: 62 loop : -1.77 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP D 221 HIS 0.005 0.001 HIS C 242 PHE 0.017 0.001 PHE B 413 TYR 0.014 0.001 TYR D 266 ARG 0.002 0.000 ARG A 569 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 181 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 MET cc_start: 0.6636 (ppp) cc_final: 0.6294 (ppp) REVERT: A 537 GLN cc_start: 0.8971 (mp10) cc_final: 0.8746 (mm-40) REVERT: B 186 LEU cc_start: 0.8354 (mt) cc_final: 0.7986 (tt) REVERT: B 276 ASN cc_start: 0.7907 (OUTLIER) cc_final: 0.7643 (t0) REVERT: B 434 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8497 (mm-30) REVERT: B 607 MET cc_start: 0.6905 (mmp) cc_final: 0.6461 (ptm) REVERT: C 175 ILE cc_start: 0.8694 (tp) cc_final: 0.8466 (tp) REVERT: C 188 CYS cc_start: 0.8264 (t) cc_final: 0.7772 (t) REVERT: C 299 ASN cc_start: 0.7468 (m110) cc_final: 0.6965 (p0) REVERT: C 422 GLN cc_start: 0.9150 (tm-30) cc_final: 0.8922 (tm-30) REVERT: C 573 TYR cc_start: 0.8680 (m-80) cc_final: 0.8297 (m-80) REVERT: C 585 MET cc_start: 0.8964 (mmp) cc_final: 0.8607 (mmp) REVERT: D 330 LYS cc_start: 0.8686 (mmmm) cc_final: 0.8300 (mmmt) REVERT: D 419 GLU cc_start: 0.7720 (pt0) cc_final: 0.7476 (pt0) REVERT: D 426 ASN cc_start: 0.8632 (OUTLIER) cc_final: 0.8333 (t0) REVERT: D 483 TYR cc_start: 0.8562 (m-80) cc_final: 0.8362 (m-80) REVERT: D 537 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8029 (tp) REVERT: D 626 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.8031 (tm-30) REVERT: D 630 HIS cc_start: 0.7322 (m-70) cc_final: 0.7046 (m-70) outliers start: 44 outliers final: 37 residues processed: 212 average time/residue: 0.2109 time to fit residues: 71.6786 Evaluate side-chains 216 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 175 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 421 LYS Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 471 ASN Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain D residue 233 CYS Chi-restraints excluded: chain D residue 264 TYR Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 369 CYS Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 426 ASN Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 626 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 137 optimal weight: 1.9990 chunk 57 optimal weight: 0.0370 chunk 141 optimal weight: 0.0670 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN D 272 GLN D 367 ASN D 426 ASN ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.141452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.110670 restraints weight = 43028.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.114463 restraints weight = 19058.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.116941 restraints weight = 11334.617| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3687 r_free = 0.3687 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3687 r_free = 0.3687 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14802 Z= 0.158 Angle : 0.584 14.171 20088 Z= 0.279 Chirality : 0.040 0.261 2283 Planarity : 0.003 0.032 2465 Dihedral : 4.138 29.731 2035 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.79 % Allowed : 21.89 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.21), residues: 1734 helix: 1.45 (0.16), residues: 1116 sheet: -0.72 (0.54), residues: 62 loop : -1.73 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 440 HIS 0.005 0.001 HIS C 242 PHE 0.017 0.001 PHE B 413 TYR 0.021 0.001 TYR D 294 ARG 0.003 0.000 ARG D 295 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2916.69 seconds wall clock time: 53 minutes 54.06 seconds (3234.06 seconds total)