Starting phenix.real_space_refine (version: 1.21rc1) on Sat Jul 8 20:45:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wug_32830/07_2023/7wug_32830.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wug_32830/07_2023/7wug_32830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wug_32830/07_2023/7wug_32830.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wug_32830/07_2023/7wug_32830.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wug_32830/07_2023/7wug_32830.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wug_32830/07_2023/7wug_32830.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 11333 2.51 5 N 2919 2.21 5 O 3171 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "5 TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 209": "OD1" <-> "OD2" Residue "5 ASP 241": "OD1" <-> "OD2" Residue "5 TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 706": "OD1" <-> "OD2" Residue "5 ASP 738": "OD1" <-> "OD2" Residue "5 ASP 754": "OD1" <-> "OD2" Residue "5 ASP 855": "OD1" <-> "OD2" Residue "5 GLU 905": "OE1" <-> "OE2" Residue "1 TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 610": "OE1" <-> "OE2" Residue "1 PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 707": "OD1" <-> "OD2" Residue "1 GLU 725": "OE1" <-> "OE2" Residue "4 GLU 178": "OE1" <-> "OE2" Residue "4 PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 313": "OD1" <-> "OD2" Residue "4 ASP 356": "OD1" <-> "OD2" Residue "Y PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 27": "OE1" <-> "OE2" Residue "Y TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 564": "OD1" <-> "OD2" Residue "Y PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 572": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 17515 Number of models: 1 Model: "" Number of chains: 5 Chain: "5" Number of atoms: 6212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 782, 6212 Classifications: {'peptide': 782} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 23, 'TRANS': 758} Chain breaks: 7 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 180 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 14, 'ARG:plan': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 105 Chain: "8" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2351 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 10, 'TRANS': 306} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 279 Unresolved non-hydrogen angles: 346 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 13, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 152 Chain: "1" Number of atoms: 3103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3103 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 13, 'TRANS': 388} Chain breaks: 10 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 213 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 101 Chain: "4" Number of atoms: 1859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1859 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "Y" Number of atoms: 3990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3990 Classifications: {'peptide': 508} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 21, 'TRANS': 486} Chain breaks: 9 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 83 Time building chain proxies: 8.75, per 1000 atoms: 0.50 Number of scatterers: 17515 At special positions: 0 Unit cell: (165.68, 113.36, 158.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 3171 8.00 N 2919 7.00 C 11333 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 Time building additional restraints: 7.09 Conformation dependent library (CDL) restraints added in 2.5 seconds 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4306 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 16 sheets defined 50.2% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain '5' and resid 6 through 17 Processing helix chain '5' and resid 21 through 30 Processing helix chain '5' and resid 34 through 41 removed outlier: 3.535A pdb=" N CYS 5 38 " --> pdb=" O GLN 5 34 " (cutoff:3.500A) Processing helix chain '5' and resid 47 through 62 Processing helix chain '5' and resid 65 through 73 Processing helix chain '5' and resid 73 through 86 removed outlier: 4.194A pdb=" N PHE 5 77 " --> pdb=" O GLY 5 73 " (cutoff:3.500A) Processing helix chain '5' and resid 97 through 115 Processing helix chain '5' and resid 122 through 137 removed outlier: 3.732A pdb=" N LEU 5 126 " --> pdb=" O ASP 5 122 " (cutoff:3.500A) Processing helix chain '5' and resid 144 through 160 removed outlier: 3.528A pdb=" N LEU 5 160 " --> pdb=" O LYS 5 156 " (cutoff:3.500A) Processing helix chain '5' and resid 187 through 205 Processing helix chain '5' and resid 207 through 211 removed outlier: 3.830A pdb=" N GLN 5 210 " --> pdb=" O TYR 5 207 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE 5 211 " --> pdb=" O LEU 5 208 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 207 through 211' Processing helix chain '5' and resid 254 through 272 Processing helix chain '5' and resid 284 through 295 Processing helix chain '5' and resid 299 through 311 Processing helix chain '5' and resid 312 through 317 removed outlier: 3.622A pdb=" N THR 5 316 " --> pdb=" O GLN 5 312 " (cutoff:3.500A) Processing helix chain '5' and resid 323 through 338 removed outlier: 3.913A pdb=" N LEU 5 327 " --> pdb=" O ASP 5 323 " (cutoff:3.500A) Proline residue: 5 332 - end of helix Processing helix chain '5' and resid 348 through 364 Processing helix chain '5' and resid 368 through 376 Processing helix chain '5' and resid 378 through 391 removed outlier: 3.949A pdb=" N CYS 5 382 " --> pdb=" O ASN 5 378 " (cutoff:3.500A) Processing helix chain '5' and resid 397 through 415 removed outlier: 3.517A pdb=" N ALA 5 415 " --> pdb=" O CYS 5 411 " (cutoff:3.500A) Processing helix chain '5' and resid 418 through 427 Processing helix chain '5' and resid 430 through 452 removed outlier: 3.562A pdb=" N HIS 5 434 " --> pdb=" O LEU 5 430 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU 5 452 " --> pdb=" O ASP 5 448 " (cutoff:3.500A) Processing helix chain '5' and resid 452 through 457 removed outlier: 3.581A pdb=" N ILE 5 456 " --> pdb=" O LEU 5 452 " (cutoff:3.500A) Processing helix chain '5' and resid 473 through 489 Processing helix chain '5' and resid 490 through 496 Processing helix chain '5' and resid 500 through 521 removed outlier: 4.131A pdb=" N ALA 5 504 " --> pdb=" O ARG 5 500 " (cutoff:3.500A) Processing helix chain '5' and resid 522 through 524 No H-bonds generated for 'chain '5' and resid 522 through 524' Processing helix chain '5' and resid 525 through 547 removed outlier: 3.538A pdb=" N MET 5 529 " --> pdb=" O GLY 5 525 " (cutoff:3.500A) Proline residue: 5 531 - end of helix Processing helix chain '5' and resid 553 through 560 Processing helix chain '5' and resid 561 through 571 removed outlier: 3.839A pdb=" N ILE 5 565 " --> pdb=" O GLY 5 561 " (cutoff:3.500A) Processing helix chain '5' and resid 585 through 593 Processing helix chain '5' and resid 597 through 612 removed outlier: 3.546A pdb=" N LYS 5 601 " --> pdb=" O VAL 5 597 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET 5 612 " --> pdb=" O LEU 5 608 " (cutoff:3.500A) Processing helix chain '5' and resid 616 through 627 removed outlier: 3.599A pdb=" N LYS 5 620 " --> pdb=" O GLN 5 616 " (cutoff:3.500A) Processing helix chain '5' and resid 628 through 635 removed outlier: 3.956A pdb=" N ILE 5 632 " --> pdb=" O PRO 5 628 " (cutoff:3.500A) Processing helix chain '5' and resid 636 through 638 No H-bonds generated for 'chain '5' and resid 636 through 638' Processing helix chain '5' and resid 640 through 656 Processing helix chain '5' and resid 658 through 669 removed outlier: 3.673A pdb=" N VAL 5 662 " --> pdb=" O SER 5 658 " (cutoff:3.500A) Processing helix chain '5' and resid 690 through 700 Processing helix chain '5' and resid 706 through 724 Processing helix chain '5' and resid 727 through 737 removed outlier: 3.545A pdb=" N LYS 5 731 " --> pdb=" O ASN 5 727 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN 5 737 " --> pdb=" O LEU 5 733 " (cutoff:3.500A) Processing helix chain '5' and resid 738 through 749 Processing helix chain '5' and resid 761 through 776 removed outlier: 3.615A pdb=" N LYS 5 765 " --> pdb=" O ASP 5 761 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU 5 776 " --> pdb=" O LEU 5 772 " (cutoff:3.500A) Processing helix chain '5' and resid 778 through 787 Processing helix chain '5' and resid 869 through 887 Processing helix chain '5' and resid 887 through 897 removed outlier: 4.144A pdb=" N LEU 5 891 " --> pdb=" O GLY 5 887 " (cutoff:3.500A) Processing helix chain '5' and resid 900 through 919 removed outlier: 3.579A pdb=" N LYS 5 919 " --> pdb=" O ASP 5 915 " (cutoff:3.500A) Processing helix chain '8' and resid 35 through 54 Processing helix chain '8' and resid 88 through 100 Processing helix chain '8' and resid 102 through 113 removed outlier: 3.813A pdb=" N SER 8 106 " --> pdb=" O TYR 8 102 " (cutoff:3.500A) Processing helix chain '8' and resid 118 through 130 Processing helix chain '8' and resid 130 through 144 Processing helix chain '8' and resid 145 through 157 Processing helix chain '8' and resid 159 through 164 removed outlier: 3.517A pdb=" N GLU 8 164 " --> pdb=" O GLU 8 160 " (cutoff:3.500A) Processing helix chain '8' and resid 193 through 212 Processing helix chain '8' and resid 220 through 234 removed outlier: 4.014A pdb=" N LEU 8 234 " --> pdb=" O SER 8 230 " (cutoff:3.500A) Processing helix chain '8' and resid 234 through 241 removed outlier: 4.143A pdb=" N SER 8 241 " --> pdb=" O LYS 8 237 " (cutoff:3.500A) Processing helix chain '8' and resid 241 through 256 removed outlier: 3.559A pdb=" N LEU 8 256 " --> pdb=" O MET 8 252 " (cutoff:3.500A) Processing helix chain '8' and resid 280 through 308 removed outlier: 3.844A pdb=" N SER 8 284 " --> pdb=" O ILE 8 280 " (cutoff:3.500A) Proline residue: 8 300 - end of helix Processing helix chain '8' and resid 352 through 357 removed outlier: 3.875A pdb=" N MET 8 357 " --> pdb=" O ASN 8 354 " (cutoff:3.500A) Processing helix chain '8' and resid 394 through 403 removed outlier: 3.506A pdb=" N GLN 8 398 " --> pdb=" O ASN 8 394 " (cutoff:3.500A) Processing helix chain '8' and resid 417 through 422 Processing helix chain '8' and resid 423 through 426 removed outlier: 3.709A pdb=" N GLU 8 426 " --> pdb=" O PHE 8 423 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 423 through 426' Processing helix chain '8' and resid 427 through 446 removed outlier: 3.608A pdb=" N GLN 8 431 " --> pdb=" O PRO 8 427 " (cutoff:3.500A) Processing helix chain '1' and resid 17 through 27 Processing helix chain '1' and resid 30 through 35 removed outlier: 3.520A pdb=" N GLN 1 33 " --> pdb=" O TYR 1 30 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN 1 34 " --> pdb=" O LEU 1 31 " (cutoff:3.500A) Proline residue: 1 35 - end of helix No H-bonds generated for 'chain '1' and resid 30 through 35' Processing helix chain '1' and resid 36 through 47 removed outlier: 3.514A pdb=" N LEU 1 40 " --> pdb=" O VAL 1 36 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS 1 47 " --> pdb=" O LEU 1 43 " (cutoff:3.500A) Processing helix chain '1' and resid 81 through 92 Processing helix chain '1' and resid 117 through 125 Processing helix chain '1' and resid 327 through 332 removed outlier: 3.650A pdb=" N GLY 1 332 " --> pdb=" O TYR 1 328 " (cutoff:3.500A) Processing helix chain '1' and resid 497 through 504 Processing helix chain '1' and resid 596 through 614 removed outlier: 3.686A pdb=" N TYR 1 600 " --> pdb=" O ASP 1 596 " (cutoff:3.500A) Processing helix chain '1' and resid 708 through 725 Processing helix chain '1' and resid 727 through 742 Processing helix chain '1' and resid 752 through 772 Processing helix chain '1' and resid 914 through 932 Processing helix chain '1' and resid 944 through 949 removed outlier: 3.652A pdb=" N ILE 1 949 " --> pdb=" O TYR 1 946 " (cutoff:3.500A) Processing helix chain '1' and resid 950 through 955 Processing helix chain '4' and resid 92 through 97 Processing helix chain '4' and resid 212 through 222 Processing helix chain '4' and resid 223 through 232 removed outlier: 3.686A pdb=" N ARG 4 227 " --> pdb=" O PHE 4 223 " (cutoff:3.500A) Processing helix chain '4' and resid 270 through 277 Processing helix chain '4' and resid 281 through 285 removed outlier: 3.627A pdb=" N GLU 4 285 " --> pdb=" O TYR 4 282 " (cutoff:3.500A) Processing helix chain 'Y' and resid 94 through 102 Processing helix chain 'Y' and resid 186 through 196 Processing helix chain 'Y' and resid 280 through 297 removed outlier: 3.712A pdb=" N VAL Y 284 " --> pdb=" O PRO Y 280 " (cutoff:3.500A) Processing helix chain 'Y' and resid 307 through 315 removed outlier: 3.644A pdb=" N VAL Y 311 " --> pdb=" O SER Y 307 " (cutoff:3.500A) Processing helix chain 'Y' and resid 319 through 328 Processing helix chain 'Y' and resid 336 through 346 Processing helix chain 'Y' and resid 543 through 553 Processing helix chain 'Y' and resid 589 through 593 removed outlier: 3.779A pdb=" N ARG Y 592 " --> pdb=" O ASN Y 589 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN Y 593 " --> pdb=" O LEU Y 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 589 through 593' Processing sheet with id=AA1, first strand: chain '5' and resid 216 through 217 removed outlier: 3.844A pdb=" N VAL 5 217 " --> pdb=" O VAL 1 110 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL 1 110 " --> pdb=" O VAL 5 217 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain '8' and resid 32 through 33 removed outlier: 6.613A pdb=" N LYS 8 32 " --> pdb=" O GLY 8 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain '8' and resid 330 through 331 removed outlier: 3.936A pdb=" N PHE 8 415 " --> pdb=" O TYR 8 331 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '1' and resid 347 through 349 Processing sheet with id=AA5, first strand: chain '1' and resid 396 through 399 removed outlier: 3.573A pdb=" N LEU 1 518 " --> pdb=" O CYS 1 513 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1' and resid 557 through 563 removed outlier: 5.591A pdb=" N HIS 1 558 " --> pdb=" O LYS 1 554 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS 1 554 " --> pdb=" O HIS 1 558 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY 1 560 " --> pdb=" O PHE 1 552 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE 1 552 " --> pdb=" O GLY 1 560 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE 1 550 " --> pdb=" O ALA 1 562 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N SER 1 582 " --> pdb=" O LEU 1 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '1' and resid 687 through 688 Processing sheet with id=AA8, first strand: chain '4' and resid 340 through 341 removed outlier: 4.131A pdb=" N GLN 4 340 " --> pdb=" O TYR 4 331 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N SER 4 164 " --> pdb=" O LYS 4 147 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N SER 4 180 " --> pdb=" O LEU 4 297 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LEU 4 297 " --> pdb=" O SER 4 180 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR 4 182 " --> pdb=" O LYS 4 295 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Y' and resid 32 through 35 removed outlier: 6.308A pdb=" N ALA Y 9 " --> pdb=" O LEU Y 677 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LEU Y 677 " --> pdb=" O ALA Y 9 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N SER Y 11 " --> pdb=" O LEU Y 675 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU Y 675 " --> pdb=" O SER Y 11 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Y' and resid 158 through 161 removed outlier: 4.724A pdb=" N TYR Y 56 " --> pdb=" O TYR Y 161 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU Y 212 " --> pdb=" O ARG Y 239 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Y' and resid 128 through 134 Processing sheet with id=AB3, first strand: chain 'Y' and resid 164 through 165 removed outlier: 6.947A pdb=" N TYR Y 165 " --> pdb=" O ILE Y 615 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N ASP Y 617 " --> pdb=" O TYR Y 165 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL Y 613 " --> pdb=" O VAL Y 633 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL Y 633 " --> pdb=" O VAL Y 613 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ILE Y 615 " --> pdb=" O HIS Y 631 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N HIS Y 631 " --> pdb=" O ILE Y 615 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR Y 635 " --> pdb=" O ASN Y 609 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Y' and resid 164 through 165 removed outlier: 6.947A pdb=" N TYR Y 165 " --> pdb=" O ILE Y 615 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N ASP Y 617 " --> pdb=" O TYR Y 165 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL Y 613 " --> pdb=" O VAL Y 633 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL Y 633 " --> pdb=" O VAL Y 613 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ILE Y 615 " --> pdb=" O HIS Y 631 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N HIS Y 631 " --> pdb=" O ILE Y 615 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU Y 640 " --> pdb=" O SER Y 636 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LYS Y 645 " --> pdb=" O LEU Y 659 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LEU Y 659 " --> pdb=" O LYS Y 645 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N GLU Y 647 " --> pdb=" O ILE Y 657 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ILE Y 657 " --> pdb=" O GLU Y 647 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Y' and resid 252 through 255 removed outlier: 6.557A pdb=" N ILE Y 274 " --> pdb=" O VAL Y 357 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Y' and resid 441 through 448 Processing sheet with id=AB7, first strand: chain 'Y' and resid 559 through 561 915 hydrogen bonds defined for protein. 2652 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: 5.88 Time building geometry restraints manager: 7.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5544 1.34 - 1.46: 4217 1.46 - 1.58: 7976 1.58 - 1.70: 0 1.70 - 1.82: 136 Bond restraints: 17873 Sorted by residual: bond pdb=" C GLN 5 312 " pdb=" N PRO 5 313 " ideal model delta sigma weight residual 1.335 1.378 -0.044 1.19e-02 7.06e+03 1.35e+01 bond pdb=" N ILE Y 570 " pdb=" CA ILE Y 570 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.21e-02 6.83e+03 9.29e+00 bond pdb=" N ASP Y 572 " pdb=" CA ASP Y 572 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.17e-02 7.31e+03 7.38e+00 bond pdb=" N GLY Y 575 " pdb=" CA GLY Y 575 " ideal model delta sigma weight residual 1.449 1.475 -0.026 9.80e-03 1.04e+04 6.80e+00 bond pdb=" N LYS 1 408 " pdb=" CA LYS 1 408 " ideal model delta sigma weight residual 1.460 1.488 -0.028 1.14e-02 7.69e+03 5.94e+00 ... (remaining 17868 not shown) Histogram of bond angle deviations from ideal: 97.48 - 104.83: 247 104.83 - 112.17: 8880 112.17 - 119.51: 5888 119.51 - 126.86: 9023 126.86 - 134.20: 189 Bond angle restraints: 24227 Sorted by residual: angle pdb=" N GLY Y 575 " pdb=" CA GLY Y 575 " pdb=" C GLY Y 575 " ideal model delta sigma weight residual 110.56 117.83 -7.27 1.36e+00 5.41e-01 2.86e+01 angle pdb=" N THR Y 573 " pdb=" CA THR Y 573 " pdb=" C THR Y 573 " ideal model delta sigma weight residual 113.38 107.41 5.97 1.23e+00 6.61e-01 2.36e+01 angle pdb=" C PHE Y 492 " pdb=" N VAL Y 493 " pdb=" CA VAL Y 493 " ideal model delta sigma weight residual 121.97 129.10 -7.13 1.80e+00 3.09e-01 1.57e+01 angle pdb=" C PHE 1 595 " pdb=" N ASP 1 596 " pdb=" CA ASP 1 596 " ideal model delta sigma weight residual 121.54 128.79 -7.25 1.91e+00 2.74e-01 1.44e+01 angle pdb=" CA VAL 5 547 " pdb=" CB VAL 5 547 " pdb=" CG1 VAL 5 547 " ideal model delta sigma weight residual 110.40 116.82 -6.42 1.70e+00 3.46e-01 1.43e+01 ... (remaining 24222 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 9653 17.49 - 34.99: 842 34.99 - 52.48: 127 52.48 - 69.98: 17 69.98 - 87.47: 11 Dihedral angle restraints: 10650 sinusoidal: 4040 harmonic: 6610 Sorted by residual: dihedral pdb=" CA TYR 5 271 " pdb=" C TYR 5 271 " pdb=" N HIS 5 272 " pdb=" CA HIS 5 272 " ideal model delta harmonic sigma weight residual 180.00 -155.16 -24.84 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA ASP Y 610 " pdb=" C ASP Y 610 " pdb=" N THR Y 611 " pdb=" CA THR Y 611 " ideal model delta harmonic sigma weight residual -180.00 -155.97 -24.03 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA PHE 1 595 " pdb=" C PHE 1 595 " pdb=" N ASP 1 596 " pdb=" CA ASP 1 596 " ideal model delta harmonic sigma weight residual -180.00 -156.13 -23.87 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 10647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1854 0.038 - 0.077: 690 0.077 - 0.115: 182 0.115 - 0.153: 58 0.153 - 0.192: 11 Chirality restraints: 2795 Sorted by residual: chirality pdb=" CB VAL 4 345 " pdb=" CA VAL 4 345 " pdb=" CG1 VAL 4 345 " pdb=" CG2 VAL 4 345 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.18e-01 chirality pdb=" CB VAL 5 749 " pdb=" CA VAL 5 749 " pdb=" CG1 VAL 5 749 " pdb=" CG2 VAL 5 749 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.94e-01 chirality pdb=" CA ILE Y 570 " pdb=" N ILE Y 570 " pdb=" C ILE Y 570 " pdb=" CB ILE Y 570 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.71e-01 ... (remaining 2792 not shown) Planarity restraints: 3049 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL 4 345 " 0.037 5.00e-02 4.00e+02 5.57e-02 4.97e+00 pdb=" N PRO 4 346 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO 4 346 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO 4 346 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG 4 124 " 0.035 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO 4 125 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO 4 125 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO 4 125 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN 1 34 " 0.032 5.00e-02 4.00e+02 4.89e-02 3.82e+00 pdb=" N PRO 1 35 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO 1 35 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO 1 35 " 0.027 5.00e-02 4.00e+02 ... (remaining 3046 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2813 2.76 - 3.30: 15372 3.30 - 3.83: 27672 3.83 - 4.37: 32080 4.37 - 4.90: 58796 Nonbonded interactions: 136733 Sorted by model distance: nonbonded pdb=" O GLY Y 249 " pdb=" OG SER Y 267 " model vdw 2.231 2.440 nonbonded pdb=" OG1 THR 4 117 " pdb=" OD1 ASP 4 150 " model vdw 2.260 2.440 nonbonded pdb=" OD2 ASP 4 321 " pdb=" OG1 THR 4 324 " model vdw 2.262 2.440 nonbonded pdb=" O ILE Y 73 " pdb=" OH TYR Y 198 " model vdw 2.269 2.440 nonbonded pdb=" OH TYR 5 889 " pdb=" OD1 ASP 5 915 " model vdw 2.287 2.440 ... (remaining 136728 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.280 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 45.160 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 17873 Z= 0.233 Angle : 0.690 11.304 24227 Z= 0.379 Chirality : 0.045 0.192 2795 Planarity : 0.005 0.056 3049 Dihedral : 13.453 87.475 6344 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.12 % Favored : 95.84 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.17), residues: 2161 helix: 0.45 (0.15), residues: 1013 sheet: 0.38 (0.31), residues: 300 loop : -1.56 (0.20), residues: 848 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 189 time to evaluate : 2.040 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 191 average time/residue: 0.2857 time to fit residues: 84.8175 Evaluate side-chains 156 residues out of total 2065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 2.008 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1515 time to fit residues: 3.0413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 0.0770 chunk 168 optimal weight: 3.9990 chunk 93 optimal weight: 20.0000 chunk 57 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 9 ASN ** 5 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 334 ASN 8 337 ASN 4 275 GLN Y 360 GLN Y 631 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.071 17873 Z= 0.404 Angle : 0.620 7.239 24227 Z= 0.323 Chirality : 0.044 0.183 2795 Planarity : 0.004 0.056 3049 Dihedral : 4.444 22.671 2383 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.93 % Favored : 96.02 % Rotamer Outliers : 0.76 % 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: 0.22 (0.18), residues: 2161 helix: 1.35 (0.16), residues: 1031 sheet: 0.46 (0.32), residues: 287 loop : -1.52 (0.20), residues: 843 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 164 time to evaluate : 2.158 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 173 average time/residue: 0.2824 time to fit residues: 76.8918 Evaluate side-chains 163 residues out of total 2065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 153 time to evaluate : 2.104 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1668 time to fit residues: 5.9594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 112 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 201 optimal weight: 8.9990 chunk 218 optimal weight: 0.8980 chunk 179 optimal weight: 0.7980 chunk 200 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 337 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 17873 Z= 0.169 Angle : 0.486 6.777 24227 Z= 0.256 Chirality : 0.040 0.144 2795 Planarity : 0.003 0.044 3049 Dihedral : 4.082 23.729 2383 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.19 % Favored : 96.76 % Rotamer Outliers : 0.70 % 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: 0.72 (0.19), residues: 2161 helix: 1.88 (0.16), residues: 1035 sheet: 0.43 (0.31), residues: 295 loop : -1.38 (0.21), residues: 831 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 171 time to evaluate : 2.042 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 176 average time/residue: 0.2935 time to fit residues: 81.1224 Evaluate side-chains 165 residues out of total 2065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 157 time to evaluate : 1.989 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1714 time to fit residues: 5.1760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 199 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 202 optimal weight: 7.9990 chunk 214 optimal weight: 0.0670 chunk 105 optimal weight: 0.9980 chunk 192 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 overall best weight: 2.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 337 ASN Y 586 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.054 17873 Z= 0.395 Angle : 0.596 8.005 24227 Z= 0.309 Chirality : 0.043 0.171 2795 Planarity : 0.004 0.047 3049 Dihedral : 4.334 23.304 2383 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.35 % Favored : 95.60 % Rotamer Outliers : 0.97 % 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: 0.63 (0.18), residues: 2161 helix: 1.83 (0.16), residues: 1032 sheet: 0.34 (0.30), residues: 294 loop : -1.42 (0.21), residues: 835 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 160 time to evaluate : 1.989 Fit side-chains outliers start: 18 outliers final: 10 residues processed: 169 average time/residue: 0.2928 time to fit residues: 76.9533 Evaluate side-chains 164 residues out of total 2065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 154 time to evaluate : 1.983 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1605 time to fit residues: 5.7271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 178 optimal weight: 10.0000 chunk 121 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 159 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 183 optimal weight: 0.0370 chunk 148 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 109 optimal weight: 0.0370 chunk 192 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 301 ASN 8 337 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 17873 Z= 0.116 Angle : 0.459 9.156 24227 Z= 0.241 Chirality : 0.039 0.146 2795 Planarity : 0.003 0.040 3049 Dihedral : 3.894 24.226 2383 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.29 % Favored : 96.67 % Rotamer Outliers : 0.76 % 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: 1.08 (0.19), residues: 2161 helix: 2.26 (0.16), residues: 1036 sheet: 0.46 (0.31), residues: 294 loop : -1.25 (0.21), residues: 831 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 171 time to evaluate : 2.326 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 180 average time/residue: 0.2891 time to fit residues: 81.7432 Evaluate side-chains 168 residues out of total 2065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 161 time to evaluate : 2.046 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1626 time to fit residues: 4.7378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 72 optimal weight: 0.9980 chunk 193 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 125 optimal weight: 0.2980 chunk 52 optimal weight: 0.4980 chunk 214 optimal weight: 4.9990 chunk 178 optimal weight: 0.0170 chunk 99 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 337 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 17873 Z= 0.130 Angle : 0.456 9.868 24227 Z= 0.237 Chirality : 0.039 0.141 2795 Planarity : 0.003 0.038 3049 Dihedral : 3.698 24.146 2383 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.38 % Favored : 96.58 % Rotamer Outliers : 0.70 % 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: 1.29 (0.19), residues: 2161 helix: 2.44 (0.16), residues: 1036 sheet: 0.58 (0.31), residues: 294 loop : -1.15 (0.22), residues: 831 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 175 time to evaluate : 2.053 Fit side-chains outliers start: 13 outliers final: 4 residues processed: 186 average time/residue: 0.2853 time to fit residues: 83.6399 Evaluate side-chains 166 residues out of total 2065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 162 time to evaluate : 2.037 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1639 time to fit residues: 3.9302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 207 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 156 optimal weight: 0.8980 chunk 121 optimal weight: 0.0770 chunk 180 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 213 optimal weight: 0.6980 chunk 133 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 337 ASN 4 176 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 17873 Z= 0.141 Angle : 0.460 12.654 24227 Z= 0.239 Chirality : 0.039 0.137 2795 Planarity : 0.003 0.038 3049 Dihedral : 3.671 23.714 2383 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.01 % Favored : 96.95 % Rotamer Outliers : 0.54 % 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: 1.31 (0.19), residues: 2161 helix: 2.42 (0.16), residues: 1044 sheet: 0.62 (0.31), residues: 294 loop : -1.16 (0.22), residues: 823 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 169 time to evaluate : 2.223 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 174 average time/residue: 0.2921 time to fit residues: 80.5169 Evaluate side-chains 166 residues out of total 2065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 161 time to evaluate : 2.101 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1763 time to fit residues: 4.2968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 132 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 41 optimal weight: 0.0770 chunk 136 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 168 optimal weight: 3.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 337 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 17873 Z= 0.154 Angle : 0.470 10.831 24227 Z= 0.243 Chirality : 0.039 0.140 2795 Planarity : 0.003 0.038 3049 Dihedral : 3.664 23.725 2383 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.24 % Favored : 96.71 % Rotamer Outliers : 0.43 % 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: 1.35 (0.19), residues: 2161 helix: 2.44 (0.16), residues: 1050 sheet: 0.61 (0.30), residues: 301 loop : -1.14 (0.22), residues: 810 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 168 time to evaluate : 2.174 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 172 average time/residue: 0.2792 time to fit residues: 75.7319 Evaluate side-chains 166 residues out of total 2065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 163 time to evaluate : 2.007 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1681 time to fit residues: 3.6705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 194 optimal weight: 4.9990 chunk 204 optimal weight: 0.8980 chunk 187 optimal weight: 3.9990 chunk 199 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 156 optimal weight: 0.0030 chunk 61 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 188 optimal weight: 7.9990 chunk 198 optimal weight: 2.9990 overall best weight: 1.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 337 ASN ** 8 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 17873 Z= 0.210 Angle : 0.506 12.474 24227 Z= 0.261 Chirality : 0.040 0.147 2795 Planarity : 0.003 0.038 3049 Dihedral : 3.794 23.890 2383 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.52 % Favored : 96.44 % Rotamer Outliers : 0.32 % 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: 1.31 (0.19), residues: 2161 helix: 2.41 (0.16), residues: 1042 sheet: 0.59 (0.30), residues: 301 loop : -1.13 (0.22), residues: 818 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 167 time to evaluate : 2.086 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 172 average time/residue: 0.2774 time to fit residues: 74.8471 Evaluate side-chains 165 residues out of total 2065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 163 time to evaluate : 1.838 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1477 time to fit residues: 3.0625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 130 optimal weight: 0.0470 chunk 210 optimal weight: 0.7980 chunk 128 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 221 optimal weight: 0.9980 chunk 203 optimal weight: 0.2980 chunk 176 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 136 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 337 ASN ** 8 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.053 17873 Z= 0.147 Angle : 0.482 12.932 24227 Z= 0.249 Chirality : 0.039 0.152 2795 Planarity : 0.003 0.039 3049 Dihedral : 3.691 24.417 2383 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.15 % Favored : 96.81 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.19), residues: 2161 helix: 2.46 (0.16), residues: 1050 sheet: 0.68 (0.31), residues: 299 loop : -1.11 (0.22), residues: 812 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 169 time to evaluate : 1.979 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 171 average time/residue: 0.2771 time to fit residues: 74.6120 Evaluate side-chains 163 residues out of total 2065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 162 time to evaluate : 1.866 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1623 time to fit residues: 2.9744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 139 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 162 optimal weight: 0.0970 chunk 26 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 176 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 337 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.122173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.097483 restraints weight = 25950.869| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.78 r_work: 0.2908 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.052 17873 Z= 0.155 Angle : 0.481 13.121 24227 Z= 0.248 Chirality : 0.039 0.144 2795 Planarity : 0.003 0.038 3049 Dihedral : 3.664 24.349 2383 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.42 % Favored : 96.53 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.19), residues: 2161 helix: 2.48 (0.16), residues: 1050 sheet: 0.65 (0.31), residues: 301 loop : -1.11 (0.22), residues: 810 =============================================================================== Job complete usr+sys time: 3233.01 seconds wall clock time: 59 minutes 50.00 seconds (3590.00 seconds total)