Starting phenix.real_space_refine on Sun Jun 15 15:26:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wug_32830/06_2025/7wug_32830.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wug_32830/06_2025/7wug_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/cci-nas-00/data/ceres_data/7wug_32830/06_2025/7wug_32830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wug_32830/06_2025/7wug_32830.map" model { file = "/net/cci-nas-00/data/ceres_data/7wug_32830/06_2025/7wug_32830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wug_32830/06_2025/7wug_32830.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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. Time to flip 33 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.03, per 1000 atoms: 0.52 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 - 3.00 Amino acid : True - 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: 3.63 Conformation dependent library (CDL) restraints added in 2.0 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: 2.15 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: 6.09 Time building geometry restraints manager: 4.39 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: 0.00 - 2.26: 23819 2.26 - 4.52: 341 4.52 - 6.78: 55 6.78 - 9.04: 11 9.04 - 11.30: 1 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 3.040 nonbonded pdb=" OG1 THR 4 117 " pdb=" OD1 ASP 4 150 " model vdw 2.260 3.040 nonbonded pdb=" OD2 ASP 4 321 " pdb=" OG1 THR 4 324 " model vdw 2.262 3.040 nonbonded pdb=" O ILE Y 73 " pdb=" OH TYR Y 198 " model vdw 2.269 3.040 nonbonded pdb=" OH TYR 5 889 " pdb=" OD1 ASP 5 915 " model vdw 2.287 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 1.230 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: 0.650 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 37.870 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.090 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:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.640 ------------------------------------------------------------------------------- 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= 0.180 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 % Allowed : 0.43 % Favored : 99.46 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 5 770 HIS 0.005 0.001 HIS 5 272 PHE 0.021 0.002 PHE 8 195 TYR 0.020 0.002 TYR Y 56 ARG 0.009 0.000 ARG 4 124 Details of bonding type rmsd hydrogen bonds : bond 0.13613 ( 909) hydrogen bonds : angle 5.60262 ( 2652) covalent geometry : bond 0.00365 (17873) covalent geometry : angle 0.69000 (24227) *********************** 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 to be fit. rotamer outliers: 2 poor density : 189 time to evaluate : 2.113 Fit side-chains revert: symmetry clash REVERT: 5 761 ASP cc_start: 0.7733 (t0) cc_final: 0.7495 (t0) REVERT: 1 720 ASP cc_start: 0.8093 (m-30) cc_final: 0.7712 (m-30) REVERT: 4 93 LYS cc_start: 0.8969 (ttmt) cc_final: 0.8622 (ttpt) REVERT: 4 115 ASN cc_start: 0.8030 (m110) cc_final: 0.7726 (m110) REVERT: Y 573 THR cc_start: 0.9166 (OUTLIER) cc_final: 0.8827 (p) outliers start: 2 outliers final: 1 residues processed: 191 average time/residue: 0.2884 time to fit residues: 85.9935 Evaluate side-chains 157 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 155 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 571 LEU Chi-restraints excluded: chain Y residue 573 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 0.7980 chunk 168 optimal weight: 3.9990 chunk 93 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 89 optimal weight: 0.7980 chunk 174 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 201 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.117379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.092173 restraints weight = 26162.650| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 1.80 r_work: 0.2788 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 17873 Z= 0.245 Angle : 0.620 7.036 24227 Z= 0.325 Chirality : 0.044 0.190 2795 Planarity : 0.004 0.054 3049 Dihedral : 4.580 37.804 2386 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.79 % Favored : 96.16 % Rotamer: Outliers : 0.54 % Allowed : 6.65 % Favored : 92.81 % 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: 0.25 (0.18), residues: 2161 helix: 1.39 (0.16), residues: 1030 sheet: 0.45 (0.31), residues: 287 loop : -1.50 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 8 39 HIS 0.005 0.001 HIS 5 272 PHE 0.017 0.002 PHE Y 54 TYR 0.022 0.002 TYR 5 333 ARG 0.005 0.001 ARG 1 694 Details of bonding type rmsd hydrogen bonds : bond 0.06209 ( 909) hydrogen bonds : angle 4.41606 ( 2652) covalent geometry : bond 0.00608 (17873) covalent geometry : angle 0.61980 (24227) *********************** 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 174 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 164 time to evaluate : 2.059 Fit side-chains revert: symmetry clash REVERT: 5 728 GLU cc_start: 0.8355 (mp0) cc_final: 0.8116 (mp0) REVERT: 1 24 ASN cc_start: 0.8609 (m110) cc_final: 0.8254 (m-40) REVERT: 1 536 ASP cc_start: 0.8464 (t0) cc_final: 0.8225 (t0) REVERT: 1 720 ASP cc_start: 0.8614 (m-30) cc_final: 0.8199 (m-30) REVERT: 4 93 LYS cc_start: 0.8558 (ttmt) cc_final: 0.8315 (ttpt) REVERT: 4 115 ASN cc_start: 0.8098 (m110) cc_final: 0.7747 (m110) REVERT: 4 300 ASP cc_start: 0.8129 (m-30) cc_final: 0.7640 (m-30) REVERT: Y 168 MET cc_start: 0.8069 (ptp) cc_final: 0.7778 (ptt) outliers start: 10 outliers final: 7 residues processed: 171 average time/residue: 0.2757 time to fit residues: 74.3365 Evaluate side-chains 161 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 154 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 534 MET Chi-restraints excluded: chain 5 residue 599 GLU Chi-restraints excluded: chain 5 residue 749 VAL Chi-restraints excluded: chain 1 residue 518 LEU Chi-restraints excluded: chain 4 residue 148 THR Chi-restraints excluded: chain 4 residue 205 VAL Chi-restraints excluded: chain 4 residue 290 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 174 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 136 optimal weight: 9.9990 chunk 38 optimal weight: 0.0470 chunk 151 optimal weight: 1.9990 chunk 210 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 123 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 147 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 337 ASN 1 957 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.121375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.096496 restraints weight = 25875.808| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.81 r_work: 0.2869 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 17873 Z= 0.105 Angle : 0.481 6.845 24227 Z= 0.254 Chirality : 0.039 0.142 2795 Planarity : 0.003 0.042 3049 Dihedral : 4.070 23.888 2383 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.05 % Favored : 96.90 % Rotamer: Outliers : 0.81 % Allowed : 8.11 % Favored : 91.08 % 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: 0.80 (0.18), residues: 2161 helix: 1.96 (0.16), residues: 1032 sheet: 0.54 (0.31), residues: 289 loop : -1.34 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 8 39 HIS 0.007 0.000 HIS 5 272 PHE 0.014 0.001 PHE 4 226 TYR 0.017 0.001 TYR 5 273 ARG 0.002 0.000 ARG 1 694 Details of bonding type rmsd hydrogen bonds : bond 0.04122 ( 909) hydrogen bonds : angle 4.08680 ( 2652) covalent geometry : bond 0.00238 (17873) covalent geometry : angle 0.48129 (24227) *********************** 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 187 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 1.891 Fit side-chains revert: symmetry clash REVERT: 8 351 GLN cc_start: 0.8948 (tt0) cc_final: 0.8721 (tt0) REVERT: 1 24 ASN cc_start: 0.8573 (m110) cc_final: 0.8226 (m-40) REVERT: 1 720 ASP cc_start: 0.8547 (m-30) cc_final: 0.8169 (m-30) REVERT: 1 925 MET cc_start: 0.9221 (mtt) cc_final: 0.8992 (mtp) REVERT: 4 93 LYS cc_start: 0.8480 (ttmt) cc_final: 0.8253 (ttpt) REVERT: 4 115 ASN cc_start: 0.8086 (m110) cc_final: 0.7698 (m110) REVERT: 4 300 ASP cc_start: 0.8160 (m-30) cc_final: 0.7758 (m-30) REVERT: Y 168 MET cc_start: 0.8041 (ptp) cc_final: 0.7742 (ptt) REVERT: Y 668 LYS cc_start: 0.8658 (mmmt) cc_final: 0.8283 (mtmt) outliers start: 15 outliers final: 11 residues processed: 178 average time/residue: 0.2862 time to fit residues: 80.0954 Evaluate side-chains 171 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 255 MET Chi-restraints excluded: chain 5 residue 324 THR Chi-restraints excluded: chain 5 residue 534 MET Chi-restraints excluded: chain 5 residue 749 VAL Chi-restraints excluded: chain 1 residue 518 LEU Chi-restraints excluded: chain 1 residue 592 ASP Chi-restraints excluded: chain 1 residue 931 GLU Chi-restraints excluded: chain 4 residue 148 THR Chi-restraints excluded: chain 4 residue 290 MET Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 264 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 170 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 chunk 202 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 189 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 337 ASN 1 957 ASN Y 586 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.117618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.092549 restraints weight = 26213.439| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.79 r_work: 0.2794 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 17873 Z= 0.208 Angle : 0.566 8.161 24227 Z= 0.295 Chirality : 0.042 0.162 2795 Planarity : 0.004 0.046 3049 Dihedral : 4.223 23.350 2383 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.98 % Favored : 95.97 % Rotamer: Outliers : 1.24 % Allowed : 10.06 % Favored : 88.70 % 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: 0.77 (0.18), residues: 2161 helix: 1.94 (0.16), residues: 1035 sheet: 0.43 (0.30), residues: 290 loop : -1.35 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 8 39 HIS 0.005 0.001 HIS 5 272 PHE 0.015 0.002 PHE 8 195 TYR 0.020 0.002 TYR 5 333 ARG 0.004 0.000 ARG 1 694 Details of bonding type rmsd hydrogen bonds : bond 0.05530 ( 909) hydrogen bonds : angle 4.18786 ( 2652) covalent geometry : bond 0.00518 (17873) covalent geometry : angle 0.56553 (24227) *********************** 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 186 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 1.884 Fit side-chains revert: symmetry clash REVERT: 8 351 GLN cc_start: 0.8998 (tt0) cc_final: 0.8690 (tt0) REVERT: 1 24 ASN cc_start: 0.8602 (m110) cc_final: 0.8264 (m-40) REVERT: 1 536 ASP cc_start: 0.8483 (t0) cc_final: 0.8145 (t0) REVERT: 1 720 ASP cc_start: 0.8611 (m-30) cc_final: 0.8143 (m-30) REVERT: 4 93 LYS cc_start: 0.8583 (ttmt) cc_final: 0.8378 (ttpt) REVERT: 4 115 ASN cc_start: 0.8116 (m110) cc_final: 0.7774 (m110) REVERT: 4 300 ASP cc_start: 0.8007 (m-30) cc_final: 0.7527 (m-30) REVERT: Y 168 MET cc_start: 0.8052 (ptp) cc_final: 0.7805 (ptt) REVERT: Y 336 ASN cc_start: 0.8142 (t0) cc_final: 0.7633 (t0) outliers start: 23 outliers final: 15 residues processed: 175 average time/residue: 0.3613 time to fit residues: 100.0934 Evaluate side-chains 171 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 3.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 324 THR Chi-restraints excluded: chain 5 residue 467 CYS Chi-restraints excluded: chain 5 residue 534 MET Chi-restraints excluded: chain 5 residue 749 VAL Chi-restraints excluded: chain 8 residue 289 LEU Chi-restraints excluded: chain 1 residue 518 LEU Chi-restraints excluded: chain 1 residue 592 ASP Chi-restraints excluded: chain 1 residue 706 ASP Chi-restraints excluded: chain 4 residue 148 THR Chi-restraints excluded: chain 4 residue 205 VAL Chi-restraints excluded: chain 4 residue 221 ILE Chi-restraints excluded: chain 4 residue 290 MET Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 264 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 69 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 chunk 204 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 chunk 192 optimal weight: 7.9990 chunk 139 optimal weight: 0.9990 chunk 156 optimal weight: 0.0060 chunk 73 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 90 optimal weight: 20.0000 chunk 85 optimal weight: 0.9980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 301 ASN 8 337 ASN 1 957 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.121181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.096317 restraints weight = 26219.457| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.81 r_work: 0.2876 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1268 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= 0.103 Angle : 0.475 9.464 24227 Z= 0.249 Chirality : 0.039 0.147 2795 Planarity : 0.003 0.041 3049 Dihedral : 3.952 23.857 2383 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.01 % Favored : 96.95 % Rotamer: Outliers : 1.57 % Allowed : 10.76 % Favored : 87.67 % 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: 1.07 (0.19), residues: 2161 helix: 2.25 (0.16), residues: 1035 sheet: 0.53 (0.30), residues: 289 loop : -1.27 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 8 39 HIS 0.007 0.000 HIS 5 272 PHE 0.016 0.001 PHE 8 195 TYR 0.018 0.001 TYR 5 273 ARG 0.005 0.000 ARG 4 124 Details of bonding type rmsd hydrogen bonds : bond 0.03938 ( 909) hydrogen bonds : angle 3.97799 ( 2652) covalent geometry : bond 0.00234 (17873) covalent geometry : angle 0.47462 (24227) *********************** 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 208 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 1.951 Fit side-chains revert: symmetry clash REVERT: 8 351 GLN cc_start: 0.8962 (tt0) cc_final: 0.8724 (tt0) REVERT: 1 24 ASN cc_start: 0.8587 (m110) cc_final: 0.8344 (m-40) REVERT: 1 720 ASP cc_start: 0.8541 (m-30) cc_final: 0.8120 (m-30) REVERT: 1 939 ASN cc_start: 0.8311 (t0) cc_final: 0.8100 (t0) REVERT: 4 93 LYS cc_start: 0.8579 (ttmt) cc_final: 0.8340 (ttpt) REVERT: 4 115 ASN cc_start: 0.8126 (m110) cc_final: 0.7773 (m110) REVERT: 4 150 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7987 (m-30) REVERT: 4 176 HIS cc_start: 0.8035 (OUTLIER) cc_final: 0.7530 (m-70) REVERT: 4 300 ASP cc_start: 0.8077 (m-30) cc_final: 0.7560 (m-30) REVERT: Y 168 MET cc_start: 0.8038 (ptp) cc_final: 0.7776 (ptt) REVERT: Y 264 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8867 (mtm) REVERT: Y 336 ASN cc_start: 0.8151 (t0) cc_final: 0.7561 (t0) REVERT: Y 668 LYS cc_start: 0.8696 (mmmt) cc_final: 0.8277 (mtmt) outliers start: 29 outliers final: 15 residues processed: 195 average time/residue: 0.2732 time to fit residues: 84.8932 Evaluate side-chains 189 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 324 THR Chi-restraints excluded: chain 5 residue 467 CYS Chi-restraints excluded: chain 5 residue 534 MET Chi-restraints excluded: chain 5 residue 544 CYS Chi-restraints excluded: chain 5 residue 749 VAL Chi-restraints excluded: chain 1 residue 123 LEU Chi-restraints excluded: chain 1 residue 706 ASP Chi-restraints excluded: chain 1 residue 931 GLU Chi-restraints excluded: chain 4 residue 148 THR Chi-restraints excluded: chain 4 residue 150 ASP Chi-restraints excluded: chain 4 residue 176 HIS Chi-restraints excluded: chain 4 residue 205 VAL Chi-restraints excluded: chain 4 residue 290 MET Chi-restraints excluded: chain 4 residue 345 VAL Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 207 ILE Chi-restraints excluded: chain Y residue 264 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 140 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 206 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 220 optimal weight: 2.9990 chunk 185 optimal weight: 0.2980 chunk 114 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 337 ASN 1 957 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.120507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.095140 restraints weight = 26034.730| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.86 r_work: 0.2862 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17873 Z= 0.121 Angle : 0.489 11.502 24227 Z= 0.256 Chirality : 0.040 0.141 2795 Planarity : 0.003 0.040 3049 Dihedral : 3.896 23.856 2383 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.70 % Favored : 96.25 % Rotamer: Outliers : 1.46 % Allowed : 11.41 % Favored : 87.13 % 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: 1.16 (0.19), residues: 2161 helix: 2.32 (0.16), residues: 1036 sheet: 0.54 (0.30), residues: 289 loop : -1.21 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 8 39 HIS 0.006 0.001 HIS 5 272 PHE 0.031 0.001 PHE Y 321 TYR 0.020 0.001 TYR 5 333 ARG 0.004 0.000 ARG 4 124 Details of bonding type rmsd hydrogen bonds : bond 0.04176 ( 909) hydrogen bonds : angle 3.93857 ( 2652) covalent geometry : bond 0.00286 (17873) covalent geometry : angle 0.48942 (24227) *********************** 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 203 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 3.020 Fit side-chains revert: symmetry clash REVERT: 5 257 ASP cc_start: 0.8833 (m-30) cc_final: 0.8501 (m-30) REVERT: 8 351 GLN cc_start: 0.8971 (tt0) cc_final: 0.8726 (tt0) REVERT: 1 24 ASN cc_start: 0.8626 (m110) cc_final: 0.8282 (m-40) REVERT: 1 720 ASP cc_start: 0.8579 (m-30) cc_final: 0.8161 (m-30) REVERT: 4 93 LYS cc_start: 0.8586 (ttmt) cc_final: 0.8353 (ttpt) REVERT: 4 115 ASN cc_start: 0.8133 (m110) cc_final: 0.7776 (m110) REVERT: 4 150 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.8002 (m-30) REVERT: 4 300 ASP cc_start: 0.8091 (m-30) cc_final: 0.7653 (m-30) REVERT: Y 168 MET cc_start: 0.8173 (ptp) cc_final: 0.7892 (ptt) REVERT: Y 172 CYS cc_start: 0.8212 (p) cc_final: 0.7912 (p) REVERT: Y 264 MET cc_start: 0.9199 (OUTLIER) cc_final: 0.8923 (mtm) REVERT: Y 336 ASN cc_start: 0.8189 (t0) cc_final: 0.7634 (t0) REVERT: Y 668 LYS cc_start: 0.8664 (mmmt) cc_final: 0.8303 (mtmt) outliers start: 27 outliers final: 18 residues processed: 191 average time/residue: 0.3124 time to fit residues: 98.9070 Evaluate side-chains 188 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 2.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 324 THR Chi-restraints excluded: chain 5 residue 467 CYS Chi-restraints excluded: chain 5 residue 534 MET Chi-restraints excluded: chain 5 residue 723 LEU Chi-restraints excluded: chain 5 residue 749 VAL Chi-restraints excluded: chain 1 residue 123 LEU Chi-restraints excluded: chain 1 residue 518 LEU Chi-restraints excluded: chain 1 residue 592 ASP Chi-restraints excluded: chain 1 residue 706 ASP Chi-restraints excluded: chain 4 residue 148 THR Chi-restraints excluded: chain 4 residue 150 ASP Chi-restraints excluded: chain 4 residue 205 VAL Chi-restraints excluded: chain 4 residue 290 MET Chi-restraints excluded: chain 4 residue 345 VAL Chi-restraints excluded: chain Y residue 81 VAL Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 207 ILE Chi-restraints excluded: chain Y residue 264 MET Chi-restraints excluded: chain Y residue 487 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 24 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 chunk 23 optimal weight: 0.0970 chunk 177 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 337 ASN 1 957 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.121475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.096465 restraints weight = 26064.834| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.85 r_work: 0.2880 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1360 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= 0.107 Angle : 0.474 9.792 24227 Z= 0.249 Chirality : 0.039 0.146 2795 Planarity : 0.003 0.040 3049 Dihedral : 3.808 23.908 2383 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.05 % Favored : 96.90 % Rotamer: Outliers : 1.62 % Allowed : 11.63 % Favored : 86.75 % 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: 1.21 (0.19), residues: 2161 helix: 2.33 (0.16), residues: 1050 sheet: 0.59 (0.30), residues: 289 loop : -1.22 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 8 39 HIS 0.007 0.000 HIS 5 272 PHE 0.015 0.001 PHE 8 195 TYR 0.019 0.001 TYR 5 333 ARG 0.005 0.000 ARG 4 124 Details of bonding type rmsd hydrogen bonds : bond 0.03836 ( 909) hydrogen bonds : angle 3.88065 ( 2652) covalent geometry : bond 0.00246 (17873) covalent geometry : angle 0.47446 (24227) *********************** 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 215 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 2.176 Fit side-chains revert: symmetry clash REVERT: 5 257 ASP cc_start: 0.8788 (m-30) cc_final: 0.8497 (m-30) REVERT: 8 351 GLN cc_start: 0.8974 (tt0) cc_final: 0.8743 (tt0) REVERT: 1 24 ASN cc_start: 0.8597 (m110) cc_final: 0.8268 (m-40) REVERT: 1 720 ASP cc_start: 0.8551 (m-30) cc_final: 0.8151 (m-30) REVERT: 4 93 LYS cc_start: 0.8559 (ttmt) cc_final: 0.8347 (ttpt) REVERT: 4 115 ASN cc_start: 0.8130 (m110) cc_final: 0.7773 (m110) REVERT: 4 150 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.8005 (m-30) REVERT: 4 176 HIS cc_start: 0.8021 (OUTLIER) cc_final: 0.7538 (m-70) REVERT: 4 300 ASP cc_start: 0.8074 (m-30) cc_final: 0.7584 (m-30) REVERT: Y 172 CYS cc_start: 0.8256 (p) cc_final: 0.7967 (p) REVERT: Y 264 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8928 (mtm) REVERT: Y 336 ASN cc_start: 0.8159 (t0) cc_final: 0.7601 (t0) REVERT: Y 549 GLN cc_start: 0.8717 (tt0) cc_final: 0.8374 (tt0) outliers start: 30 outliers final: 21 residues processed: 202 average time/residue: 0.3039 time to fit residues: 99.0976 Evaluate side-chains 193 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 324 THR Chi-restraints excluded: chain 5 residue 467 CYS Chi-restraints excluded: chain 5 residue 534 MET Chi-restraints excluded: chain 5 residue 544 CYS Chi-restraints excluded: chain 5 residue 599 GLU Chi-restraints excluded: chain 5 residue 723 LEU Chi-restraints excluded: chain 5 residue 749 VAL Chi-restraints excluded: chain 1 residue 123 LEU Chi-restraints excluded: chain 1 residue 518 LEU Chi-restraints excluded: chain 1 residue 592 ASP Chi-restraints excluded: chain 1 residue 706 ASP Chi-restraints excluded: chain 4 residue 148 THR Chi-restraints excluded: chain 4 residue 150 ASP Chi-restraints excluded: chain 4 residue 176 HIS Chi-restraints excluded: chain 4 residue 205 VAL Chi-restraints excluded: chain 4 residue 290 MET Chi-restraints excluded: chain 4 residue 345 VAL Chi-restraints excluded: chain Y residue 81 VAL Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 207 ILE Chi-restraints excluded: chain Y residue 252 THR Chi-restraints excluded: chain Y residue 264 MET Chi-restraints excluded: chain Y residue 306 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 53 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 185 optimal weight: 3.9990 chunk 188 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 160 optimal weight: 0.5980 chunk 203 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 337 ASN 1 957 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.120488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.095528 restraints weight = 26007.353| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.85 r_work: 0.2870 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17873 Z= 0.126 Angle : 0.497 11.855 24227 Z= 0.260 Chirality : 0.040 0.150 2795 Planarity : 0.003 0.040 3049 Dihedral : 3.836 23.969 2383 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.47 % Favored : 96.48 % Rotamer: Outliers : 1.51 % Allowed : 12.33 % Favored : 86.15 % 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: 1.23 (0.19), residues: 2161 helix: 2.36 (0.16), residues: 1042 sheet: 0.56 (0.30), residues: 291 loop : -1.17 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 8 39 HIS 0.006 0.001 HIS 5 272 PHE 0.016 0.001 PHE 8 195 TYR 0.020 0.001 TYR 5 333 ARG 0.006 0.000 ARG 4 124 Details of bonding type rmsd hydrogen bonds : bond 0.04174 ( 909) hydrogen bonds : angle 3.90415 ( 2652) covalent geometry : bond 0.00300 (17873) covalent geometry : angle 0.49667 (24227) *********************** 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 200 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 2.170 Fit side-chains revert: symmetry clash REVERT: 5 257 ASP cc_start: 0.8828 (m-30) cc_final: 0.8539 (m-30) REVERT: 5 915 ASP cc_start: 0.8820 (OUTLIER) cc_final: 0.8457 (m-30) REVERT: 8 351 GLN cc_start: 0.8971 (tt0) cc_final: 0.8730 (tt0) REVERT: 1 24 ASN cc_start: 0.8685 (m110) cc_final: 0.8368 (m-40) REVERT: 1 720 ASP cc_start: 0.8569 (m-30) cc_final: 0.8143 (m-30) REVERT: 4 93 LYS cc_start: 0.8590 (ttmt) cc_final: 0.8365 (ttpt) REVERT: 4 115 ASN cc_start: 0.8136 (m110) cc_final: 0.7778 (m110) REVERT: 4 150 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.8051 (m-30) REVERT: 4 300 ASP cc_start: 0.8059 (m-30) cc_final: 0.7574 (m-30) REVERT: Y 172 CYS cc_start: 0.8321 (p) cc_final: 0.8024 (p) REVERT: Y 264 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.8932 (mtm) REVERT: Y 336 ASN cc_start: 0.8145 (t0) cc_final: 0.7587 (t0) outliers start: 28 outliers final: 20 residues processed: 188 average time/residue: 0.4175 time to fit residues: 126.4069 Evaluate side-chains 189 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 2.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 324 THR Chi-restraints excluded: chain 5 residue 467 CYS Chi-restraints excluded: chain 5 residue 534 MET Chi-restraints excluded: chain 5 residue 599 GLU Chi-restraints excluded: chain 5 residue 723 LEU Chi-restraints excluded: chain 5 residue 749 VAL Chi-restraints excluded: chain 5 residue 915 ASP Chi-restraints excluded: chain 1 residue 123 LEU Chi-restraints excluded: chain 1 residue 518 LEU Chi-restraints excluded: chain 1 residue 592 ASP Chi-restraints excluded: chain 1 residue 706 ASP Chi-restraints excluded: chain 4 residue 148 THR Chi-restraints excluded: chain 4 residue 150 ASP Chi-restraints excluded: chain 4 residue 205 VAL Chi-restraints excluded: chain 4 residue 290 MET Chi-restraints excluded: chain 4 residue 345 VAL Chi-restraints excluded: chain Y residue 81 VAL Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 207 ILE Chi-restraints excluded: chain Y residue 252 THR Chi-restraints excluded: chain Y residue 264 MET Chi-restraints excluded: chain Y residue 487 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 28 optimal weight: 0.6980 chunk 159 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 151 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 210 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 337 ASN 1 957 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.121094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.096093 restraints weight = 25924.604| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.85 r_work: 0.2876 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17873 Z= 0.116 Angle : 0.489 10.246 24227 Z= 0.256 Chirality : 0.040 0.142 2795 Planarity : 0.003 0.040 3049 Dihedral : 3.804 24.204 2383 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.10 % Favored : 96.85 % Rotamer: Outliers : 1.41 % Allowed : 12.76 % Favored : 85.83 % 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: 1.28 (0.19), residues: 2161 helix: 2.39 (0.16), residues: 1042 sheet: 0.59 (0.30), residues: 291 loop : -1.13 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 8 39 HIS 0.006 0.001 HIS 5 272 PHE 0.016 0.001 PHE 8 195 TYR 0.020 0.001 TYR 5 333 ARG 0.004 0.000 ARG 4 124 Details of bonding type rmsd hydrogen bonds : bond 0.03971 ( 909) hydrogen bonds : angle 3.89231 ( 2652) covalent geometry : bond 0.00272 (17873) covalent geometry : angle 0.48859 (24227) *********************** 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 197 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 2.062 Fit side-chains revert: symmetry clash REVERT: 5 257 ASP cc_start: 0.8807 (m-30) cc_final: 0.8518 (m-30) REVERT: 5 915 ASP cc_start: 0.8796 (OUTLIER) cc_final: 0.8416 (m-30) REVERT: 8 351 GLN cc_start: 0.8963 (tt0) cc_final: 0.8728 (tt0) REVERT: 1 24 ASN cc_start: 0.8697 (m110) cc_final: 0.8366 (m-40) REVERT: 1 720 ASP cc_start: 0.8566 (m-30) cc_final: 0.8165 (m-30) REVERT: 4 93 LYS cc_start: 0.8593 (ttmt) cc_final: 0.8375 (ttpt) REVERT: 4 115 ASN cc_start: 0.8140 (m110) cc_final: 0.7757 (m110) REVERT: 4 150 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7957 (m-30) REVERT: 4 300 ASP cc_start: 0.8073 (m-30) cc_final: 0.7596 (m-30) REVERT: Y 172 CYS cc_start: 0.8332 (p) cc_final: 0.8034 (p) REVERT: Y 264 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8943 (mtm) REVERT: Y 336 ASN cc_start: 0.8170 (t0) cc_final: 0.7579 (t0) outliers start: 26 outliers final: 20 residues processed: 186 average time/residue: 0.2699 time to fit residues: 80.6718 Evaluate side-chains 191 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 324 THR Chi-restraints excluded: chain 5 residue 467 CYS Chi-restraints excluded: chain 5 residue 534 MET Chi-restraints excluded: chain 5 residue 599 GLU Chi-restraints excluded: chain 5 residue 723 LEU Chi-restraints excluded: chain 5 residue 749 VAL Chi-restraints excluded: chain 5 residue 915 ASP Chi-restraints excluded: chain 1 residue 123 LEU Chi-restraints excluded: chain 1 residue 518 LEU Chi-restraints excluded: chain 1 residue 592 ASP Chi-restraints excluded: chain 1 residue 706 ASP Chi-restraints excluded: chain 4 residue 148 THR Chi-restraints excluded: chain 4 residue 150 ASP Chi-restraints excluded: chain 4 residue 205 VAL Chi-restraints excluded: chain 4 residue 290 MET Chi-restraints excluded: chain 4 residue 345 VAL Chi-restraints excluded: chain Y residue 81 VAL Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 207 ILE Chi-restraints excluded: chain Y residue 252 THR Chi-restraints excluded: chain Y residue 264 MET Chi-restraints excluded: chain Y residue 487 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 125 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 164 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 126 optimal weight: 0.0270 chunk 2 optimal weight: 0.9980 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 337 ASN 1 957 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.120985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.095961 restraints weight = 26003.192| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.86 r_work: 0.2868 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17873 Z= 0.119 Angle : 0.497 13.383 24227 Z= 0.259 Chirality : 0.040 0.140 2795 Planarity : 0.003 0.040 3049 Dihedral : 3.799 24.220 2383 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.38 % Favored : 96.58 % Rotamer: Outliers : 1.41 % Allowed : 12.76 % Favored : 85.83 % 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: 1.28 (0.19), residues: 2161 helix: 2.39 (0.16), residues: 1043 sheet: 0.52 (0.30), residues: 299 loop : -1.11 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 8 39 HIS 0.006 0.001 HIS 5 272 PHE 0.015 0.001 PHE 8 195 TYR 0.019 0.001 TYR 5 333 ARG 0.004 0.000 ARG 4 124 Details of bonding type rmsd hydrogen bonds : bond 0.04010 ( 909) hydrogen bonds : angle 3.89659 ( 2652) covalent geometry : bond 0.00281 (17873) covalent geometry : angle 0.49735 (24227) ********************** 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 198 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 2.039 Fit side-chains revert: symmetry clash REVERT: 5 257 ASP cc_start: 0.8810 (m-30) cc_final: 0.8520 (m-30) REVERT: 5 915 ASP cc_start: 0.8803 (OUTLIER) cc_final: 0.8422 (m-30) REVERT: 8 351 GLN cc_start: 0.8959 (tt0) cc_final: 0.8717 (tt0) REVERT: 1 24 ASN cc_start: 0.8684 (m110) cc_final: 0.8356 (m-40) REVERT: 1 536 ASP cc_start: 0.8451 (t0) cc_final: 0.8178 (t0) REVERT: 1 720 ASP cc_start: 0.8576 (m-30) cc_final: 0.8183 (m-30) REVERT: 4 93 LYS cc_start: 0.8586 (ttmt) cc_final: 0.8372 (ttpt) REVERT: 4 115 ASN cc_start: 0.8141 (m110) cc_final: 0.7777 (m110) REVERT: 4 150 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7973 (m-30) REVERT: 4 300 ASP cc_start: 0.8051 (m-30) cc_final: 0.7567 (m-30) REVERT: Y 172 CYS cc_start: 0.8380 (p) cc_final: 0.8061 (p) REVERT: Y 192 PHE cc_start: 0.9225 (t80) cc_final: 0.8980 (t80) REVERT: Y 264 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8945 (mtm) REVERT: Y 336 ASN cc_start: 0.8126 (t0) cc_final: 0.7553 (t0) outliers start: 26 outliers final: 21 residues processed: 188 average time/residue: 0.2624 time to fit residues: 79.2913 Evaluate side-chains 192 residues out of total 2065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 324 THR Chi-restraints excluded: chain 5 residue 467 CYS Chi-restraints excluded: chain 5 residue 534 MET Chi-restraints excluded: chain 5 residue 544 CYS Chi-restraints excluded: chain 5 residue 599 GLU Chi-restraints excluded: chain 5 residue 723 LEU Chi-restraints excluded: chain 5 residue 749 VAL Chi-restraints excluded: chain 5 residue 915 ASP Chi-restraints excluded: chain 1 residue 123 LEU Chi-restraints excluded: chain 1 residue 518 LEU Chi-restraints excluded: chain 1 residue 592 ASP Chi-restraints excluded: chain 1 residue 706 ASP Chi-restraints excluded: chain 4 residue 148 THR Chi-restraints excluded: chain 4 residue 150 ASP Chi-restraints excluded: chain 4 residue 205 VAL Chi-restraints excluded: chain 4 residue 290 MET Chi-restraints excluded: chain 4 residue 345 VAL Chi-restraints excluded: chain Y residue 81 VAL Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 207 ILE Chi-restraints excluded: chain Y residue 252 THR Chi-restraints excluded: chain Y residue 264 MET Chi-restraints excluded: chain Y residue 487 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 70 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 chunk 217 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 190 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 193 optimal weight: 4.9990 chunk 205 optimal weight: 4.9990 chunk 213 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 337 ASN 1 957 ASN 4 322 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.119304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.093639 restraints weight = 26114.666| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.86 r_work: 0.2839 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1471 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= 0.160 Angle : 0.535 13.259 24227 Z= 0.279 Chirality : 0.041 0.150 2795 Planarity : 0.003 0.040 3049 Dihedral : 3.947 24.190 2383 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.38 % Favored : 96.58 % Rotamer: Outliers : 1.51 % Allowed : 12.71 % Favored : 85.78 % 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: 1.18 (0.19), residues: 2161 helix: 2.28 (0.16), residues: 1041 sheet: 0.50 (0.30), residues: 294 loop : -1.13 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 8 39 HIS 0.006 0.001 HIS 5 272 PHE 0.016 0.001 PHE 8 195 TYR 0.023 0.001 TYR 5 333 ARG 0.004 0.000 ARG 4 124 Details of bonding type rmsd hydrogen bonds : bond 0.04685 ( 909) hydrogen bonds : angle 3.99460 ( 2652) covalent geometry : bond 0.00393 (17873) covalent geometry : angle 0.53539 (24227) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10402.40 seconds wall clock time: 184 minutes 50.85 seconds (11090.85 seconds total)