Starting phenix.real_space_refine on Sun Dec 10 17:26:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8r_14561/12_2023/7z8r_14561.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8r_14561/12_2023/7z8r_14561.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8r_14561/12_2023/7z8r_14561.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8r_14561/12_2023/7z8r_14561.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8r_14561/12_2023/7z8r_14561.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8r_14561/12_2023/7z8r_14561.pdb" } resolution = 2.7 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 3 6.06 5 S 91 5.16 5 C 9647 2.51 5 N 2576 2.21 5 O 2807 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ASP 22": "OD1" <-> "OD2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 112": "OD1" <-> "OD2" Residue "C TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 169": "OD1" <-> "OD2" Residue "C GLU 210": "OE1" <-> "OE2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C ASP 312": "OD1" <-> "OD2" Residue "C GLU 341": "OE1" <-> "OE2" Residue "C GLU 353": "OE1" <-> "OE2" Residue "C ASP 362": "OD1" <-> "OD2" Residue "C ASP 396": "OD1" <-> "OD2" Residue "C PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 443": "OE1" <-> "OE2" Residue "C PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 510": "OD1" <-> "OD2" Residue "C ASP 754": "OD1" <-> "OD2" Residue "C TYR 761": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 366": "OE1" <-> "OE2" Residue "D GLU 387": "OE1" <-> "OE2" Residue "D TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 554": "OD1" <-> "OD2" Residue "D GLU 587": "OE1" <-> "OE2" Residue "D GLU 696": "OE1" <-> "OE2" Residue "D GLU 737": "OE1" <-> "OE2" Residue "D ASP 850": "OD1" <-> "OD2" Residue "D PHE 865": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 878": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 915": "OE1" <-> "OE2" Residue "D TYR 973": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 980": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1110": "OE1" <-> "OE2" Residue "D GLU 1171": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 15124 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 5626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 715, 5626 Classifications: {'peptide': 715} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 12, 'TRANS': 702} Chain breaks: 3 Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 282 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 157 Chain: "D" Number of atoms: 8792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1149, 8792 Classifications: {'peptide': 1149} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 55, 'TRANS': 1093} Chain breaks: 5 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 140 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 16, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 115 Chain: "R" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 706 Unusual residues: {' ZN': 3} Classifications: {'peptide': 86, 'undetermined': 3} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 84, None: 3} Not linked: pdbres="TYR R 106 " pdbres=" ZN R 201 " Not linked: pdbres=" ZN R 201 " pdbres=" ZN R 202 " Not linked: pdbres=" ZN R 202 " pdbres=" ZN R 203 " Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14603 SG CYS R 42 134.188 53.405 48.693 1.00 81.63 S ATOM 14622 SG CYS R 45 136.854 51.786 51.212 1.00 84.76 S ATOM 14910 SG CYS R 83 133.928 53.681 52.490 1.00 73.53 S ATOM 14839 SG CYS R 75 126.568 60.641 41.209 1.00 60.58 S ATOM 15006 SG CYS R 94 129.949 61.609 42.973 1.00 68.92 S ATOM 14686 SG CYS R 53 132.795 49.611 56.110 1.00 88.77 S ATOM 14709 SG CYS R 56 131.786 49.413 59.780 1.00 94.10 S ATOM 14789 SG CYS R 68 129.591 47.803 56.925 1.00 85.00 S Time building chain proxies: 8.07, per 1000 atoms: 0.53 Number of scatterers: 15124 At special positions: 0 Unit cell: (150.662, 129.382, 115.763, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 3 29.99 S 91 16.00 O 2807 8.00 N 2576 7.00 C 9647 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.12 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 80 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 45 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 42 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 83 " pdb=" ZN R 202 " pdb="ZN ZN R 202 " - pdb=" ND1 HIS R 77 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 75 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 94 " pdb=" ZN R 203 " pdb="ZN ZN R 203 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 68 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 56 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 53 " Number of angles added : 6 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3760 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 5 sheets defined 77.2% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'C' and resid 18 through 32 removed outlier: 3.715A pdb=" N ASP C 23 " --> pdb=" O GLN C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 54 Processing helix chain 'C' and resid 85 through 105 removed outlier: 3.839A pdb=" N LYS C 105 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 137 removed outlier: 3.736A pdb=" N LEU C 116 " --> pdb=" O ASP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 152 removed outlier: 4.265A pdb=" N VAL C 145 " --> pdb=" O ASN C 141 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARG C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 171 Processing helix chain 'C' and resid 175 through 192 Processing helix chain 'C' and resid 197 through 211 removed outlier: 4.356A pdb=" N ILE C 201 " --> pdb=" O ASN C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 232 Processing helix chain 'C' and resid 232 through 253 removed outlier: 3.860A pdb=" N THR C 249 " --> pdb=" O THR C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 279 removed outlier: 3.608A pdb=" N LYS C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU C 279 " --> pdb=" O VAL C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'C' and resid 283 through 297 Processing helix chain 'C' and resid 299 through 313 removed outlier: 3.744A pdb=" N GLN C 308 " --> pdb=" O HIS C 304 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN C 309 " --> pdb=" O THR C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 327 Processing helix chain 'C' and resid 333 through 356 removed outlier: 3.943A pdb=" N CYS C 355 " --> pdb=" O ALA C 351 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLY C 356 " --> pdb=" O ILE C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 362 through 385 removed outlier: 3.511A pdb=" N TYR C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 405 removed outlier: 3.789A pdb=" N ASN C 404 " --> pdb=" O GLY C 400 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 413 Processing helix chain 'C' and resid 416 through 431 removed outlier: 3.604A pdb=" N GLU C 420 " --> pdb=" O SER C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 454 removed outlier: 3.584A pdb=" N LYS C 454 " --> pdb=" O MET C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 476 removed outlier: 4.328A pdb=" N PHE C 462 " --> pdb=" O ASP C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 496 Processing helix chain 'C' and resid 498 through 527 removed outlier: 4.016A pdb=" N MET C 507 " --> pdb=" O LYS C 503 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE C 508 " --> pdb=" O LEU C 504 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU C 519 " --> pdb=" O LYS C 515 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN C 520 " --> pdb=" O ASP C 516 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN C 527 " --> pdb=" O LYS C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 558 No H-bonds generated for 'chain 'C' and resid 556 through 558' Processing helix chain 'C' and resid 559 through 574 Processing helix chain 'C' and resid 605 through 613 removed outlier: 3.714A pdb=" N GLN C 613 " --> pdb=" O ALA C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 616 No H-bonds generated for 'chain 'C' and resid 614 through 616' Processing helix chain 'C' and resid 622 through 630 removed outlier: 4.126A pdb=" N ASP C 627 " --> pdb=" O GLN C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 646 removed outlier: 3.545A pdb=" N SER C 646 " --> pdb=" O ILE C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 722 removed outlier: 4.088A pdb=" N GLN C 692 " --> pdb=" O MET C 688 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS C 693 " --> pdb=" O LYS C 689 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE C 703 " --> pdb=" O THR C 699 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU C 704 " --> pdb=" O HIS C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 739 Processing helix chain 'C' and resid 745 through 759 Processing helix chain 'D' and resid 7 through 15 Processing helix chain 'D' and resid 19 through 34 Processing helix chain 'D' and resid 45 through 57 removed outlier: 3.687A pdb=" N LYS D 51 " --> pdb=" O ARG D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 77 removed outlier: 3.686A pdb=" N GLN D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLY D 73 " --> pdb=" O VAL D 69 " (cutoff:3.500A) Proline residue: D 74 - end of helix removed outlier: 4.157A pdb=" N SER D 77 " --> pdb=" O GLY D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 96 removed outlier: 3.606A pdb=" N VAL D 84 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU D 85 " --> pdb=" O GLU D 81 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR D 86 " --> pdb=" O TYR D 82 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU D 96 " --> pdb=" O CYS D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 117 Processing helix chain 'D' and resid 128 through 144 removed outlier: 3.622A pdb=" N ARG D 137 " --> pdb=" O LYS D 133 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER D 140 " --> pdb=" O GLY D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 165 removed outlier: 3.828A pdb=" N ARG D 164 " --> pdb=" O ASP D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 181 Processing helix chain 'D' and resid 182 through 186 removed outlier: 3.544A pdb=" N THR D 185 " --> pdb=" O PRO D 182 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER D 186 " --> pdb=" O GLN D 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 182 through 186' Processing helix chain 'D' and resid 188 through 205 removed outlier: 3.676A pdb=" N ARG D 192 " --> pdb=" O ARG D 188 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 225 Processing helix chain 'D' and resid 227 through 245 removed outlier: 3.546A pdb=" N THR D 231 " --> pdb=" O SER D 227 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG D 232 " --> pdb=" O MET D 228 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR D 233 " --> pdb=" O SER D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 264 Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 268 through 286 removed outlier: 3.610A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR D 274 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 292 No H-bonds generated for 'chain 'D' and resid 290 through 292' Processing helix chain 'D' and resid 293 through 306 removed outlier: 4.493A pdb=" N THR D 306 " --> pdb=" O LEU D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 363 removed outlier: 3.967A pdb=" N ARG D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR D 363 " --> pdb=" O ALA D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 382 removed outlier: 4.847A pdb=" N SER D 376 " --> pdb=" O TYR D 372 " (cutoff:3.500A) Proline residue: D 377 - end of helix Processing helix chain 'D' and resid 383 through 385 No H-bonds generated for 'chain 'D' and resid 383 through 385' Processing helix chain 'D' and resid 387 through 406 removed outlier: 3.582A pdb=" N ARG D 406 " --> pdb=" O LEU D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 443 Proline residue: D 433 - end of helix removed outlier: 3.933A pdb=" N LYS D 441 " --> pdb=" O LYS D 437 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 465 removed outlier: 4.073A pdb=" N ARG D 451 " --> pdb=" O SER D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 485 Proline residue: D 478 - end of helix Processing helix chain 'D' and resid 490 through 507 Processing helix chain 'D' and resid 509 through 515 removed outlier: 3.523A pdb=" N VAL D 512 " --> pdb=" O SER D 509 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE D 513 " --> pdb=" O PRO D 510 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS D 514 " --> pdb=" O GLN D 511 " (cutoff:3.500A) Proline residue: D 515 - end of helix No H-bonds generated for 'chain 'D' and resid 509 through 515' Processing helix chain 'D' and resid 516 through 529 Proline residue: D 522 - end of helix removed outlier: 3.648A pdb=" N GLY D 529 " --> pdb=" O VAL D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 551 removed outlier: 3.624A pdb=" N GLN D 545 " --> pdb=" O LEU D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 577 removed outlier: 3.809A pdb=" N ILE D 565 " --> pdb=" O ALA D 561 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS D 566 " --> pdb=" O THR D 562 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASP D 567 " --> pdb=" O PRO D 563 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS D 574 " --> pdb=" O THR D 570 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG D 575 " --> pdb=" O CYS D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 601 Processing helix chain 'D' and resid 606 through 619 removed outlier: 4.576A pdb=" N ASN D 610 " --> pdb=" O SER D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 637 removed outlier: 4.056A pdb=" N THR D 628 " --> pdb=" O THR D 624 " (cutoff:3.500A) Processing helix chain 'D' and resid 644 through 658 removed outlier: 3.923A pdb=" N GLY D 649 " --> pdb=" O ARG D 645 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLU D 650 " --> pdb=" O PRO D 646 " (cutoff:3.500A) Proline residue: D 653 - end of helix Processing helix chain 'D' and resid 659 through 661 No H-bonds generated for 'chain 'D' and resid 659 through 661' Processing helix chain 'D' and resid 663 through 681 Processing helix chain 'D' and resid 682 through 685 removed outlier: 3.508A pdb=" N LEU D 685 " --> pdb=" O SER D 682 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 682 through 685' Processing helix chain 'D' and resid 686 through 695 Processing helix chain 'D' and resid 705 through 723 removed outlier: 3.816A pdb=" N SER D 709 " --> pdb=" O ASP D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 730 removed outlier: 3.664A pdb=" N LEU D 727 " --> pdb=" O PRO D 724 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N SER D 728 " --> pdb=" O SER D 725 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS D 729 " --> pdb=" O SER D 726 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE D 730 " --> pdb=" O LEU D 727 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 724 through 730' Processing helix chain 'D' and resid 732 through 743 removed outlier: 3.603A pdb=" N ASN D 736 " --> pdb=" O GLY D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 766 removed outlier: 3.741A pdb=" N VAL D 764 " --> pdb=" O GLN D 760 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR D 765 " --> pdb=" O ALA D 761 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLY D 766 " --> pdb=" O LEU D 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 771 through 786 Proline residue: D 782 - end of helix Processing helix chain 'D' and resid 792 through 810 removed outlier: 4.216A pdb=" N TYR D 796 " --> pdb=" O HIS D 792 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR D 797 " --> pdb=" O LYS D 793 " (cutoff:3.500A) Processing helix chain 'D' and resid 813 through 827 removed outlier: 3.626A pdb=" N VAL D 817 " --> pdb=" O GLU D 813 " (cutoff:3.500A) Processing helix chain 'D' and resid 831 through 849 removed outlier: 4.315A pdb=" N HIS D 848 " --> pdb=" O GLU D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 856 through 866 removed outlier: 4.076A pdb=" N SER D 866 " --> pdb=" O LEU D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 869 through 887 removed outlier: 3.577A pdb=" N LYS D 873 " --> pdb=" O SER D 869 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER D 884 " --> pdb=" O LEU D 880 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL D 885 " --> pdb=" O GLY D 881 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLY D 886 " --> pdb=" O SER D 882 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN D 887 " --> pdb=" O ILE D 883 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 902 Proline residue: D 893 - end of helix removed outlier: 3.706A pdb=" N THR D 900 " --> pdb=" O LEU D 896 " (cutoff:3.500A) Processing helix chain 'D' and resid 908 through 919 Processing helix chain 'D' and resid 921 through 926 removed outlier: 3.529A pdb=" N LYS D 926 " --> pdb=" O VAL D 922 " (cutoff:3.500A) Processing helix chain 'D' and resid 928 through 940 Processing helix chain 'D' and resid 946 through 961 removed outlier: 3.677A pdb=" N VAL D 950 " --> pdb=" O GLY D 946 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL D 951 " --> pdb=" O THR D 947 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D 960 " --> pdb=" O GLY D 956 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE D 961 " --> pdb=" O LYS D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 962 through 973 removed outlier: 3.545A pdb=" N LEU D 966 " --> pdb=" O ASP D 962 " (cutoff:3.500A) Proline residue: D 968 - end of helix removed outlier: 3.923A pdb=" N TYR D 973 " --> pdb=" O ARG D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 978 through 990 removed outlier: 3.540A pdb=" N ARG D 982 " --> pdb=" O SER D 978 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS D 990 " --> pdb=" O VAL D 986 " (cutoff:3.500A) Processing helix chain 'D' and resid 991 through 993 No H-bonds generated for 'chain 'D' and resid 991 through 993' Processing helix chain 'D' and resid 1000 through 1013 removed outlier: 3.564A pdb=" N ASN D1006 " --> pdb=" O PRO D1002 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLY D1009 " --> pdb=" O LYS D1005 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ASP D1010 " --> pdb=" O ASN D1006 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE D1011 " --> pdb=" O CYS D1007 " (cutoff:3.500A) Processing helix chain 'D' and resid 1014 through 1016 No H-bonds generated for 'chain 'D' and resid 1014 through 1016' Processing helix chain 'D' and resid 1019 through 1037 removed outlier: 3.918A pdb=" N ARG D1023 " --> pdb=" O ASP D1019 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG D1024 " --> pdb=" O LEU D1020 " (cutoff:3.500A) Processing helix chain 'D' and resid 1038 through 1043 removed outlier: 4.573A pdb=" N ARG D1042 " --> pdb=" O SER D1039 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ASP D1043 " --> pdb=" O LEU D1040 " (cutoff:3.500A) Processing helix chain 'D' and resid 1044 through 1055 Proline residue: D1050 - end of helix Processing helix chain 'D' and resid 1078 through 1096 removed outlier: 3.617A pdb=" N ASP D1094 " --> pdb=" O TYR D1090 " (cutoff:3.500A) Processing helix chain 'D' and resid 1103 through 1113 removed outlier: 3.734A pdb=" N ASN D1107 " --> pdb=" O PHE D1103 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N HIS D1108 " --> pdb=" O GLU D1104 " (cutoff:3.500A) Processing helix chain 'D' and resid 1116 through 1131 Processing helix chain 'D' and resid 1134 through 1141 removed outlier: 3.972A pdb=" N VAL D1138 " --> pdb=" O CYS D1134 " (cutoff:3.500A) Processing helix chain 'D' and resid 1141 through 1154 removed outlier: 4.131A pdb=" N GLU D1147 " --> pdb=" O ASP D1143 " (cutoff:3.500A) Proline residue: D1148 - end of helix Processing helix chain 'D' and resid 1162 through 1185 removed outlier: 3.912A pdb=" N PHE D1166 " --> pdb=" O VAL D1162 " (cutoff:3.500A) Processing helix chain 'D' and resid 1192 through 1205 Processing helix chain 'D' and resid 1205 through 1215 removed outlier: 3.530A pdb=" N ILE D1211 " --> pdb=" O GLU D1207 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 58 Processing helix chain 'R' and resid 62 through 67 removed outlier: 4.321A pdb=" N GLU R 67 " --> pdb=" O ALA R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 88 Processing sheet with id=AA1, first strand: chain 'C' and resid 534 through 541 removed outlier: 6.410A pdb=" N ASP C 534 " --> pdb=" O TRP R 27 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ALA R 29 " --> pdb=" O ASP C 534 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER C 536 " --> pdb=" O ALA R 29 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ALA R 31 " --> pdb=" O SER C 536 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N GLN C 538 " --> pdb=" O ALA R 31 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N TRP R 33 " --> pdb=" O GLN C 538 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU C 540 " --> pdb=" O TRP R 33 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N TRP R 35 " --> pdb=" O LEU C 540 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N PHE R 22 " --> pdb=" O LEU C 590 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N LEU C 590 " --> pdb=" O PHE R 22 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N VAL R 24 " --> pdb=" O GLY C 588 " (cutoff:3.500A) removed outlier: 10.282A pdb=" N GLY C 588 " --> pdb=" O VAL R 24 " (cutoff:3.500A) removed outlier: 11.415A pdb=" N LYS R 26 " --> pdb=" O SER C 586 " (cutoff:3.500A) removed outlier: 10.519A pdb=" N SER C 586 " --> pdb=" O LYS R 26 " (cutoff:3.500A) removed outlier: 11.405A pdb=" N ASN R 28 " --> pdb=" O GLN C 584 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N GLN C 584 " --> pdb=" O ASN R 28 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL R 30 " --> pdb=" O LEU C 582 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR C 599 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL C 682 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 619 through 621 removed outlier: 3.731A pdb=" N VAL C 650 " --> pdb=" O LYS C 670 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 724 through 726 Processing sheet with id=AA4, first strand: chain 'D' and resid 1064 through 1068 removed outlier: 3.644A pdb=" N MET D1068 " --> pdb=" O PHE D1071 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'R' and resid 78 through 80 removed outlier: 6.630A pdb=" N TRP R 72 " --> pdb=" O GLN R 104 " (cutoff:3.500A) 967 hydrogen bonds defined for protein. 2886 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.54 Time building geometry restraints manager: 6.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2667 1.32 - 1.45: 3625 1.45 - 1.57: 8950 1.57 - 1.69: 2 1.69 - 1.81: 133 Bond restraints: 15377 Sorted by residual: bond pdb=" C GLY D1112 " pdb=" O GLY D1112 " ideal model delta sigma weight residual 1.235 1.201 0.033 1.23e-02 6.61e+03 7.26e+00 bond pdb=" C LEU D1113 " pdb=" O LEU D1113 " ideal model delta sigma weight residual 1.236 1.204 0.032 1.29e-02 6.01e+03 6.01e+00 bond pdb=" N LEU D1113 " pdb=" CA LEU D1113 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.35e-02 5.49e+03 5.54e+00 bond pdb=" N ASP D1111 " pdb=" CA ASP D1111 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.21e-02 6.83e+03 3.56e+00 bond pdb=" CB PRO C 223 " pdb=" CG PRO C 223 " ideal model delta sigma weight residual 1.492 1.571 -0.079 5.00e-02 4.00e+02 2.50e+00 ... (remaining 15372 not shown) Histogram of bond angle deviations from ideal: 99.17 - 106.14: 329 106.14 - 113.11: 8603 113.11 - 120.08: 5283 120.08 - 127.05: 6498 127.05 - 134.02: 136 Bond angle restraints: 20849 Sorted by residual: angle pdb=" N ILE D1102 " pdb=" CA ILE D1102 " pdb=" C ILE D1102 " ideal model delta sigma weight residual 112.83 108.75 4.08 9.90e-01 1.02e+00 1.70e+01 angle pdb=" C ASP D1111 " pdb=" N GLY D1112 " pdb=" CA GLY D1112 " ideal model delta sigma weight residual 120.22 125.24 -5.02 1.27e+00 6.20e-01 1.56e+01 angle pdb=" N LYS D1114 " pdb=" CA LYS D1114 " pdb=" C LYS D1114 " ideal model delta sigma weight residual 112.92 108.11 4.81 1.23e+00 6.61e-01 1.53e+01 angle pdb=" C ARG C 401 " pdb=" N PHE C 402 " pdb=" CA PHE C 402 " ideal model delta sigma weight residual 122.06 116.02 6.04 1.86e+00 2.89e-01 1.06e+01 angle pdb=" C LYS D 661 " pdb=" N ASN D 662 " pdb=" CA ASN D 662 " ideal model delta sigma weight residual 121.54 127.33 -5.79 1.91e+00 2.74e-01 9.19e+00 ... (remaining 20844 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.33: 8468 16.33 - 32.67: 745 32.67 - 49.00: 159 49.00 - 65.34: 31 65.34 - 81.67: 13 Dihedral angle restraints: 9416 sinusoidal: 3653 harmonic: 5763 Sorted by residual: dihedral pdb=" CA PHE C 232 " pdb=" C PHE C 232 " pdb=" N GLU C 233 " pdb=" CA GLU C 233 " ideal model delta harmonic sigma weight residual -180.00 -164.13 -15.87 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA ASN C 683 " pdb=" CB ASN C 683 " pdb=" CG ASN C 683 " pdb=" OD1 ASN C 683 " ideal model delta sinusoidal sigma weight residual 120.00 -173.68 -66.32 2 2.00e+01 2.50e-03 1.01e+01 dihedral pdb=" CA ARG D 284 " pdb=" C ARG D 284 " pdb=" N ARG D 285 " pdb=" CA ARG D 285 " ideal model delta harmonic sigma weight residual 180.00 -164.19 -15.81 0 5.00e+00 4.00e-02 9.99e+00 ... (remaining 9413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1936 0.045 - 0.090: 460 0.090 - 0.135: 93 0.135 - 0.180: 2 0.180 - 0.225: 2 Chirality restraints: 2493 Sorted by residual: chirality pdb=" CA LYS D1114 " pdb=" N LYS D1114 " pdb=" C LYS D1114 " pdb=" CB LYS D1114 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA LEU D1113 " pdb=" N LEU D1113 " pdb=" C LEU D1113 " pdb=" CB LEU D1113 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA LEU D 181 " pdb=" N LEU D 181 " pdb=" C LEU D 181 " pdb=" CB LEU D 181 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.92e-01 ... (remaining 2490 not shown) Planarity restraints: 2631 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 664 " 0.036 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO C 665 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 665 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 665 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU D1113 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.37e+00 pdb=" C LEU D1113 " 0.036 2.00e-02 2.50e+03 pdb=" O LEU D1113 " -0.014 2.00e-02 2.50e+03 pdb=" N LYS D1114 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN D 902 " -0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO D 903 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO D 903 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 903 " -0.028 5.00e-02 4.00e+02 ... (remaining 2628 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 59 2.57 - 3.15: 12043 3.15 - 3.74: 22993 3.74 - 4.32: 29793 4.32 - 4.90: 52321 Nonbonded interactions: 117209 Sorted by model distance: nonbonded pdb=" OD2 ASP R 97 " pdb="ZN ZN R 202 " model vdw 1.991 2.230 nonbonded pdb=" OH TYR C 244 " pdb=" OE2 GLU C 271 " model vdw 2.220 2.440 nonbonded pdb=" OD1 ASP D 774 " pdb=" NH2 ARG D 777 " model vdw 2.258 2.520 nonbonded pdb=" OH TYR C 599 " pdb=" O ASN C 677 " model vdw 2.259 2.440 nonbonded pdb=" NH1 ARG D 350 " pdb=" OE2 GLU D 385 " model vdw 2.275 2.520 ... (remaining 117204 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.430 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 45.560 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 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 : 0.002 0.079 15377 Z= 0.156 Angle : 0.518 10.384 20849 Z= 0.273 Chirality : 0.038 0.225 2493 Planarity : 0.004 0.055 2631 Dihedral : 13.268 81.673 5656 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.12 % Allowed : 0.30 % Favored : 99.58 % 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: 1.79 (0.20), residues: 1928 helix: 2.18 (0.15), residues: 1333 sheet: 1.75 (1.11), residues: 29 loop : -1.35 (0.24), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 33 HIS 0.003 0.001 HIS D1108 PHE 0.019 0.001 PHE C 95 TYR 0.014 0.001 TYR C 377 ARG 0.004 0.000 ARG C 573 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 286 time to evaluate : 1.882 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 286 average time/residue: 1.4396 time to fit residues: 448.9813 Evaluate side-chains 140 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.877 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 162 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 151 optimal weight: 0.3980 chunk 58 optimal weight: 10.0000 chunk 91 optimal weight: 0.4980 chunk 112 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN C 293 GLN C 694 GLN D 10 ASN D 66 ASN D 101 GLN D 145 GLN D 151 GLN D 662 ASN D 902 GLN D1199 GLN R 76 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15377 Z= 0.210 Angle : 0.525 9.548 20849 Z= 0.272 Chirality : 0.039 0.142 2493 Planarity : 0.004 0.045 2631 Dihedral : 3.556 16.566 2085 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.54 % Allowed : 9.56 % Favored : 87.90 % 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: 1.89 (0.20), residues: 1928 helix: 2.19 (0.14), residues: 1355 sheet: 1.92 (1.08), residues: 29 loop : -1.29 (0.24), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 33 HIS 0.005 0.001 HIS D1108 PHE 0.026 0.002 PHE C 402 TYR 0.019 0.001 TYR C 377 ARG 0.010 0.001 ARG R 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 146 time to evaluate : 1.864 Fit side-chains outliers start: 42 outliers final: 17 residues processed: 174 average time/residue: 1.2584 time to fit residues: 243.6192 Evaluate side-chains 154 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 1.995 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 11 residues processed: 6 average time/residue: 0.3422 time to fit residues: 5.3622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 97 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 145 optimal weight: 0.5980 chunk 119 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 175 optimal weight: 6.9990 chunk 189 optimal weight: 20.0000 chunk 156 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 140 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 662 ASN D 820 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15377 Z= 0.183 Angle : 0.488 9.493 20849 Z= 0.253 Chirality : 0.038 0.138 2493 Planarity : 0.004 0.044 2631 Dihedral : 3.486 16.603 2085 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.48 % Allowed : 11.55 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.20), residues: 1928 helix: 2.28 (0.14), residues: 1364 sheet: 2.06 (1.10), residues: 29 loop : -1.35 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 33 HIS 0.003 0.001 HIS D1108 PHE 0.025 0.001 PHE C 569 TYR 0.018 0.001 TYR C 377 ARG 0.005 0.000 ARG R 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 142 time to evaluate : 2.042 Fit side-chains outliers start: 41 outliers final: 21 residues processed: 166 average time/residue: 1.2978 time to fit residues: 239.0841 Evaluate side-chains 152 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 1.854 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 14 residues processed: 7 average time/residue: 0.5102 time to fit residues: 7.0981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 173 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 91 optimal weight: 0.0770 chunk 19 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 176 optimal weight: 0.7980 chunk 186 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1199 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15377 Z= 0.157 Angle : 0.471 9.384 20849 Z= 0.243 Chirality : 0.037 0.134 2493 Planarity : 0.004 0.042 2631 Dihedral : 3.409 16.059 2085 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.54 % Allowed : 12.22 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.20), residues: 1928 helix: 2.38 (0.14), residues: 1362 sheet: 2.15 (1.10), residues: 29 loop : -1.28 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 33 HIS 0.003 0.001 HIS D1108 PHE 0.030 0.001 PHE C 569 TYR 0.017 0.001 TYR C 377 ARG 0.007 0.000 ARG R 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 134 time to evaluate : 1.609 Fit side-chains outliers start: 42 outliers final: 20 residues processed: 163 average time/residue: 1.2233 time to fit residues: 222.2810 Evaluate side-chains 146 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 1.852 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 16 residues processed: 4 average time/residue: 0.5473 time to fit residues: 5.0328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 155 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 95 optimal weight: 0.0270 chunk 167 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 overall best weight: 1.1240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 386 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15377 Z= 0.195 Angle : 0.498 9.790 20849 Z= 0.255 Chirality : 0.039 0.158 2493 Planarity : 0.004 0.042 2631 Dihedral : 3.465 16.582 2085 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.30 % Allowed : 12.70 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.20), residues: 1928 helix: 2.38 (0.14), residues: 1362 sheet: 2.00 (1.08), residues: 29 loop : -1.26 (0.24), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 33 HIS 0.003 0.001 HIS D1108 PHE 0.023 0.001 PHE C 569 TYR 0.020 0.001 TYR C 377 ARG 0.010 0.000 ARG C 573 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 133 time to evaluate : 1.903 Fit side-chains outliers start: 38 outliers final: 21 residues processed: 159 average time/residue: 1.2834 time to fit residues: 227.2563 Evaluate side-chains 144 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 2.050 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 14 residues processed: 7 average time/residue: 0.6327 time to fit residues: 8.1709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 62 optimal weight: 0.5980 chunk 168 optimal weight: 0.0770 chunk 36 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 186 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15377 Z= 0.153 Angle : 0.473 8.822 20849 Z= 0.243 Chirality : 0.037 0.157 2493 Planarity : 0.004 0.041 2631 Dihedral : 3.374 16.304 2085 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.18 % Allowed : 13.43 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.20), residues: 1928 helix: 2.46 (0.14), residues: 1363 sheet: 2.01 (1.10), residues: 29 loop : -1.21 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 33 HIS 0.003 0.001 HIS D1108 PHE 0.021 0.001 PHE C 569 TYR 0.017 0.001 TYR C 377 ARG 0.009 0.000 ARG C 573 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 131 time to evaluate : 1.874 Fit side-chains outliers start: 36 outliers final: 20 residues processed: 158 average time/residue: 1.2870 time to fit residues: 226.0731 Evaluate side-chains 142 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 122 time to evaluate : 1.832 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 16 residues processed: 4 average time/residue: 0.4691 time to fit residues: 4.9492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 180 optimal weight: 9.9990 chunk 21 optimal weight: 0.4980 chunk 106 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 186 optimal weight: 8.9990 chunk 116 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 602 GLN D1199 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15377 Z= 0.216 Angle : 0.510 8.182 20849 Z= 0.262 Chirality : 0.039 0.169 2493 Planarity : 0.004 0.042 2631 Dihedral : 3.489 16.761 2085 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.18 % Allowed : 13.85 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.20), residues: 1928 helix: 2.34 (0.14), residues: 1368 sheet: 1.85 (1.08), residues: 29 loop : -1.17 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 33 HIS 0.004 0.001 HIS D1108 PHE 0.021 0.002 PHE C 402 TYR 0.020 0.001 TYR C 377 ARG 0.010 0.000 ARG C 573 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 125 time to evaluate : 1.837 Fit side-chains outliers start: 36 outliers final: 20 residues processed: 153 average time/residue: 1.2379 time to fit residues: 210.6832 Evaluate side-chains 141 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 1.820 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 16 residues processed: 4 average time/residue: 0.2205 time to fit residues: 3.8653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 115 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 chunk 169 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15377 Z= 0.221 Angle : 0.517 11.035 20849 Z= 0.266 Chirality : 0.039 0.173 2493 Planarity : 0.004 0.041 2631 Dihedral : 3.540 16.927 2085 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.06 % Allowed : 14.16 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.20), residues: 1928 helix: 2.32 (0.14), residues: 1367 sheet: 1.95 (1.10), residues: 29 loop : -1.21 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 33 HIS 0.004 0.001 HIS D1108 PHE 0.021 0.002 PHE C 402 TYR 0.019 0.001 TYR C 377 ARG 0.011 0.000 ARG C 573 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 124 time to evaluate : 1.848 Fit side-chains outliers start: 34 outliers final: 18 residues processed: 149 average time/residue: 1.3602 time to fit residues: 224.8738 Evaluate side-chains 138 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 1.952 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 15 residues processed: 3 average time/residue: 0.2109 time to fit residues: 3.5630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 178 optimal weight: 3.9990 chunk 162 optimal weight: 7.9990 chunk 173 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 156 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 113 optimal weight: 0.4980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 599 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15377 Z= 0.240 Angle : 0.538 12.186 20849 Z= 0.274 Chirality : 0.040 0.175 2493 Planarity : 0.004 0.043 2631 Dihedral : 3.601 17.183 2085 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.39 % Allowed : 15.00 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.20), residues: 1928 helix: 2.29 (0.14), residues: 1366 sheet: 1.93 (1.10), residues: 29 loop : -1.17 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 33 HIS 0.004 0.001 HIS D1108 PHE 0.021 0.002 PHE C 402 TYR 0.020 0.001 TYR C 377 ARG 0.012 0.000 ARG C 573 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 118 time to evaluate : 1.776 Fit side-chains outliers start: 23 outliers final: 17 residues processed: 139 average time/residue: 1.3049 time to fit residues: 201.8375 Evaluate side-chains 133 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 116 time to evaluate : 1.736 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 16 residues processed: 1 average time/residue: 0.1782 time to fit residues: 2.7551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 183 optimal weight: 30.0000 chunk 111 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 127 optimal weight: 0.6980 chunk 192 optimal weight: 8.9990 chunk 176 optimal weight: 1.9990 chunk 153 optimal weight: 0.3980 chunk 15 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15377 Z= 0.177 Angle : 0.506 11.336 20849 Z= 0.259 Chirality : 0.038 0.162 2493 Planarity : 0.004 0.047 2631 Dihedral : 3.491 16.745 2085 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.27 % Allowed : 15.00 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.20), residues: 1928 helix: 2.37 (0.14), residues: 1368 sheet: 1.92 (1.11), residues: 29 loop : -1.16 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 33 HIS 0.003 0.001 HIS D1108 PHE 0.019 0.001 PHE C 402 TYR 0.018 0.001 TYR D 6 ARG 0.012 0.000 ARG C 573 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 117 time to evaluate : 1.902 Fit side-chains outliers start: 21 outliers final: 19 residues processed: 134 average time/residue: 1.3367 time to fit residues: 199.0709 Evaluate side-chains 134 residues out of total 1754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 1.804 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 15 residues processed: 4 average time/residue: 0.2514 time to fit residues: 3.9774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 163 optimal weight: 0.3980 chunk 46 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 157 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 134 optimal weight: 0.0010 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.123235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.086833 restraints weight = 22468.302| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.14 r_work: 0.2959 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15377 Z= 0.152 Angle : 0.493 11.256 20849 Z= 0.250 Chirality : 0.037 0.155 2493 Planarity : 0.004 0.048 2631 Dihedral : 3.382 16.112 2085 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.27 % Allowed : 15.18 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.20), residues: 1928 helix: 2.48 (0.14), residues: 1366 sheet: 1.97 (1.12), residues: 29 loop : -1.13 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 33 HIS 0.003 0.001 HIS D1108 PHE 0.019 0.001 PHE C 402 TYR 0.017 0.001 TYR D1117 ARG 0.012 0.000 ARG C 573 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4950.72 seconds wall clock time: 88 minutes 57.89 seconds (5337.89 seconds total)