Starting phenix.real_space_refine on Fri Nov 17 14:23:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jeu_36196/11_2023/8jeu_36196.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jeu_36196/11_2023/8jeu_36196.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jeu_36196/11_2023/8jeu_36196.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jeu_36196/11_2023/8jeu_36196.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jeu_36196/11_2023/8jeu_36196.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jeu_36196/11_2023/8jeu_36196.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.051 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 84 5.16 5 C 12658 2.51 5 N 3298 2.21 5 O 3398 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 473": "OE1" <-> "OE2" Residue "C GLU 103": "OE1" <-> "OE2" Residue "B GLU 103": "OE1" <-> "OE2" Residue "B GLU 399": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 19438 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4779 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 658, 4770 Classifications: {'peptide': 658} Incomplete info: {'truncation_to_alanine': 156} Link IDs: {'PTRANS': 18, 'TRANS': 639} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 556 Unresolved non-hydrogen angles: 689 Unresolved non-hydrogen dihedrals: 454 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 17, 'PHE:plan': 2, 'GLU:plan': 21, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 324 Conformer: "B" Number of residues, atoms: 658, 4770 Classifications: {'peptide': 658} Incomplete info: {'truncation_to_alanine': 156} Link IDs: {'PTRANS': 18, 'TRANS': 639} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 556 Unresolved non-hydrogen angles: 689 Unresolved non-hydrogen dihedrals: 454 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 17, 'PHE:plan': 2, 'GLU:plan': 21, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 324 bond proxies already assigned to first conformer: 4861 Chain: "D" Number of atoms: 4940 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 662, 4931 Classifications: {'peptide': 662} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'PTRANS': 18, 'TRANS': 643} Chain breaks: 1 Unresolved non-hydrogen bonds: 420 Unresolved non-hydrogen angles: 521 Unresolved non-hydrogen dihedrals: 341 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 16, 'PHE:plan': 2, 'GLU:plan': 21, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 254 Conformer: "B" Number of residues, atoms: 662, 4931 Classifications: {'peptide': 662} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'PTRANS': 18, 'TRANS': 643} Chain breaks: 1 Unresolved non-hydrogen bonds: 420 Unresolved non-hydrogen angles: 521 Unresolved non-hydrogen dihedrals: 341 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 16, 'PHE:plan': 2, 'GLU:plan': 21, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 254 bond proxies already assigned to first conformer: 5026 Chain: "C" Number of atoms: 4779 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 658, 4770 Classifications: {'peptide': 658} Incomplete info: {'truncation_to_alanine': 156} Link IDs: {'PTRANS': 18, 'TRANS': 639} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 556 Unresolved non-hydrogen angles: 689 Unresolved non-hydrogen dihedrals: 454 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 17, 'PHE:plan': 2, 'GLU:plan': 21, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 324 Conformer: "B" Number of residues, atoms: 658, 4770 Classifications: {'peptide': 658} Incomplete info: {'truncation_to_alanine': 156} Link IDs: {'PTRANS': 18, 'TRANS': 639} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 556 Unresolved non-hydrogen angles: 689 Unresolved non-hydrogen dihedrals: 454 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 17, 'PHE:plan': 2, 'GLU:plan': 21, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 324 bond proxies already assigned to first conformer: 4861 Chain: "B" Number of atoms: 4940 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 662, 4931 Classifications: {'peptide': 662} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'PTRANS': 18, 'TRANS': 643} Chain breaks: 1 Unresolved non-hydrogen bonds: 420 Unresolved non-hydrogen angles: 521 Unresolved non-hydrogen dihedrals: 341 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 16, 'PHE:plan': 2, 'GLU:plan': 21, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 254 Conformer: "B" Number of residues, atoms: 662, 4931 Classifications: {'peptide': 662} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'PTRANS': 18, 'TRANS': 643} Chain breaks: 1 Unresolved non-hydrogen bonds: 420 Unresolved non-hydrogen angles: 521 Unresolved non-hydrogen dihedrals: 341 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 16, 'PHE:plan': 2, 'GLU:plan': 21, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 254 bond proxies already assigned to first conformer: 5026 Time building chain proxies: 19.25, per 1000 atoms: 0.99 Number of scatterers: 19438 At special positions: 0 Unit cell: (106.05, 99.99, 184.83, 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 84 16.00 O 3398 8.00 N 3298 7.00 C 12658 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.16 Conformation dependent library (CDL) restraints added in 7.1 seconds 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4988 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 8 sheets defined 67.0% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'A' and resid 81 through 107 removed outlier: 3.961A pdb=" N MET A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE A 91 " --> pdb=" O MET A 87 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TRP A 92 " --> pdb=" O PHE A 88 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) Proline residue: A 101 - end of helix removed outlier: 3.724A pdb=" N PHE A 107 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 114 through 132 removed outlier: 3.521A pdb=" N ASP A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR A 132 " --> pdb=" O ASP A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 150 through 169 removed outlier: 3.623A pdb=" N SER A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ILE A 162 " --> pdb=" O LYS A 158 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.920A pdb=" N ILE A 174 " --> pdb=" O PRO A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 194 Processing helix chain 'A' and resid 195 through 208 Processing helix chain 'A' and resid 212 through 242 removed outlier: 3.655A pdb=" N THR A 216 " --> pdb=" O ASN A 212 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG A 217 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS A 220 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 240 " --> pdb=" O PHE A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 251 removed outlier: 3.505A pdb=" N GLU A 248 " --> pdb=" O ALA A 245 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N GLY A 249 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A 250 " --> pdb=" O GLN A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 287 removed outlier: 3.706A pdb=" N THR A 277 " --> pdb=" O THR A 273 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER A 278 " --> pdb=" O ARG A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 329 removed outlier: 3.674A pdb=" N ILE A 314 " --> pdb=" O SER A 310 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE A 320 " --> pdb=" O GLY A 316 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A 325 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 329 " --> pdb=" O ALA A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 348 removed outlier: 3.527A pdb=" N ASP A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR A 346 " --> pdb=" O ASP A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 371 removed outlier: 3.503A pdb=" N ARG A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY A 358 " --> pdb=" O ARG A 354 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN A 359 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN A 367 " --> pdb=" O HIS A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 394 removed outlier: 3.635A pdb=" N ILE A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 400 removed outlier: 3.750A pdb=" N LYS A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 416 Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'A' and resid 472 through 478 removed outlier: 3.526A pdb=" N LEU A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS A 478 " --> pdb=" O ILE A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 509 removed outlier: 3.525A pdb=" N ILE A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 506 " --> pdb=" O PHE A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 527 removed outlier: 3.762A pdb=" N ARG A 515 " --> pdb=" O HIS A 511 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 517 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN A 518 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN A 519 " --> pdb=" O ARG A 515 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 520 " --> pdb=" O ILE A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 543 removed outlier: 3.669A pdb=" N HIS A 540 " --> pdb=" O ASP A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 558 removed outlier: 3.633A pdb=" N LEU A 548 " --> pdb=" O GLN A 544 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA A 549 " --> pdb=" O GLU A 545 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 583 through 591 removed outlier: 3.521A pdb=" N LEU A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG A 591 " --> pdb=" O LEU A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 601 removed outlier: 3.973A pdb=" N LEU A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N TYR A 599 " --> pdb=" O ASP A 595 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU A 600 " --> pdb=" O ILE A 596 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ILE A 601 " --> pdb=" O THR A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 604 No H-bonds generated for 'chain 'A' and resid 602 through 604' Processing helix chain 'A' and resid 618 through 624 removed outlier: 3.646A pdb=" N ILE A 622 " --> pdb=" O LEU A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 636 Processing helix chain 'A' and resid 644 through 656 removed outlier: 3.517A pdb=" N GLY A 656 " --> pdb=" O VAL A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 666 removed outlier: 4.191A pdb=" N LEU A 661 " --> pdb=" O ASP A 657 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS A 662 " --> pdb=" O SER A 658 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG A 663 " --> pdb=" O ASP A 659 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A 664 " --> pdb=" O PHE A 660 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 665 " --> pdb=" O LEU A 661 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER A 666 " --> pdb=" O LYS A 662 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 657 through 666' Processing helix chain 'A' and resid 680 through 689 removed outlier: 3.785A pdb=" N VAL A 684 " --> pdb=" O THR A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 693 No H-bonds generated for 'chain 'A' and resid 691 through 693' Processing helix chain 'A' and resid 694 through 699 Processing helix chain 'A' and resid 713 through 722 Processing helix chain 'A' and resid 723 through 740 Processing helix chain 'D' and resid 79 through 106 removed outlier: 3.503A pdb=" N ALA D 84 " --> pdb=" O ARG D 80 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TRP D 92 " --> pdb=" O PHE D 88 " (cutoff:3.500A) Proline residue: D 101 - end of helix Processing helix chain 'D' and resid 111 through 113 No H-bonds generated for 'chain 'D' and resid 111 through 113' Processing helix chain 'D' and resid 114 through 132 removed outlier: 3.592A pdb=" N GLN D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE D 125 " --> pdb=" O GLY D 121 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP D 128 " --> pdb=" O ALA D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 135 No H-bonds generated for 'chain 'D' and resid 133 through 135' Processing helix chain 'D' and resid 148 through 158 removed outlier: 3.635A pdb=" N ALA D 153 " --> pdb=" O ARG D 149 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS D 158 " --> pdb=" O LEU D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 169 removed outlier: 4.057A pdb=" N LEU D 166 " --> pdb=" O ILE D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 178 Processing helix chain 'D' and resid 181 through 187 removed outlier: 4.163A pdb=" N ARG D 185 " --> pdb=" O LYS D 181 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 194 Processing helix chain 'D' and resid 195 through 208 removed outlier: 3.747A pdb=" N ASP D 208 " --> pdb=" O LYS D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 243 removed outlier: 3.948A pdb=" N CYS D 228 " --> pdb=" O VAL D 224 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU D 243 " --> pdb=" O LEU D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 251 removed outlier: 3.660A pdb=" N GLU D 248 " --> pdb=" O ALA D 245 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLY D 249 " --> pdb=" O SER D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 287 removed outlier: 3.696A pdb=" N THR D 277 " --> pdb=" O THR D 273 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER D 278 " --> pdb=" O ARG D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 330 removed outlier: 3.567A pdb=" N MET D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE D 303 " --> pdb=" O MET D 299 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE D 304 " --> pdb=" O ARG D 300 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE D 320 " --> pdb=" O GLY D 316 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU D 326 " --> pdb=" O ASN D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 350 removed outlier: 3.726A pdb=" N ASN D 350 " --> pdb=" O TYR D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 370 removed outlier: 4.336A pdb=" N GLY D 358 " --> pdb=" O ARG D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 392 Processing helix chain 'D' and resid 394 through 398 Processing helix chain 'D' and resid 401 through 405 removed outlier: 3.560A pdb=" N ARG D 405 " --> pdb=" O PRO D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 416 removed outlier: 3.602A pdb=" N ILE D 412 " --> pdb=" O SER D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 478 Processing helix chain 'D' and resid 499 through 509 removed outlier: 3.958A pdb=" N MET D 503 " --> pdb=" O LYS D 499 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASN D 504 " --> pdb=" O GLN D 500 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ILE D 505 " --> pdb=" O SER D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 524 Processing helix chain 'D' and resid 535 through 559 removed outlier: 3.627A pdb=" N SER D 542 " --> pdb=" O THR D 538 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS D 551 " --> pdb=" O GLU D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 570 removed outlier: 3.631A pdb=" N LEU D 564 " --> pdb=" O ASP D 560 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS D 565 " --> pdb=" O LEU D 561 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER D 566 " --> pdb=" O TYR D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 589 removed outlier: 3.621A pdb=" N ALA D 589 " --> pdb=" O LEU D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 603 removed outlier: 3.620A pdb=" N LEU D 598 " --> pdb=" O GLU D 594 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N TYR D 599 " --> pdb=" O ASP D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 625 Processing helix chain 'D' and resid 626 through 637 removed outlier: 3.516A pdb=" N ALA D 630 " --> pdb=" O ASN D 626 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA D 631 " --> pdb=" O ASP D 627 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU D 632 " --> pdb=" O ARG D 628 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 633 " --> pdb=" O VAL D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 644 through 656 removed outlier: 3.951A pdb=" N VAL D 653 " --> pdb=" O LEU D 649 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA D 654 " --> pdb=" O CYS D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 667 removed outlier: 3.521A pdb=" N ASN D 667 " --> pdb=" O ARG D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 689 removed outlier: 3.550A pdb=" N VAL D 684 " --> pdb=" O THR D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 691 through 701 Processing helix chain 'D' and resid 713 through 722 Processing helix chain 'D' and resid 723 through 740 removed outlier: 3.941A pdb=" N LEU D 729 " --> pdb=" O MET D 725 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 107 removed outlier: 3.951A pdb=" N MET C 87 " --> pdb=" O LYS C 83 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE C 91 " --> pdb=" O MET C 87 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TRP C 92 " --> pdb=" O PHE C 88 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR C 100 " --> pdb=" O SER C 96 " (cutoff:3.500A) Proline residue: C 101 - end of helix removed outlier: 3.707A pdb=" N PHE C 107 " --> pdb=" O GLU C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 132 removed outlier: 3.659A pdb=" N ASP C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE C 119 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN C 122 " --> pdb=" O ASP C 118 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP C 128 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL C 130 " --> pdb=" O LEU C 126 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR C 132 " --> pdb=" O ASP C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 150 through 169 removed outlier: 3.627A pdb=" N SER C 159 " --> pdb=" O ARG C 155 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE C 161 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ILE C 162 " --> pdb=" O LYS C 158 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE C 163 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS C 168 " --> pdb=" O ASP C 164 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.832A pdb=" N ILE C 174 " --> pdb=" O PRO C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 194 Processing helix chain 'C' and resid 195 through 208 Processing helix chain 'C' and resid 214 through 242 removed outlier: 3.980A pdb=" N LYS C 220 " --> pdb=" O THR C 216 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA C 240 " --> pdb=" O PHE C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 251 removed outlier: 3.567A pdb=" N GLU C 248 " --> pdb=" O ALA C 245 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLY C 249 " --> pdb=" O SER C 246 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR C 250 " --> pdb=" O GLN C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 287 removed outlier: 3.626A pdb=" N THR C 277 " --> pdb=" O THR C 273 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER C 278 " --> pdb=" O ARG C 274 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE C 281 " --> pdb=" O THR C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 329 removed outlier: 3.762A pdb=" N ILE C 314 " --> pdb=" O SER C 310 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE C 320 " --> pdb=" O GLY C 316 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA C 325 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 326 " --> pdb=" O ASN C 322 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS C 329 " --> pdb=" O ALA C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 348 removed outlier: 3.555A pdb=" N ASP C 338 " --> pdb=" O GLU C 334 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR C 346 " --> pdb=" O ASP C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 370 removed outlier: 3.521A pdb=" N ARG C 357 " --> pdb=" O GLY C 353 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY C 358 " --> pdb=" O ARG C 354 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN C 359 " --> pdb=" O ASN C 355 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN C 367 " --> pdb=" O HIS C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 394 removed outlier: 3.661A pdb=" N ILE C 389 " --> pdb=" O ILE C 385 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 393 " --> pdb=" O ILE C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 400 removed outlier: 3.741A pdb=" N LYS C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 416 Processing helix chain 'C' and resid 417 through 419 No H-bonds generated for 'chain 'C' and resid 417 through 419' Processing helix chain 'C' and resid 473 through 479 removed outlier: 3.990A pdb=" N LEU C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS C 478 " --> pdb=" O ILE C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 503 Processing helix chain 'C' and resid 504 through 509 Processing helix chain 'C' and resid 509 through 527 removed outlier: 3.758A pdb=" N ARG C 515 " --> pdb=" O HIS C 511 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 517 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN C 518 " --> pdb=" O ARG C 514 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN C 519 " --> pdb=" O ARG C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 530 through 543 removed outlier: 3.691A pdb=" N HIS C 540 " --> pdb=" O ASP C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 558 removed outlier: 3.629A pdb=" N LEU C 548 " --> pdb=" O GLN C 544 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ALA C 549 " --> pdb=" O GLU C 545 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 552 " --> pdb=" O LEU C 548 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER C 554 " --> pdb=" O LEU C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 570 Processing helix chain 'C' and resid 583 through 589 removed outlier: 3.544A pdb=" N LEU C 587 " --> pdb=" O SER C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 603 removed outlier: 3.956A pdb=" N LEU C 598 " --> pdb=" O GLU C 594 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N TYR C 599 " --> pdb=" O ASP C 595 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU C 600 " --> pdb=" O ILE C 596 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE C 601 " --> pdb=" O THR C 597 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN C 602 " --> pdb=" O LEU C 598 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU C 603 " --> pdb=" O TYR C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 624 Processing helix chain 'C' and resid 626 through 637 removed outlier: 3.587A pdb=" N LYS C 635 " --> pdb=" O ALA C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 656 removed outlier: 3.745A pdb=" N CYS C 650 " --> pdb=" O GLY C 646 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR C 651 " --> pdb=" O THR C 647 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL C 653 " --> pdb=" O LEU C 649 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C 654 " --> pdb=" O CYS C 650 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS C 655 " --> pdb=" O THR C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 658 through 667 removed outlier: 3.759A pdb=" N ASN C 667 " --> pdb=" O ARG C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 680 through 689 removed outlier: 3.832A pdb=" N VAL C 684 " --> pdb=" O THR C 680 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU C 688 " --> pdb=" O VAL C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 700 removed outlier: 4.120A pdb=" N LEU C 697 " --> pdb=" O LEU C 693 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL C 698 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA C 700 " --> pdb=" O GLN C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 722 Processing helix chain 'C' and resid 723 through 740 Processing helix chain 'B' and resid 79 through 106 removed outlier: 3.514A pdb=" N MET B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TRP B 92 " --> pdb=" O PHE B 88 " (cutoff:3.500A) Proline residue: B 101 - end of helix Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 114 through 132 removed outlier: 3.543A pdb=" N GLN B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP B 128 " --> pdb=" O ALA B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 158 removed outlier: 3.605A pdb=" N ALA B 153 " --> pdb=" O ARG B 149 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 169 removed outlier: 4.107A pdb=" N LEU B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 178 Processing helix chain 'B' and resid 181 through 187 removed outlier: 4.164A pdb=" N ARG B 185 " --> pdb=" O LYS B 181 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 194 Processing helix chain 'B' and resid 195 through 207 Processing helix chain 'B' and resid 212 through 243 removed outlier: 3.899A pdb=" N CYS B 228 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA B 240 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 251 removed outlier: 3.637A pdb=" N GLU B 248 " --> pdb=" O ALA B 245 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N GLY B 249 " --> pdb=" O SER B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 287 removed outlier: 3.693A pdb=" N THR B 277 " --> pdb=" O THR B 273 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER B 278 " --> pdb=" O ARG B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 330 removed outlier: 3.867A pdb=" N ILE B 303 " --> pdb=" O MET B 299 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE B 314 " --> pdb=" O SER B 310 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 320 " --> pdb=" O GLY B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 350 removed outlier: 3.702A pdb=" N ASN B 350 " --> pdb=" O TYR B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 370 removed outlier: 4.372A pdb=" N GLY B 358 " --> pdb=" O ARG B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 392 Processing helix chain 'B' and resid 394 through 398 Processing helix chain 'B' and resid 401 through 405 removed outlier: 3.535A pdb=" N ARG B 405 " --> pdb=" O PRO B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 416 Processing helix chain 'B' and resid 472 through 478 removed outlier: 3.528A pdb=" N ILE B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 509 removed outlier: 4.057A pdb=" N MET B 503 " --> pdb=" O LYS B 499 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASN B 504 " --> pdb=" O GLN B 500 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ILE B 505 " --> pdb=" O SER B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 524 removed outlier: 3.750A pdb=" N LEU B 517 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 520 " --> pdb=" O ILE B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 559 removed outlier: 3.911A pdb=" N LYS B 551 " --> pdb=" O GLU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 570 removed outlier: 3.645A pdb=" N LEU B 564 " --> pdb=" O ASP B 560 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS B 565 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER B 566 " --> pdb=" O TYR B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 589 Processing helix chain 'B' and resid 593 through 603 removed outlier: 3.624A pdb=" N LEU B 598 " --> pdb=" O GLU B 594 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TYR B 599 " --> pdb=" O ASP B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 625 Processing helix chain 'B' and resid 626 through 637 removed outlier: 3.702A pdb=" N ALA B 630 " --> pdb=" O ASN B 626 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B 631 " --> pdb=" O ASP B 627 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU B 632 " --> pdb=" O ARG B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 656 removed outlier: 3.745A pdb=" N PHE B 648 " --> pdb=" O ASN B 644 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 649 " --> pdb=" O ALA B 645 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N CYS B 650 " --> pdb=" O GLY B 646 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR B 651 " --> pdb=" O THR B 647 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL B 653 " --> pdb=" O LEU B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 667 removed outlier: 3.550A pdb=" N LEU B 665 " --> pdb=" O LEU B 661 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN B 667 " --> pdb=" O ARG B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 689 removed outlier: 3.514A pdb=" N VAL B 684 " --> pdb=" O THR B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 701 removed outlier: 3.600A pdb=" N GLU B 699 " --> pdb=" O ILE B 695 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 700 " --> pdb=" O GLN B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 722 Processing helix chain 'B' and resid 723 through 740 removed outlier: 4.002A pdb=" N LEU B 729 " --> pdb=" O MET B 725 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 420 through 424 removed outlier: 6.532A pdb=" N ARG A 493 " --> pdb=" O CYS A 444 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR A 441 " --> pdb=" O PHE A 471 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N HIS A 469 " --> pdb=" O VAL A 443 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 463 through 465 removed outlier: 3.808A pdb=" N ALA A 463 " --> pdb=" O GLU A 450 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 420 through 424 removed outlier: 3.864A pdb=" N CYS D 492 " --> pdb=" O PHE D 424 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR D 441 " --> pdb=" O PHE D 471 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE D 471 " --> pdb=" O TYR D 441 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 429 through 431 removed outlier: 7.649A pdb=" N VAL D 486 " --> pdb=" O ILE D 430 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU D 448 " --> pdb=" O VAL D 464 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N VAL D 464 " --> pdb=" O LEU D 448 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N GLU D 450 " --> pdb=" O VAL D 462 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL D 462 " --> pdb=" O GLU D 450 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 420 through 424 removed outlier: 6.986A pdb=" N ARG C 493 " --> pdb=" O CYS C 444 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR C 441 " --> pdb=" O PHE C 471 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N HIS C 469 " --> pdb=" O VAL C 443 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 463 through 465 removed outlier: 3.786A pdb=" N ALA C 463 " --> pdb=" O GLU C 450 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 420 through 424 removed outlier: 3.876A pdb=" N CYS B 492 " --> pdb=" O PHE B 424 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR B 441 " --> pdb=" O PHE B 471 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE B 471 " --> pdb=" O TYR B 441 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 429 through 431 removed outlier: 6.178A pdb=" N VAL B 429 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL B 488 " --> pdb=" O VAL B 429 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N MET B 431 " --> pdb=" O VAL B 486 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL B 486 " --> pdb=" O MET B 431 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA B 463 " --> pdb=" O GLU B 450 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLY B 452 " --> pdb=" O ILE B 461 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ILE B 461 " --> pdb=" O GLY B 452 " (cutoff:3.500A) 1050 hydrogen bonds defined for protein. 2988 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: 6.43 Time building geometry restraints manager: 7.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6247 1.34 - 1.46: 4781 1.46 - 1.58: 8694 1.58 - 1.70: 0 1.70 - 1.82: 140 Bond restraints: 19862 Sorted by residual: bond pdb=" C ILE A 381 " pdb=" N PRO A 382 " ideal model delta sigma weight residual 1.331 1.364 -0.032 1.27e-02 6.20e+03 6.53e+00 bond pdb=" C ALA A 120 " pdb=" N GLY A 121 " ideal model delta sigma weight residual 1.334 1.303 0.031 1.21e-02 6.83e+03 6.52e+00 bond pdb=" C ILE C 381 " pdb=" N PRO C 382 " ideal model delta sigma weight residual 1.331 1.363 -0.032 1.27e-02 6.20e+03 6.34e+00 bond pdb=" C PHE C 107 " pdb=" N ARG C 108 " ideal model delta sigma weight residual 1.329 1.299 0.030 1.33e-02 5.65e+03 5.02e+00 bond pdb=" CB GLN B 466 " pdb=" CG GLN B 466 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.03e+00 ... (remaining 19857 not shown) Histogram of bond angle deviations from ideal: 100.26 - 107.02: 414 107.02 - 113.79: 11017 113.79 - 120.56: 8435 120.56 - 127.32: 7073 127.32 - 134.09: 157 Bond angle restraints: 27096 Sorted by residual: angle pdb=" C LEU C 378 " pdb=" N GLN C 379 " pdb=" CA GLN C 379 " ideal model delta sigma weight residual 121.54 129.80 -8.26 1.91e+00 2.74e-01 1.87e+01 angle pdb=" C LEU A 378 " pdb=" N GLN A 379 " pdb=" CA GLN A 379 " ideal model delta sigma weight residual 121.54 129.78 -8.24 1.91e+00 2.74e-01 1.86e+01 angle pdb=" CB MET C 344 " pdb=" CG MET C 344 " pdb=" SD MET C 344 " ideal model delta sigma weight residual 112.70 124.76 -12.06 3.00e+00 1.11e-01 1.62e+01 angle pdb=" CB MET A 344 " pdb=" CG MET A 344 " pdb=" SD MET A 344 " ideal model delta sigma weight residual 112.70 123.36 -10.66 3.00e+00 1.11e-01 1.26e+01 angle pdb=" CB MET C 205 " pdb=" CG MET C 205 " pdb=" SD MET C 205 " ideal model delta sigma weight residual 112.70 122.45 -9.75 3.00e+00 1.11e-01 1.06e+01 ... (remaining 27091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 10187 17.88 - 35.76: 1118 35.76 - 53.64: 271 53.64 - 71.52: 35 71.52 - 89.40: 9 Dihedral angle restraints: 11620 sinusoidal: 3864 harmonic: 7756 Sorted by residual: dihedral pdb=" CA ASP D 128 " pdb=" CB ASP D 128 " pdb=" CG ASP D 128 " pdb=" OD1 ASP D 128 " ideal model delta sinusoidal sigma weight residual -30.00 -88.68 58.68 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASP B 128 " pdb=" CB ASP B 128 " pdb=" CG ASP B 128 " pdb=" OD1 ASP B 128 " ideal model delta sinusoidal sigma weight residual -30.00 -88.56 58.56 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ARG A 194 " pdb=" C ARG A 194 " pdb=" N VAL A 195 " pdb=" CA VAL A 195 " ideal model delta harmonic sigma weight residual 180.00 163.12 16.88 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 11617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1923 0.028 - 0.056: 862 0.056 - 0.085: 292 0.085 - 0.113: 113 0.113 - 0.141: 18 Chirality restraints: 3208 Sorted by residual: chirality pdb=" CA ILE B 294 " pdb=" N ILE B 294 " pdb=" C ILE B 294 " pdb=" CB ILE B 294 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA ILE B 381 " pdb=" N ILE B 381 " pdb=" C ILE B 381 " pdb=" CB ILE B 381 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 chirality pdb=" CA ILE D 381 " pdb=" N ILE D 381 " pdb=" C ILE D 381 " pdb=" CB ILE D 381 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 ... (remaining 3205 not shown) Planarity restraints: 3426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 381 " 0.036 5.00e-02 4.00e+02 5.51e-02 4.85e+00 pdb=" N PRO C 382 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 382 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 382 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 573 " 0.035 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO B 574 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 574 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 574 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 381 " -0.035 5.00e-02 4.00e+02 5.30e-02 4.49e+00 pdb=" N PRO A 382 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 382 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 382 " -0.030 5.00e-02 4.00e+02 ... (remaining 3423 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1423 2.74 - 3.28: 20859 3.28 - 3.82: 31159 3.82 - 4.36: 34408 4.36 - 4.90: 58928 Nonbonded interactions: 146777 Sorted by model distance: nonbonded pdb=" O GLN C 563 " pdb=" OG SER C 566 " model vdw 2.202 2.440 nonbonded pdb=" O MET D 431 " pdb=" OG1 THR D 485 " model vdw 2.216 2.440 nonbonded pdb=" OG1 THR A 285 " pdb=" OH TYR B 291 " model vdw 2.235 2.440 nonbonded pdb=" OH TYR D 291 " pdb=" OG1 THR C 285 " model vdw 2.239 2.440 nonbonded pdb=" O MET D 306 " pdb=" OG SER D 310 " model vdw 2.242 2.440 ... (remaining 146772 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 75 through 180 or (resid 181 through 183 and (name N or na \ me CA or name C or name O or name CB )) or resid 184 through 249 or resid 251 th \ rough 344 or (resid 345 and (name N or name CA or name C or name O or name CB )) \ or resid 346 through 377 or (resid 378 through 381 and (name N or name CA or na \ me C or name O or name CB )) or resid 382 through 472 or (resid 473 and (name N \ or name CA or name C or name O or name CB )) or resid 474 through 490 or (resid \ 491 through 492 and (name N or name CA or name C or name O or name CB )) or resi \ d 493 through 546 or (resid 547 and (name N or name CA or name C or name O or na \ me CB )) or resid 548 through 561 or (resid 562 and (name N or name CA or name C \ or name O or name CB )) or resid 563 through 572 or (resid 573 and (name N or n \ ame CA or name C or name O or name CB )) or resid 574 through 575 or (resid 576 \ and (name N or name CA or name C or name O or name CB )) or resid 577 through 60 \ 2 or (resid 603 and (name N or name CA or name C or name O or name CB )) or resi \ d 604 through 605 or (resid 606 and (name N or name CA or name C or name O or na \ me CB )) or resid 607 through 609 or (resid 610 and (name N or name CA or name C \ or name O or name CB )) or resid 611 through 638 or (resid 639 and (name N or n \ ame CA or name C or name O or name CB )) or resid 640 through 656 or (resid 657 \ and (name N or name CA or name C or name O or name CB )) or resid 658 through 66 \ 9 or (resid 670 and (name N or name CA or name C or name O or name CB )) or resi \ d 671 or (resid 672 and (name N or name CA or name C or name O or name CB )) or \ resid 673 through 681 or (resid 682 and (name N or name CA or name C or name O o \ r name CB )) or resid 683 through 686 or (resid 687 through 688 and (name N or n \ ame CA or name C or name O or name CB )) or resid 689 or (resid 690 through 692 \ and (name N or name CA or name C or name O or name CB )) or resid 693 through 69 \ 4 or (resid 695 and (name N or name CA or name C or name O or name CB )) or resi \ d 696 through 697 or (resid 698 through 710 and (name N or name CA or name C or \ name O or name CB )) or resid 711 through 740)) selection = (chain 'B' and ((resid 75 through 80 and (name N or name CA or name C or name O \ or name CB )) or resid 81 through 82 or (resid 83 through 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 86 or (resid 87 and (n \ ame N or name CA or name C or name O or name CB )) or resid 88 through 111 or (r \ esid 112 through 113 and (name N or name CA or name C or name O or name CB )) or \ resid 114 through 118 or (resid 119 through 120 and (name N or name CA or name \ C or name O or name CB )) or resid 121 through 122 or (resid 123 through 124 and \ (name N or name CA or name C or name O or name CB )) or resid 125 or (resid 126 \ and (name N or name CA or name C or name O or name CB )) or resid 127 through 1 \ 28 or (resid 129 and (name N or name CA or name C or name O or name CB )) or res \ id 130 through 134 or (resid 135 through 154 and (name N or name CA or name C or \ name O or name CB )) or resid 155 through 168 or (resid 169 and (name N or name \ CA or name C or name O or name CB )) or resid 170 through 181 or (resid 182 thr \ ough 183 and (name N or name CA or name C or name O or name CB )) or resid 184 t \ hrough 207 or (resid 208 and (name N or name CA or name C or name O or name CB ) \ ) or resid 209 through 210 or (resid 211 and (name N or name CA or name C or nam \ e O or name CB )) or resid 212 through 215 or (resid 216 and (name N or name CA \ or name C or name O or name CB )) or resid 217 through 249 or resid 251 through \ 380 or (resid 381 and (name N or name CA or name C or name O or name CB )) or re \ sid 382 or (resid 383 through 385 and (name N or name CA or name C or name O or \ name CB )) or resid 386 through 387 or (resid 388 and (name N or name CA or name \ C or name O or name CB )) or resid 389 through 399 or (resid 400 and (name N or \ name CA or name C or name O or name CB )) or resid 401 through 404 or (resid 40 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 406 or (resi \ d 407 and (name N or name CA or name C or name O or name CB )) or resid 408 thro \ ugh 431 or (resid 432 and (name N or name CA or name C or name O or name CB )) o \ r resid 433 through 434 or (resid 435 and (name N or name CA or name C or name O \ or name CB )) or resid 436 through 451 or resid 460 through 465 or (resid 466 a \ nd (name N or name CA or name C or name O or name CB )) or resid 467 or (resid 4 \ 68 and (name N or name CA or name C or name O or name CB )) or resid 469 through \ 474 or (resid 475 and (name N or name CA or name C or name O or name CB )) or r \ esid 476 through 478 or (resid 479 and (name N or name CA or name C or name O or \ name CB )) or resid 480 through 499 or (resid 500 and (name N or name CA or nam \ e C or name O or name CB )) or resid 501 through 502 or (resid 503 and (name N o \ r name CA or name C or name O or name CB )) or resid 504 through 506 or (resid 5 \ 07 and (name N or name CA or name C or name O or name CB )) or resid 508 through \ 511 or (resid 512 and (name N or name CA or name C or name O or name CB )) or r \ esid 513 or (resid 514 and (name N or name CA or name C or name O or name CB )) \ or resid 515 or (resid 516 and (name N or name CA or name C or name O or name CB \ )) or resid 517 or (resid 518 and (name N or name CA or name C or name O or nam \ e CB )) or resid 519 through 520 or (resid 521 through 522 and (name N or name C \ A or name C or name O or name CB )) or (resid 523 through 544 and (name N or nam \ e CA or name C or name O or name CB )) or resid 545 through 612 or (resid 613 an \ d (name N or name CA or name C or name O or name CB )) or resid 614 through 625 \ or (resid 626 and (name N or name CA or name C or name O or name CB )) or resid \ 627 or (resid 628 and (name N or name CA or name C or name O or name CB )) or re \ sid 629 through 674 or (resid 675 and (name N or name CA or name C or name O or \ name CB )) or resid 676 or (resid 677 and (name N or name CA or name C or name O \ or name CB )) or resid 678 through 683 or (resid 684 through 688 and (name N or \ name CA or name C or name O or name CB )) or resid 689 through 708 or (resid 70 \ 9 through 710 and (name N or name CA or name C or name O or name CB )) or resid \ 711 through 740)) selection = (chain 'C' and (resid 75 through 180 or (resid 181 through 183 and (name N or na \ me CA or name C or name O or name CB )) or resid 184 through 249 or resid 251 th \ rough 344 or (resid 345 and (name N or name CA or name C or name O or name CB )) \ or resid 346 through 377 or (resid 378 through 381 and (name N or name CA or na \ me C or name O or name CB )) or resid 382 through 472 or (resid 473 and (name N \ or name CA or name C or name O or name CB )) or resid 474 through 490 or (resid \ 491 through 492 and (name N or name CA or name C or name O or name CB )) or resi \ d 493 through 546 or (resid 547 and (name N or name CA or name C or name O or na \ me CB )) or resid 548 through 561 or (resid 562 and (name N or name CA or name C \ or name O or name CB )) or resid 563 through 572 or (resid 573 and (name N or n \ ame CA or name C or name O or name CB )) or resid 574 through 575 or (resid 576 \ and (name N or name CA or name C or name O or name CB )) or resid 577 through 60 \ 2 or (resid 603 and (name N or name CA or name C or name O or name CB )) or resi \ d 604 through 605 or (resid 606 and (name N or name CA or name C or name O or na \ me CB )) or resid 607 through 609 or (resid 610 and (name N or name CA or name C \ or name O or name CB )) or resid 611 through 638 or (resid 639 and (name N or n \ ame CA or name C or name O or name CB )) or resid 640 through 656 or (resid 657 \ and (name N or name CA or name C or name O or name CB )) or resid 658 through 66 \ 9 or (resid 670 and (name N or name CA or name C or name O or name CB )) or resi \ d 671 or (resid 672 and (name N or name CA or name C or name O or name CB )) or \ resid 673 through 681 or (resid 682 and (name N or name CA or name C or name O o \ r name CB )) or resid 683 through 686 or (resid 687 through 688 and (name N or n \ ame CA or name C or name O or name CB )) or resid 689 or (resid 690 through 692 \ and (name N or name CA or name C or name O or name CB )) or resid 693 through 69 \ 4 or (resid 695 and (name N or name CA or name C or name O or name CB )) or resi \ d 696 through 697 or (resid 698 through 710 and (name N or name CA or name C or \ name O or name CB )) or resid 711 through 740)) selection = (chain 'D' and ((resid 75 through 80 and (name N or name CA or name C or name O \ or name CB )) or resid 81 through 82 or (resid 83 through 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 86 or (resid 87 and (n \ ame N or name CA or name C or name O or name CB )) or resid 88 through 111 or (r \ esid 112 through 113 and (name N or name CA or name C or name O or name CB )) or \ resid 114 through 118 or (resid 119 through 120 and (name N or name CA or name \ C or name O or name CB )) or resid 121 through 122 or (resid 123 through 124 and \ (name N or name CA or name C or name O or name CB )) or resid 125 or (resid 126 \ and (name N or name CA or name C or name O or name CB )) or resid 127 through 1 \ 28 or (resid 129 and (name N or name CA or name C or name O or name CB )) or res \ id 130 through 134 or (resid 135 through 154 and (name N or name CA or name C or \ name O or name CB )) or resid 155 through 168 or (resid 169 and (name N or name \ CA or name C or name O or name CB )) or resid 170 through 181 or (resid 182 thr \ ough 183 and (name N or name CA or name C or name O or name CB )) or resid 184 t \ hrough 207 or (resid 208 and (name N or name CA or name C or name O or name CB ) \ ) or resid 209 through 210 or (resid 211 and (name N or name CA or name C or nam \ e O or name CB )) or resid 212 through 215 or (resid 216 and (name N or name CA \ or name C or name O or name CB )) or resid 217 through 249 or resid 251 through \ 380 or (resid 381 and (name N or name CA or name C or name O or name CB )) or re \ sid 382 or (resid 383 through 385 and (name N or name CA or name C or name O or \ name CB )) or resid 386 through 387 or (resid 388 and (name N or name CA or name \ C or name O or name CB )) or resid 389 through 399 or (resid 400 and (name N or \ name CA or name C or name O or name CB )) or resid 401 through 404 or (resid 40 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 406 or (resi \ d 407 and (name N or name CA or name C or name O or name CB )) or resid 408 thro \ ugh 431 or (resid 432 and (name N or name CA or name C or name O or name CB )) o \ r resid 433 through 434 or (resid 435 and (name N or name CA or name C or name O \ or name CB )) or resid 436 through 451 or resid 460 through 465 or (resid 466 a \ nd (name N or name CA or name C or name O or name CB )) or resid 467 or (resid 4 \ 68 and (name N or name CA or name C or name O or name CB )) or resid 469 through \ 474 or (resid 475 and (name N or name CA or name C or name O or name CB )) or r \ esid 476 through 478 or (resid 479 and (name N or name CA or name C or name O or \ name CB )) or resid 480 through 499 or (resid 500 and (name N or name CA or nam \ e C or name O or name CB )) or resid 501 through 502 or (resid 503 and (name N o \ r name CA or name C or name O or name CB )) or resid 504 through 506 or (resid 5 \ 07 and (name N or name CA or name C or name O or name CB )) or resid 508 through \ 511 or (resid 512 and (name N or name CA or name C or name O or name CB )) or r \ esid 513 or (resid 514 and (name N or name CA or name C or name O or name CB )) \ or resid 515 or (resid 516 and (name N or name CA or name C or name O or name CB \ )) or resid 517 or (resid 518 and (name N or name CA or name C or name O or nam \ e CB )) or resid 519 through 520 or (resid 521 through 522 and (name N or name C \ A or name C or name O or name CB )) or (resid 523 through 544 and (name N or nam \ e CA or name C or name O or name CB )) or resid 545 through 612 or (resid 613 an \ d (name N or name CA or name C or name O or name CB )) or resid 614 through 625 \ or (resid 626 and (name N or name CA or name C or name O or name CB )) or resid \ 627 or (resid 628 and (name N or name CA or name C or name O or name CB )) or re \ sid 629 through 674 or (resid 675 and (name N or name CA or name C or name O or \ name CB )) or resid 676 or (resid 677 and (name N or name CA or name C or name O \ or name CB )) or resid 678 through 683 or (resid 684 through 688 and (name N or \ name CA or name C or name O or name CB )) or resid 689 through 708 or (resid 70 \ 9 through 710 and (name N or name CA or name C or name O or name CB )) or resid \ 711 through 740)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.890 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 65.110 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.140 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 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 0.043 19862 Z= 0.122 Angle : 0.518 12.061 27096 Z= 0.259 Chirality : 0.037 0.141 3208 Planarity : 0.003 0.055 3426 Dihedral : 15.899 89.396 6632 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.99 % Favored : 94.70 % Rotamer: Outliers : 0.17 % Allowed : 30.98 % Favored : 68.85 % 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: -0.27 (0.16), residues: 2628 helix: 0.30 (0.14), residues: 1456 sheet: 0.72 (0.52), residues: 94 loop : -0.80 (0.19), residues: 1078 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 182 time to evaluate : 2.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 184 average time/residue: 0.2618 time to fit residues: 80.8017 Evaluate side-chains 164 residues out of total 2298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 161 time to evaluate : 2.341 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1797 time to fit residues: 3.8193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 221 optimal weight: 5.9990 chunk 198 optimal weight: 0.9990 chunk 110 optimal weight: 50.0000 chunk 67 optimal weight: 0.1980 chunk 133 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 205 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 124 optimal weight: 30.0000 chunk 152 optimal weight: 0.8980 chunk 237 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 HIS A 575 ASN ** A 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 ASN ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 ASN ** C 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 HIS B 322 ASN ** B 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19862 Z= 0.169 Angle : 0.568 9.350 27096 Z= 0.292 Chirality : 0.040 0.143 3208 Planarity : 0.004 0.058 3426 Dihedral : 3.752 17.823 2884 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.69 % Favored : 95.01 % Rotamer: Outliers : 1.77 % Allowed : 29.27 % Favored : 68.96 % 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: 0.27 (0.17), residues: 2628 helix: 0.85 (0.13), residues: 1492 sheet: 0.93 (0.51), residues: 90 loop : -0.81 (0.20), residues: 1046 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 181 time to evaluate : 2.419 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 12 residues processed: 207 average time/residue: 0.2703 time to fit residues: 92.7015 Evaluate side-chains 168 residues out of total 2298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 156 time to evaluate : 2.206 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1892 time to fit residues: 7.1118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 132 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 198 optimal weight: 0.7980 chunk 162 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 238 optimal weight: 2.9990 chunk 257 optimal weight: 0.0030 chunk 212 optimal weight: 0.8980 chunk 236 optimal weight: 0.4980 chunk 81 optimal weight: 0.9980 chunk 191 optimal weight: 20.0000 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 ASN ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 GLN ** D 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 563 GLN ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 ASN ** B 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19862 Z= 0.140 Angle : 0.522 12.871 27096 Z= 0.266 Chirality : 0.039 0.135 3208 Planarity : 0.004 0.059 3426 Dihedral : 3.619 19.475 2884 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.69 % Favored : 95.01 % Rotamer: Outliers : 1.59 % Allowed : 28.82 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.17), residues: 2628 helix: 1.15 (0.13), residues: 1498 sheet: 0.87 (0.51), residues: 90 loop : -0.83 (0.20), residues: 1040 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 189 time to evaluate : 2.041 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 10 residues processed: 210 average time/residue: 0.2575 time to fit residues: 90.6195 Evaluate side-chains 177 residues out of total 2298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 167 time to evaluate : 2.116 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1784 time to fit residues: 6.2927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 235 optimal weight: 0.9980 chunk 179 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 160 optimal weight: 6.9990 chunk 239 optimal weight: 0.2980 chunk 253 optimal weight: 5.9990 chunk 124 optimal weight: 0.0010 chunk 226 optimal weight: 0.2980 chunk 68 optimal weight: 0.0000 overall best weight: 0.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 553 ASN ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19862 Z= 0.124 Angle : 0.496 9.753 27096 Z= 0.253 Chirality : 0.039 0.137 3208 Planarity : 0.004 0.061 3426 Dihedral : 3.498 18.709 2884 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.99 % Favored : 94.70 % Rotamer: Outliers : 1.31 % Allowed : 28.19 % Favored : 70.50 % 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: 0.81 (0.17), residues: 2628 helix: 1.40 (0.14), residues: 1492 sheet: 0.86 (0.51), residues: 90 loop : -0.72 (0.20), residues: 1046 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 192 time to evaluate : 2.154 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 9 residues processed: 206 average time/residue: 0.2591 time to fit residues: 89.9012 Evaluate side-chains 177 residues out of total 2298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 168 time to evaluate : 2.316 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2052 time to fit residues: 6.4910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 210 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 188 optimal weight: 20.0000 chunk 104 optimal weight: 0.0000 chunk 216 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 129 optimal weight: 50.0000 chunk 227 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 553 ASN ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 ASN ** B 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 GLN ** B 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19862 Z= 0.193 Angle : 0.531 8.991 27096 Z= 0.273 Chirality : 0.040 0.143 3208 Planarity : 0.004 0.058 3426 Dihedral : 3.597 18.265 2884 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.26 % Favored : 94.44 % Rotamer: Outliers : 1.59 % Allowed : 28.42 % Favored : 69.99 % 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: 0.87 (0.17), residues: 2628 helix: 1.50 (0.14), residues: 1492 sheet: 0.83 (0.51), residues: 90 loop : -0.78 (0.20), residues: 1046 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 161 time to evaluate : 2.417 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 19 residues processed: 185 average time/residue: 0.2570 time to fit residues: 80.1579 Evaluate side-chains 179 residues out of total 2298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 160 time to evaluate : 2.246 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1725 time to fit residues: 9.4435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 85 optimal weight: 0.6980 chunk 228 optimal weight: 0.0470 chunk 50 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 62 optimal weight: 0.1980 chunk 253 optimal weight: 2.9990 chunk 210 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 133 optimal weight: 0.5980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 GLN ** B 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19862 Z= 0.125 Angle : 0.500 9.945 27096 Z= 0.254 Chirality : 0.039 0.137 3208 Planarity : 0.003 0.062 3426 Dihedral : 3.476 18.709 2884 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.80 % Favored : 94.89 % Rotamer: Outliers : 0.80 % Allowed : 28.36 % Favored : 70.84 % 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: 1.01 (0.17), residues: 2628 helix: 1.60 (0.14), residues: 1494 sheet: 0.89 (0.52), residues: 90 loop : -0.70 (0.20), residues: 1044 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 184 time to evaluate : 2.044 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 191 average time/residue: 0.2610 time to fit residues: 83.6409 Evaluate side-chains 174 residues out of total 2298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 168 time to evaluate : 2.087 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2105 time to fit residues: 5.1470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 244 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 185 optimal weight: 8.9990 chunk 143 optimal weight: 0.9990 chunk 213 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 252 optimal weight: 0.0010 chunk 158 optimal weight: 0.9980 chunk 153 optimal weight: 0.4980 chunk 116 optimal weight: 0.0370 overall best weight: 0.5066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 ASN ** B 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19862 Z= 0.124 Angle : 0.504 10.316 27096 Z= 0.254 Chirality : 0.039 0.140 3208 Planarity : 0.003 0.062 3426 Dihedral : 3.435 18.185 2884 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.07 % Favored : 94.63 % Rotamer: Outliers : 0.57 % Allowed : 28.64 % Favored : 70.79 % 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: 1.10 (0.17), residues: 2628 helix: 1.68 (0.14), residues: 1498 sheet: 0.96 (0.51), residues: 90 loop : -0.69 (0.20), residues: 1040 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 184 time to evaluate : 2.232 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 191 average time/residue: 0.2619 time to fit residues: 85.4597 Evaluate side-chains 176 residues out of total 2298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 172 time to evaluate : 2.330 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2123 time to fit residues: 4.7063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 156 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 150 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 49 optimal weight: 0.0970 chunk 48 optimal weight: 0.0040 chunk 160 optimal weight: 0.7980 chunk 172 optimal weight: 0.7980 chunk 124 optimal weight: 0.0870 chunk 23 optimal weight: 0.7980 chunk 198 optimal weight: 0.0000 overall best weight: 0.1772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 GLN ** B 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19862 Z= 0.116 Angle : 0.502 10.761 27096 Z= 0.252 Chirality : 0.039 0.151 3208 Planarity : 0.003 0.060 3426 Dihedral : 3.393 18.082 2884 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.69 % Favored : 95.08 % Rotamer: Outliers : 0.46 % Allowed : 28.08 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.17), residues: 2628 helix: 1.65 (0.14), residues: 1514 sheet: 0.92 (0.51), residues: 90 loop : -0.63 (0.20), residues: 1024 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 204 time to evaluate : 2.535 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 208 average time/residue: 0.2653 time to fit residues: 93.7102 Evaluate side-chains 186 residues out of total 2298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 184 time to evaluate : 2.186 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3284 time to fit residues: 4.7271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 229 optimal weight: 0.8980 chunk 241 optimal weight: 1.9990 chunk 220 optimal weight: 0.9990 chunk 235 optimal weight: 8.9990 chunk 141 optimal weight: 0.2980 chunk 102 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 212 optimal weight: 0.9980 chunk 222 optimal weight: 2.9990 chunk 234 optimal weight: 0.1980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 ASN ** B 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 GLN ** B 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19862 Z= 0.133 Angle : 0.506 10.230 27096 Z= 0.254 Chirality : 0.039 0.167 3208 Planarity : 0.004 0.066 3426 Dihedral : 3.396 16.349 2884 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.95 % Favored : 94.82 % Rotamer: Outliers : 0.57 % Allowed : 28.76 % Favored : 70.67 % 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: 1.16 (0.17), residues: 2628 helix: 1.67 (0.14), residues: 1524 sheet: 0.89 (0.51), residues: 90 loop : -0.60 (0.21), residues: 1014 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 179 time to evaluate : 2.286 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 184 average time/residue: 0.2642 time to fit residues: 82.5060 Evaluate side-chains 182 residues out of total 2298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 178 time to evaluate : 2.065 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1728 time to fit residues: 4.4109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 154 optimal weight: 0.9990 chunk 248 optimal weight: 0.0010 chunk 151 optimal weight: 0.8980 chunk 118 optimal weight: 8.9990 chunk 172 optimal weight: 0.3980 chunk 261 optimal weight: 8.9990 chunk 240 optimal weight: 2.9990 chunk 207 optimal weight: 0.2980 chunk 21 optimal weight: 0.7980 chunk 160 optimal weight: 0.0270 chunk 127 optimal weight: 50.0000 overall best weight: 0.3044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 ASN ** B 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19862 Z= 0.118 Angle : 0.502 10.515 27096 Z= 0.250 Chirality : 0.039 0.137 3208 Planarity : 0.004 0.068 3426 Dihedral : 3.358 17.241 2884 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.99 % Favored : 94.78 % Rotamer: Outliers : 0.11 % Allowed : 28.93 % Favored : 70.96 % 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: 1.21 (0.17), residues: 2628 helix: 1.72 (0.14), residues: 1516 sheet: 0.98 (0.51), residues: 90 loop : -0.60 (0.21), residues: 1022 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 2.250 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.2632 time to fit residues: 85.7028 Evaluate side-chains 182 residues out of total 2298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 2.327 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 165 optimal weight: 4.9990 chunk 221 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 191 optimal weight: 30.0000 chunk 30 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 208 optimal weight: 0.4980 chunk 87 optimal weight: 3.9990 chunk 213 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 HIS ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 ASN ** B 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.123869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.081270 restraints weight = 58640.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.084145 restraints weight = 21975.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.085907 restraints weight = 11889.809| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3255 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3255 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19862 Z= 0.240 Angle : 0.564 9.926 27096 Z= 0.287 Chirality : 0.041 0.235 3208 Planarity : 0.004 0.065 3426 Dihedral : 3.611 17.865 2884 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.22 % Favored : 94.55 % Rotamer: Outliers : 0.28 % Allowed : 28.99 % Favored : 70.73 % 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: 1.09 (0.17), residues: 2628 helix: 1.70 (0.14), residues: 1494 sheet: 0.87 (0.51), residues: 90 loop : -0.72 (0.20), residues: 1044 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3507.16 seconds wall clock time: 64 minutes 54.15 seconds (3894.15 seconds total)