Starting phenix.real_space_refine on Sat Jul 4 14:17:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7b1g_11985/07_2026/7b1g_11985.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b1g_11985/07_2026/7b1g_11985.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7b1g_11985/07_2026/7b1g_11985.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b1g_11985/07_2026/7b1g_11985.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7b1g_11985/07_2026/7b1g_11985.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7b1g_11985/07_2026/7b1g_11985.cif" model { file = "/net/cci-nas-00/data/ceres_data/7b1g_11985/07_2026/7b1g_11985.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b1g_11985/07_2026/7b1g_11985.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 P 4 5.49 5 S 108 5.16 5 C 14134 2.51 5 N 3555 2.21 5 O 3856 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 180 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21661 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 5497 Classifications: {'peptide': 691} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 24, 'TRANS': 666} Chain breaks: 3 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 8, 'TYR:plan': 2, 'PHE:plan': 2, 'ARG:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 97 Chain: "E" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 392 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 47} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 5226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5226 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 22, 'TRANS': 627} Chain breaks: 4 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 72 Planarities with less than four sites: {'GLU:plan': 7, 'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "C" Number of atoms: 5226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5226 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 22, 'TRANS': 627} Chain breaks: 4 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 72 Planarities with less than four sites: {'GLU:plan': 7, 'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "D" Number of atoms: 5220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5220 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 22, 'TRANS': 627} Chain breaks: 4 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 77 Planarities with less than four sites: {'GLU:plan': 7, 'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {' CA': 1, '44E': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 49 Unusual residues: {' CA': 1, '44E': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {' CA': 1, '44E': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.02, per 1000 atoms: 0.19 Number of scatterers: 21661 At special positions: 0 Unit cell: (144.5, 130.05, 133.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 108 16.00 P 4 15.00 O 3856 8.00 N 3555 7.00 C 14134 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 780.1 milliseconds 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5162 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 71.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 32 through 42 removed outlier: 3.587A pdb=" N TYR A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 58 removed outlier: 3.823A pdb=" N GLU A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 82 through 92 Processing helix chain 'A' and resid 98 through 106 Processing helix chain 'A' and resid 108 through 117 Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 154 through 164 removed outlier: 3.817A pdb=" N MET A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 204 Processing helix chain 'A' and resid 205 through 212 removed outlier: 3.629A pdb=" N LEU A 211 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 235 removed outlier: 4.249A pdb=" N LYS A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 258 removed outlier: 3.676A pdb=" N GLN A 258 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 270 removed outlier: 3.524A pdb=" N LEU A 267 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 303 through 315 Processing helix chain 'A' and resid 327 through 350 removed outlier: 3.653A pdb=" N THR A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) Proline residue: A 341 - end of helix removed outlier: 3.834A pdb=" N TYR A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 361 removed outlier: 3.676A pdb=" N ILE A 359 " --> pdb=" O TYR A 355 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 383 Processing helix chain 'A' and resid 400 through 425 Proline residue: A 408 - end of helix removed outlier: 3.615A pdb=" N ASP A 423 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 458 removed outlier: 3.924A pdb=" N LYS A 458 " --> pdb=" O VAL A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 468 Processing helix chain 'A' and resid 472 through 492 removed outlier: 4.027A pdb=" N LEU A 492 " --> pdb=" O SER A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 498 Processing helix chain 'A' and resid 501 through 511 removed outlier: 4.472A pdb=" N LEU A 505 " --> pdb=" O HIS A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 538 removed outlier: 3.636A pdb=" N ILE A 522 " --> pdb=" O LYS A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 574 Processing helix chain 'A' and resid 575 through 577 No H-bonds generated for 'chain 'A' and resid 575 through 577' Processing helix chain 'A' and resid 590 through 610 Processing helix chain 'A' and resid 611 through 626 removed outlier: 3.937A pdb=" N ASN A 622 " --> pdb=" O ALA A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 648 removed outlier: 3.623A pdb=" N GLU A 634 " --> pdb=" O HIS A 630 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER A 645 " --> pdb=" O LYS A 641 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR A 646 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU A 648 " --> pdb=" O MET A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 658 Processing helix chain 'A' and resid 668 through 674 Processing helix chain 'A' and resid 677 through 681 Processing helix chain 'A' and resid 694 through 722 removed outlier: 3.817A pdb=" N ARG A 722 " --> pdb=" O ALA A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 752 Processing helix chain 'E' and resid 108 through 113 removed outlier: 3.948A pdb=" N LEU E 113 " --> pdb=" O VAL E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 123 Processing helix chain 'E' and resid 124 through 126 No H-bonds generated for 'chain 'E' and resid 124 through 126' Processing helix chain 'B' and resid 31 through 43 removed outlier: 3.803A pdb=" N SER B 35 " --> pdb=" O THR B 31 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER B 38 " --> pdb=" O LYS B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 58 removed outlier: 3.556A pdb=" N LYS B 49 " --> pdb=" O TYR B 45 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE B 57 " --> pdb=" O GLU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 removed outlier: 3.987A pdb=" N ALA B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 91 removed outlier: 4.114A pdb=" N LEU B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 106 removed outlier: 3.530A pdb=" N HIS B 102 " --> pdb=" O ASP B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 117 removed outlier: 3.729A pdb=" N GLU B 113 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU B 114 " --> pdb=" O GLY B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 154 through 164 removed outlier: 4.158A pdb=" N MET B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 203 removed outlier: 3.740A pdb=" N LEU B 197 " --> pdb=" O SER B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 212 Processing helix chain 'B' and resid 217 through 235 removed outlier: 3.596A pdb=" N SER B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS B 232 " --> pdb=" O GLN B 228 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 246 removed outlier: 4.079A pdb=" N LEU B 244 " --> pdb=" O GLU B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 257 removed outlier: 3.534A pdb=" N LYS B 253 " --> pdb=" O LYS B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 270 removed outlier: 3.533A pdb=" N LEU B 267 " --> pdb=" O ARG B 263 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE B 268 " --> pdb=" O GLU B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 294 Processing helix chain 'B' and resid 305 through 315 removed outlier: 3.749A pdb=" N LEU B 309 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 339 removed outlier: 4.025A pdb=" N ILE B 331 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR B 332 " --> pdb=" O GLY B 328 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET B 339 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 350 removed outlier: 3.669A pdb=" N LEU B 343 " --> pdb=" O MET B 339 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N CYS B 346 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N TYR B 347 " --> pdb=" O LEU B 343 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 382 removed outlier: 3.843A pdb=" N PHE B 376 " --> pdb=" O SER B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 385 No H-bonds generated for 'chain 'B' and resid 383 through 385' Processing helix chain 'B' and resid 400 through 425 removed outlier: 3.798A pdb=" N LEU B 407 " --> pdb=" O GLU B 403 " (cutoff:3.500A) Proline residue: B 408 - end of helix removed outlier: 3.667A pdb=" N LYS B 419 " --> pdb=" O TRP B 415 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLN B 420 " --> pdb=" O THR B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 457 removed outlier: 3.601A pdb=" N LEU B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N MET B 437 " --> pdb=" O TRP B 433 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR B 445 " --> pdb=" O MET B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 468 Processing helix chain 'B' and resid 472 through 489 Processing helix chain 'B' and resid 490 through 498 removed outlier: 3.742A pdb=" N THR B 497 " --> pdb=" O SER B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 512 removed outlier: 4.116A pdb=" N LEU B 505 " --> pdb=" O HIS B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 520 removed outlier: 3.976A pdb=" N ILE B 516 " --> pdb=" O MET B 512 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 517 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 539 removed outlier: 3.860A pdb=" N LEU B 528 " --> pdb=" O CYS B 524 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN B 536 " --> pdb=" O ASN B 532 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 574 removed outlier: 3.677A pdb=" N GLN B 569 " --> pdb=" O PHE B 565 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER B 570 " --> pdb=" O GLU B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 601 Processing helix chain 'B' and resid 601 through 608 removed outlier: 3.523A pdb=" N ASN B 605 " --> pdb=" O PHE B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 627 removed outlier: 3.656A pdb=" N ILE B 617 " --> pdb=" O LEU B 613 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASN B 622 " --> pdb=" O ALA B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 644 Processing helix chain 'B' and resid 645 through 647 No H-bonds generated for 'chain 'B' and resid 645 through 647' Processing helix chain 'B' and resid 654 through 659 removed outlier: 3.912A pdb=" N ILE B 659 " --> pdb=" O PRO B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 722 removed outlier: 3.507A pdb=" N GLU B 707 " --> pdb=" O HIS B 703 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL B 708 " --> pdb=" O GLN B 704 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN B 711 " --> pdb=" O GLU B 707 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 718 " --> pdb=" O LYS B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 753 removed outlier: 3.571A pdb=" N LEU B 738 " --> pdb=" O ASN B 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 43 removed outlier: 4.140A pdb=" N SER C 35 " --> pdb=" O THR C 31 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 58 removed outlier: 3.767A pdb=" N ILE C 57 " --> pdb=" O GLU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 82 through 92 removed outlier: 3.890A pdb=" N LEU C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 106 Processing helix chain 'C' and resid 108 through 117 removed outlier: 3.570A pdb=" N VAL C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU C 113 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU C 114 " --> pdb=" O GLY C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 153 Processing helix chain 'C' and resid 154 through 164 removed outlier: 3.591A pdb=" N GLN C 163 " --> pdb=" O LYS C 159 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS C 164 " --> pdb=" O MET C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 204 removed outlier: 3.572A pdb=" N ARG C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER C 195 " --> pdb=" O ARG C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 212 removed outlier: 3.529A pdb=" N LEU C 211 " --> pdb=" O SER C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 235 removed outlier: 3.624A pdb=" N SER C 224 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LYS C 232 " --> pdb=" O GLN C 228 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 257 removed outlier: 4.171A pdb=" N LEU C 244 " --> pdb=" O GLU C 240 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN C 247 " --> pdb=" O GLU C 243 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N HIS C 250 " --> pdb=" O HIS C 246 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS C 253 " --> pdb=" O LYS C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 270 removed outlier: 3.865A pdb=" N ILE C 268 " --> pdb=" O GLU C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 Processing helix chain 'C' and resid 297 through 302 removed outlier: 3.555A pdb=" N VAL C 301 " --> pdb=" O GLN C 297 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA C 302 " --> pdb=" O LYS C 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 297 through 302' Processing helix chain 'C' and resid 303 through 315 Processing helix chain 'C' and resid 327 through 338 removed outlier: 3.834A pdb=" N THR C 332 " --> pdb=" O GLY C 328 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS C 333 " --> pdb=" O LYS C 329 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE C 336 " --> pdb=" O THR C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 350 removed outlier: 4.198A pdb=" N TYR C 347 " --> pdb=" O LEU C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 360 removed outlier: 3.744A pdb=" N ILE C 359 " --> pdb=" O TYR C 355 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG C 360 " --> pdb=" O GLY C 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 355 through 360' Processing helix chain 'C' and resid 361 through 384 removed outlier: 3.833A pdb=" N SER C 384 " --> pdb=" O LEU C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 423 Proline residue: C 408 - end of helix Processing helix chain 'C' and resid 434 through 457 removed outlier: 3.825A pdb=" N VAL C 440 " --> pdb=" O LEU C 436 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR C 445 " --> pdb=" O MET C 441 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C 451 " --> pdb=" O ALA C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 468 Processing helix chain 'C' and resid 472 through 490 Processing helix chain 'C' and resid 491 through 498 removed outlier: 3.636A pdb=" N SER C 494 " --> pdb=" O ARG C 491 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA C 498 " --> pdb=" O LEU C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 511 Processing helix chain 'C' and resid 513 through 518 Processing helix chain 'C' and resid 519 through 539 removed outlier: 3.714A pdb=" N LEU C 528 " --> pdb=" O CYS C 524 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN C 535 " --> pdb=" O ALA C 531 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN C 536 " --> pdb=" O ASN C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 575 removed outlier: 3.711A pdb=" N ILE C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 609 Processing helix chain 'C' and resid 611 through 627 removed outlier: 3.907A pdb=" N ASN C 622 " --> pdb=" O ALA C 618 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE C 627 " --> pdb=" O SER C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 648 removed outlier: 3.990A pdb=" N SER C 645 " --> pdb=" O LYS C 641 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR C 646 " --> pdb=" O LEU C 642 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU C 648 " --> pdb=" O MET C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 658 Processing helix chain 'C' and resid 698 through 718 removed outlier: 3.945A pdb=" N GLU C 707 " --> pdb=" O HIS C 703 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL C 708 " --> pdb=" O GLN C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 731 through 750 removed outlier: 3.724A pdb=" N PHE C 745 " --> pdb=" O ASP C 741 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU C 748 " --> pdb=" O SER C 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 42 removed outlier: 3.686A pdb=" N SER D 35 " --> pdb=" O THR D 31 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR D 36 " --> pdb=" O GLN D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 55 removed outlier: 3.599A pdb=" N LYS D 49 " --> pdb=" O TYR D 45 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 80 removed outlier: 3.803A pdb=" N ALA D 77 " --> pdb=" O ALA D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 92 removed outlier: 3.501A pdb=" N ILE D 86 " --> pdb=" O ASN D 82 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU D 88 " --> pdb=" O GLU D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 106 removed outlier: 3.504A pdb=" N ARG D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 117 removed outlier: 4.430A pdb=" N GLU D 113 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N LEU D 114 " --> pdb=" O GLY D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 154 through 163 Processing helix chain 'D' and resid 190 through 201 removed outlier: 3.849A pdb=" N ILE D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 212 Processing helix chain 'D' and resid 215 through 235 removed outlier: 3.883A pdb=" N LYS D 232 " --> pdb=" O GLN D 228 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL D 233 " --> pdb=" O GLU D 229 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 257 removed outlier: 4.021A pdb=" N LYS D 253 " --> pdb=" O LYS D 249 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU D 256 " --> pdb=" O ALA D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 270 removed outlier: 3.705A pdb=" N ILE D 268 " --> pdb=" O GLU D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 295 Processing helix chain 'D' and resid 307 through 315 Processing helix chain 'D' and resid 325 through 338 Processing helix chain 'D' and resid 339 through 350 removed outlier: 4.463A pdb=" N TYR D 347 " --> pdb=" O LEU D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 360 removed outlier: 3.645A pdb=" N ILE D 359 " --> pdb=" O TYR D 355 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG D 360 " --> pdb=" O GLY D 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 355 through 360' Processing helix chain 'D' and resid 361 through 384 removed outlier: 4.015A pdb=" N PHE D 378 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 382 " --> pdb=" O PHE D 378 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER D 384 " --> pdb=" O LEU D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 425 removed outlier: 3.780A pdb=" N LEU D 407 " --> pdb=" O GLU D 403 " (cutoff:3.500A) Proline residue: D 408 - end of helix removed outlier: 3.955A pdb=" N ASP D 423 " --> pdb=" O LYS D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 457 removed outlier: 3.570A pdb=" N LEU D 436 " --> pdb=" O ASP D 432 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET D 437 " --> pdb=" O TRP D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 468 Processing helix chain 'D' and resid 472 through 490 Processing helix chain 'D' and resid 491 through 498 removed outlier: 3.533A pdb=" N SER D 494 " --> pdb=" O ARG D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 509 removed outlier: 4.175A pdb=" N LEU D 505 " --> pdb=" O HIS D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 522 through 539 removed outlier: 3.804A pdb=" N LEU D 528 " --> pdb=" O CYS D 524 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY D 533 " --> pdb=" O ALA D 529 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU D 534 " --> pdb=" O PHE D 530 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN D 536 " --> pdb=" O ASN D 532 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR D 538 " --> pdb=" O LEU D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 568 Processing helix chain 'D' and resid 590 through 609 Processing helix chain 'D' and resid 611 through 627 removed outlier: 3.970A pdb=" N ASN D 622 " --> pdb=" O ALA D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 648 removed outlier: 3.857A pdb=" N SER D 645 " --> pdb=" O LYS D 641 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N TYR D 646 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE D 647 " --> pdb=" O TRP D 643 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLU D 648 " --> pdb=" O MET D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 659 removed outlier: 4.088A pdb=" N ILE D 659 " --> pdb=" O PRO D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 698 through 725 removed outlier: 3.578A pdb=" N GLU D 707 " --> pdb=" O HIS D 703 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL D 708 " --> pdb=" O GLN D 704 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS D 714 " --> pdb=" O ARG D 710 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG D 722 " --> pdb=" O ALA D 718 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASP D 723 " --> pdb=" O ALA D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 731 through 753 removed outlier: 3.616A pdb=" N GLU D 748 " --> pdb=" O SER D 744 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY D 751 " --> pdb=" O TYR D 747 " (cutoff:3.500A) 1168 hydrogen bonds defined for protein. 3417 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: 3.53 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3438 1.31 - 1.43: 6155 1.43 - 1.56: 12404 1.56 - 1.69: 4 1.69 - 1.81: 177 Bond restraints: 22178 Sorted by residual: bond pdb=" O13 44E B1002 " pdb=" P 44E B1002 " ideal model delta sigma weight residual 1.684 1.500 0.184 2.00e-02 2.50e+03 8.42e+01 bond pdb=" O13 44E C1002 " pdb=" P 44E C1002 " ideal model delta sigma weight residual 1.684 1.502 0.182 2.00e-02 2.50e+03 8.26e+01 bond pdb=" O13 44E A1002 " pdb=" P 44E A1002 " ideal model delta sigma weight residual 1.684 1.503 0.181 2.00e-02 2.50e+03 8.21e+01 bond pdb=" O13 44E B1001 " pdb=" P 44E B1001 " ideal model delta sigma weight residual 1.684 1.504 0.180 2.00e-02 2.50e+03 8.08e+01 bond pdb=" O14 44E B1001 " pdb=" P 44E B1001 " ideal model delta sigma weight residual 1.668 1.504 0.164 2.00e-02 2.50e+03 6.74e+01 ... (remaining 22173 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.01: 30066 11.01 - 22.03: 19 22.03 - 33.04: 0 33.04 - 44.06: 0 44.06 - 55.07: 4 Bond angle restraints: 30089 Sorted by residual: angle pdb=" O13 44E B1001 " pdb=" P 44E B1001 " pdb=" O14 44E B1001 " ideal model delta sigma weight residual 54.79 109.86 -55.07 3.00e+00 1.11e-01 3.37e+02 angle pdb=" O13 44E B1002 " pdb=" P 44E B1002 " pdb=" O14 44E B1002 " ideal model delta sigma weight residual 54.79 109.47 -54.68 3.00e+00 1.11e-01 3.32e+02 angle pdb=" O13 44E C1002 " pdb=" P 44E C1002 " pdb=" O14 44E C1002 " ideal model delta sigma weight residual 54.79 109.26 -54.47 3.00e+00 1.11e-01 3.30e+02 angle pdb=" O13 44E A1002 " pdb=" P 44E A1002 " pdb=" O14 44E A1002 " ideal model delta sigma weight residual 54.79 108.53 -53.74 3.00e+00 1.11e-01 3.21e+02 angle pdb=" O12 44E A1002 " pdb=" P 44E A1002 " pdb=" O14 44E A1002 " ideal model delta sigma weight residual 127.76 109.83 17.93 3.00e+00 1.11e-01 3.57e+01 ... (remaining 30084 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.54: 12374 27.54 - 55.09: 690 55.09 - 82.63: 65 82.63 - 110.17: 6 110.17 - 137.72: 2 Dihedral angle restraints: 13137 sinusoidal: 5203 harmonic: 7934 Sorted by residual: dihedral pdb=" CA MET D 470 " pdb=" C MET D 470 " pdb=" N TRP D 471 " pdb=" CA TRP D 471 " ideal model delta harmonic sigma weight residual -180.00 -157.22 -22.78 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" C33 44E B1001 " pdb=" C31 44E B1001 " pdb=" C32 44E B1001 " pdb=" O32 44E B1001 " ideal model delta sinusoidal sigma weight residual 7.95 145.67 -137.72 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" C33 44E B1001 " pdb=" C31 44E B1001 " pdb=" C32 44E B1001 " pdb=" O31 44E B1001 " ideal model delta sinusoidal sigma weight residual -170.09 -34.38 -135.71 1 3.00e+01 1.11e-03 1.83e+01 ... (remaining 13134 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2073 0.039 - 0.078: 1060 0.078 - 0.116: 222 0.116 - 0.155: 41 0.155 - 0.194: 6 Chirality restraints: 3402 Sorted by residual: chirality pdb=" C2 44E A1002 " pdb=" C1 44E A1002 " pdb=" C3 44E A1002 " pdb=" O21 44E A1002 " both_signs ideal model delta sigma weight residual False -2.57 -2.37 -0.19 2.00e-01 2.50e+01 9.39e-01 chirality pdb=" CA ASN C 559 " pdb=" N ASN C 559 " pdb=" C ASN C 559 " pdb=" CB ASN C 559 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.95e-01 chirality pdb=" CA ARG A 553 " pdb=" N ARG A 553 " pdb=" C ARG A 553 " pdb=" CB ARG A 553 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.93e-01 ... (remaining 3399 not shown) Planarity restraints: 3748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 433 " -0.016 2.00e-02 2.50e+03 1.32e-02 4.34e+00 pdb=" CG TRP D 433 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP D 433 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP D 433 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 433 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP D 433 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 433 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 433 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 433 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 433 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 205 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO C 206 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 206 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 206 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 303 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.22e+00 pdb=" N PRO A 304 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 304 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 304 " 0.028 5.00e-02 4.00e+02 ... (remaining 3745 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3749 2.75 - 3.29: 22749 3.29 - 3.83: 34648 3.83 - 4.36: 42683 4.36 - 4.90: 70535 Nonbonded interactions: 174364 Sorted by model distance: nonbonded pdb=" OD1 ASN D 153 " pdb=" OG SER D 207 " model vdw 2.213 3.040 nonbonded pdb=" NH1 ARG A 272 " pdb=" OD1 ASP A 274 " model vdw 2.215 3.120 nonbonded pdb=" O LEU B 571 " pdb=" OH TYR B 604 " model vdw 2.216 3.040 nonbonded pdb=" O ARG E 107 " pdb=" OG1 THR E 111 " model vdw 2.218 3.040 nonbonded pdb=" OH TYR C 523 " pdb=" OH TYR C 604 " model vdw 2.220 3.040 ... (remaining 174359 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 272 or resid 284 through 660 or resid 696 throu \ gh 721 or (resid 722 and (name N or name CA or name C or name O or name CB )) or \ resid 723 through 753)) selection = (chain 'B' and (resid 28 through 458 or (resid 459 and (name N or name CA or nam \ e C or name O or name CB )) or resid 460 through 461 or (resid 462 and (name N o \ r name CA or name C or name O or name CB )) or resid 463 through 721 or (resid 7 \ 22 and (name N or name CA or name C or name O or name CB )) or resid 723 through \ 753)) selection = (chain 'C' and (resid 28 through 458 or (resid 459 and (name N or name CA or nam \ e C or name O or name CB )) or resid 460 through 461 or (resid 462 and (name N o \ r name CA or name C or name O or name CB )) or resid 463 through 721 or (resid 7 \ 22 and (name N or name CA or name C or name O or name CB )) or resid 723 through \ 753)) selection = (chain 'D' and (resid 28 through 458 or (resid 459 and (name N or name CA or nam \ e C or name O or name CB )) or resid 460 through 461 or (resid 462 and (name N o \ r name CA or name C or name O or name CB )) or resid 463 through 753)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.150 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 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 : 0.007 0.184 22178 Z= 0.329 Angle : 1.040 55.074 30089 Z= 0.449 Chirality : 0.045 0.194 3402 Planarity : 0.005 0.051 3748 Dihedral : 16.012 137.718 7975 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 0.09 % Allowed : 1.04 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.16), residues: 2643 helix: -1.15 (0.12), residues: 1792 sheet: None (None), residues: 0 loop : -1.88 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 722 TYR 0.030 0.002 TYR D 200 PHE 0.023 0.002 PHE B 300 TRP 0.035 0.002 TRP D 433 HIS 0.008 0.001 HIS B 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00738 / 0.33 (22178) covalent geometry : angle 1.03972 / 0.45 (30089) hydrogen bonds : bond 0.24431 / 16.45 ( 1168) hydrogen bonds : angle 8.42408 / 5.90 ( 3417) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 279 time to evaluate : 0.847 Fit side-chains REVERT: A 429 TYR cc_start: 0.8418 (t80) cc_final: 0.7744 (t80) REVERT: C 83 LEU cc_start: 0.9041 (mp) cc_final: 0.8824 (mp) outliers start: 2 outliers final: 0 residues processed: 280 average time/residue: 0.1260 time to fit residues: 56.7960 Evaluate side-chains 225 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.0000 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.0040 chunk 111 optimal weight: 3.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 ASN A 630 HIS ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN B 532 ASN ** B 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN C 308 GLN C 605 ASN ** C 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 704 GLN ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN D 442 ASN ** D 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.114520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.095836 restraints weight = 42121.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.098265 restraints weight = 23342.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.099883 restraints weight = 15914.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.100795 restraints weight = 12399.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.101583 restraints weight = 10677.995| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22178 Z= 0.145 Angle : 0.650 9.387 30089 Z= 0.329 Chirality : 0.041 0.196 3402 Planarity : 0.005 0.045 3748 Dihedral : 7.702 89.867 2977 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.96 % Allowed : 9.05 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.16), residues: 2643 helix: -0.35 (0.12), residues: 1864 sheet: None (None), residues: 0 loop : -1.76 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 511 TYR 0.020 0.001 TYR A 582 PHE 0.020 0.002 PHE A 271 TRP 0.021 0.001 TRP D 326 HIS 0.005 0.001 HIS B 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 (22178) covalent geometry : angle 0.64969 / 0.33 (30089) hydrogen bonds : bond 0.04883 / 3.30 ( 1168) hydrogen bonds : angle 4.78279 / 3.41 ( 3417) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 288 time to evaluate : 0.863 Fit side-chains REVERT: B 722 ARG cc_start: 0.7015 (mpt180) cc_final: 0.6596 (mpt180) outliers start: 22 outliers final: 14 residues processed: 298 average time/residue: 0.1320 time to fit residues: 62.9880 Evaluate side-chains 249 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 235 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 404 TRP Chi-restraints excluded: chain B residue 466 ASP Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 704 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 124 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 chunk 146 optimal weight: 0.3980 chunk 125 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 ASN A 559 ASN B 303 GLN ** B 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 734 ASN C 614 ASN C 621 ASN ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 485 ASN D 614 ASN D 622 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.114060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.095337 restraints weight = 42365.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.097736 restraints weight = 23552.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.099355 restraints weight = 16122.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.100400 restraints weight = 12557.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.100980 restraints weight = 10688.658| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22178 Z= 0.140 Angle : 0.592 9.590 30089 Z= 0.300 Chirality : 0.041 0.213 3402 Planarity : 0.004 0.046 3748 Dihedral : 7.306 63.332 2977 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.52 % Allowed : 12.71 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.16), residues: 2643 helix: 0.05 (0.12), residues: 1858 sheet: None (None), residues: 0 loop : -1.70 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 511 TYR 0.017 0.001 TYR D 582 PHE 0.017 0.001 PHE A 300 TRP 0.020 0.001 TRP D 326 HIS 0.019 0.001 HIS C 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (22178) covalent geometry : angle 0.59222 / 0.30 (30089) hydrogen bonds : bond 0.03992 / 2.70 ( 1168) hydrogen bonds : angle 4.27230 / 3.05 ( 3417) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 261 time to evaluate : 0.934 Fit side-chains REVERT: B 438 ASP cc_start: 0.7734 (t0) cc_final: 0.7298 (t0) REVERT: B 445 TYR cc_start: 0.8039 (m-80) cc_final: 0.7779 (m-80) REVERT: B 566 GLU cc_start: 0.8208 (tp30) cc_final: 0.7986 (tp30) REVERT: D 394 ARG cc_start: 0.7860 (tpt90) cc_final: 0.7552 (tpt170) REVERT: D 554 CYS cc_start: 0.7920 (t) cc_final: 0.7155 (t) outliers start: 35 outliers final: 17 residues processed: 285 average time/residue: 0.1426 time to fit residues: 65.5139 Evaluate side-chains 248 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 231 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 704 GLN Chi-restraints excluded: chain D residue 738 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 184 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 203 optimal weight: 9.9990 chunk 46 optimal weight: 0.5980 chunk 135 optimal weight: 0.9990 chunk 173 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 209 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 94 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 ASN A 559 ASN B 442 ASN B 558 ASN B 734 ASN ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 630 HIS C 704 GLN ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.116023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.097569 restraints weight = 42241.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.099932 restraints weight = 23808.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.101533 restraints weight = 16381.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.102426 restraints weight = 12818.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.103184 restraints weight = 11065.705| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22178 Z= 0.112 Angle : 0.560 11.299 30089 Z= 0.283 Chirality : 0.040 0.227 3402 Planarity : 0.004 0.046 3748 Dihedral : 6.932 59.919 2977 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.65 % Allowed : 15.45 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.16), residues: 2643 helix: 0.34 (0.12), residues: 1863 sheet: None (None), residues: 0 loop : -1.63 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 511 TYR 0.016 0.001 TYR D 582 PHE 0.025 0.001 PHE A 271 TRP 0.031 0.001 TRP D 326 HIS 0.013 0.001 HIS C 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (22178) covalent geometry : angle 0.56045 / 0.28 (30089) hydrogen bonds : bond 0.03510 / 2.39 ( 1168) hydrogen bonds : angle 3.97601 / 2.85 ( 3417) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 279 time to evaluate : 0.853 Fit side-chains REVERT: A 535 ASN cc_start: 0.8474 (t0) cc_final: 0.8058 (t0) REVERT: B 438 ASP cc_start: 0.7701 (t0) cc_final: 0.7288 (t0) REVERT: D 343 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8349 (tt) REVERT: D 394 ARG cc_start: 0.7745 (tpt90) cc_final: 0.7465 (tpt170) outliers start: 38 outliers final: 22 residues processed: 302 average time/residue: 0.1426 time to fit residues: 68.3701 Evaluate side-chains 257 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 234 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain D residue 200 TYR Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 704 GLN Chi-restraints excluded: chain D residue 738 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 215 optimal weight: 0.0170 chunk 54 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 241 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 180 optimal weight: 0.9990 chunk 240 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 223 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 overall best weight: 1.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 HIS A 559 ASN A 590 HIS B 734 ASN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 ASN C 621 ASN ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.115435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.096920 restraints weight = 42296.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.099256 restraints weight = 23936.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.100813 restraints weight = 16528.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.101869 restraints weight = 13001.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.102423 restraints weight = 11083.983| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22178 Z= 0.124 Angle : 0.552 9.494 30089 Z= 0.280 Chirality : 0.040 0.193 3402 Planarity : 0.004 0.047 3748 Dihedral : 6.699 58.755 2977 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.05 % Allowed : 16.23 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.17), residues: 2643 helix: 0.51 (0.12), residues: 1873 sheet: None (None), residues: 0 loop : -1.52 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 511 TYR 0.016 0.001 TYR D 582 PHE 0.027 0.001 PHE A 539 TRP 0.036 0.001 TRP D 326 HIS 0.007 0.001 HIS C 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (22178) covalent geometry : angle 0.55246 / 0.28 (30089) hydrogen bonds : bond 0.03375 / 2.30 ( 1168) hydrogen bonds : angle 3.85418 / 2.76 ( 3417) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 262 time to evaluate : 0.865 Fit side-chains REVERT: A 535 ASN cc_start: 0.8498 (t0) cc_final: 0.8099 (t0) REVERT: B 90 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8738 (mm) REVERT: B 339 MET cc_start: 0.6925 (mtt) cc_final: 0.6589 (mtp) REVERT: C 372 SER cc_start: 0.9128 (m) cc_final: 0.8698 (p) REVERT: D 343 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8344 (tt) outliers start: 47 outliers final: 26 residues processed: 296 average time/residue: 0.1462 time to fit residues: 69.3568 Evaluate side-chains 267 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 239 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 200 TYR Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 704 GLN Chi-restraints excluded: chain D residue 738 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 163 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 70 optimal weight: 0.0050 chunk 188 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 241 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 225 optimal weight: 4.9990 chunk 147 optimal weight: 0.3980 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 ASN A 559 ASN B 734 ASN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 HIS C 250 HIS ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 ASN C 621 ASN C 622 ASN C 704 GLN ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.116059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.097478 restraints weight = 42413.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.099792 restraints weight = 24036.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.101376 restraints weight = 16649.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.102388 restraints weight = 13100.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.102952 restraints weight = 11216.323| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22178 Z= 0.117 Angle : 0.555 11.386 30089 Z= 0.277 Chirality : 0.040 0.193 3402 Planarity : 0.004 0.046 3748 Dihedral : 6.590 56.520 2977 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.05 % Allowed : 16.97 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.17), residues: 2643 helix: 0.68 (0.12), residues: 1869 sheet: None (None), residues: 0 loop : -1.53 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 511 TYR 0.015 0.001 TYR B 445 PHE 0.018 0.001 PHE B 300 TRP 0.027 0.001 TRP D 326 HIS 0.005 0.001 HIS C 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (22178) covalent geometry : angle 0.55457 / 0.28 (30089) hydrogen bonds : bond 0.03233 / 2.20 ( 1168) hydrogen bonds : angle 3.74062 / 2.68 ( 3417) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 262 time to evaluate : 0.588 Fit side-chains REVERT: A 314 TRP cc_start: 0.8684 (OUTLIER) cc_final: 0.7669 (t60) REVERT: A 535 ASN cc_start: 0.8525 (t0) cc_final: 0.8122 (t0) REVERT: A 538 TYR cc_start: 0.8057 (m-80) cc_final: 0.7773 (m-80) REVERT: E 140 GLU cc_start: 0.6704 (tp30) cc_final: 0.6388 (tp30) REVERT: B 90 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8719 (mm) REVERT: C 417 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7370 (tp30) REVERT: C 744 SER cc_start: 0.8709 (OUTLIER) cc_final: 0.8483 (t) REVERT: D 343 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8380 (tt) REVERT: D 439 PHE cc_start: 0.8949 (t80) cc_final: 0.8728 (t80) REVERT: D 600 MET cc_start: 0.7700 (mtm) cc_final: 0.7484 (mtm) outliers start: 47 outliers final: 29 residues processed: 295 average time/residue: 0.1291 time to fit residues: 61.2846 Evaluate side-chains 275 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 242 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 314 TRP Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 630 HIS Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 644 MET Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 200 TYR Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 704 GLN Chi-restraints excluded: chain D residue 738 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 87 optimal weight: 0.0770 chunk 109 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 249 optimal weight: 0.9980 chunk 258 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 227 optimal weight: 4.9990 chunk 62 optimal weight: 30.0000 chunk 99 optimal weight: 0.9980 overall best weight: 2.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 ASN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 ASN C 621 ASN D 153 ASN D 442 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.112972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.094087 restraints weight = 42646.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.096379 restraints weight = 24177.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.097962 restraints weight = 16798.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.098984 restraints weight = 13246.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.099431 restraints weight = 11338.673| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22178 Z= 0.181 Angle : 0.600 10.648 30089 Z= 0.301 Chirality : 0.042 0.183 3402 Planarity : 0.004 0.046 3748 Dihedral : 6.738 60.075 2977 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.35 % Allowed : 18.06 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.17), residues: 2643 helix: 0.61 (0.12), residues: 1878 sheet: None (None), residues: 0 loop : -1.53 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 511 TYR 0.015 0.001 TYR D 582 PHE 0.021 0.002 PHE B 300 TRP 0.023 0.001 TRP D 326 HIS 0.005 0.001 HIS B 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 (22178) covalent geometry : angle 0.59970 / 0.30 (30089) hydrogen bonds : bond 0.03464 / 2.36 ( 1168) hydrogen bonds : angle 3.87610 / 2.77 ( 3417) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 246 time to evaluate : 0.825 Fit side-chains REVERT: A 314 TRP cc_start: 0.8763 (OUTLIER) cc_final: 0.7795 (t60) REVERT: A 535 ASN cc_start: 0.8626 (t0) cc_final: 0.8279 (t0) REVERT: A 644 MET cc_start: 0.8837 (mmm) cc_final: 0.8611 (mmm) REVERT: B 445 TYR cc_start: 0.7977 (m-80) cc_final: 0.7637 (m-80) REVERT: B 568 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8774 (mm) REVERT: C 417 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7450 (tp30) REVERT: D 343 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8367 (tt) outliers start: 54 outliers final: 41 residues processed: 284 average time/residue: 0.1411 time to fit residues: 64.3614 Evaluate side-chains 276 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 232 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 314 TRP Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 630 HIS Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 644 MET Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain D residue 200 TYR Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 433 TRP Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 704 GLN Chi-restraints excluded: chain D residue 738 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 116 optimal weight: 0.9990 chunk 262 optimal weight: 9.9990 chunk 32 optimal weight: 0.0050 chunk 44 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 142 optimal weight: 0.6980 chunk 242 optimal weight: 9.9990 chunk 259 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 221 optimal weight: 5.9990 chunk 178 optimal weight: 0.9980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 ASN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 621 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.115490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.096871 restraints weight = 41924.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.099263 restraints weight = 23192.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.100887 restraints weight = 15787.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.101963 restraints weight = 12304.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.102396 restraints weight = 10421.285| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22178 Z= 0.112 Angle : 0.565 10.601 30089 Z= 0.284 Chirality : 0.040 0.165 3402 Planarity : 0.004 0.046 3748 Dihedral : 6.578 59.282 2977 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.96 % Allowed : 19.23 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.17), residues: 2643 helix: 0.81 (0.12), residues: 1876 sheet: None (None), residues: 0 loop : -1.49 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 511 TYR 0.013 0.001 TYR A 582 PHE 0.016 0.001 PHE C 340 TRP 0.029 0.001 TRP D 326 HIS 0.009 0.001 HIS C 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (22178) covalent geometry : angle 0.56512 / 0.28 (30089) hydrogen bonds : bond 0.03165 / 2.16 ( 1168) hydrogen bonds : angle 3.72354 / 2.66 ( 3417) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 255 time to evaluate : 0.696 Fit side-chains REVERT: A 314 TRP cc_start: 0.8684 (OUTLIER) cc_final: 0.7639 (t60) REVERT: A 535 ASN cc_start: 0.8579 (t0) cc_final: 0.8197 (t0) REVERT: E 140 GLU cc_start: 0.6661 (tp30) cc_final: 0.6321 (tp30) REVERT: B 568 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8705 (mm) REVERT: C 417 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7521 (tp30) REVERT: D 343 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8332 (tt) REVERT: D 439 PHE cc_start: 0.8733 (t80) cc_final: 0.8452 (t80) outliers start: 45 outliers final: 32 residues processed: 288 average time/residue: 0.1389 time to fit residues: 64.1241 Evaluate side-chains 269 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 234 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 314 TRP Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 630 HIS Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 644 MET Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain D residue 200 TYR Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 704 GLN Chi-restraints excluded: chain D residue 738 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 25 optimal weight: 6.9990 chunk 70 optimal weight: 0.0980 chunk 124 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 261 optimal weight: 0.7980 chunk 199 optimal weight: 4.9990 chunk 197 optimal weight: 0.0060 chunk 152 optimal weight: 0.7980 chunk 167 optimal weight: 0.8980 chunk 189 optimal weight: 0.9990 chunk 173 optimal weight: 7.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 ASN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 ASN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.117189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.098762 restraints weight = 42413.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.101115 restraints weight = 23864.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.102695 restraints weight = 16433.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.103582 restraints weight = 12900.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.104374 restraints weight = 11141.297| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 22178 Z= 0.108 Angle : 0.576 12.892 30089 Z= 0.285 Chirality : 0.040 0.163 3402 Planarity : 0.004 0.044 3748 Dihedral : 6.336 59.673 2977 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.74 % Allowed : 19.41 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.17), residues: 2643 helix: 0.95 (0.12), residues: 1876 sheet: None (None), residues: 0 loop : -1.37 (0.23), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 511 TYR 0.016 0.001 TYR B 445 PHE 0.025 0.001 PHE C 439 TRP 0.031 0.001 TRP D 326 HIS 0.012 0.001 HIS C 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (22178) covalent geometry : angle 0.57582 / 0.29 (30089) hydrogen bonds : bond 0.03080 / 2.10 ( 1168) hydrogen bonds : angle 3.65598 / 2.62 ( 3417) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 255 time to evaluate : 0.780 Fit side-chains REVERT: A 314 TRP cc_start: 0.8642 (OUTLIER) cc_final: 0.7728 (t60) REVERT: A 535 ASN cc_start: 0.8520 (t0) cc_final: 0.8148 (t0) REVERT: E 140 GLU cc_start: 0.6563 (tp30) cc_final: 0.6240 (tp30) REVERT: B 568 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8709 (mm) REVERT: C 744 SER cc_start: 0.8678 (OUTLIER) cc_final: 0.8455 (t) REVERT: D 343 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8389 (tt) outliers start: 40 outliers final: 32 residues processed: 283 average time/residue: 0.1357 time to fit residues: 61.3451 Evaluate side-chains 273 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 237 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 314 TRP Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 630 HIS Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain D residue 200 TYR Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 704 GLN Chi-restraints excluded: chain D residue 738 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 72 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 143 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 202 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 177 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 535 ASN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.115382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.096839 restraints weight = 42163.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.099244 restraints weight = 23338.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.100844 restraints weight = 15879.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.101746 restraints weight = 12364.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.102406 restraints weight = 10632.199| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22178 Z= 0.130 Angle : 0.593 14.807 30089 Z= 0.293 Chirality : 0.041 0.189 3402 Planarity : 0.004 0.045 3748 Dihedral : 6.312 59.221 2977 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.78 % Allowed : 19.63 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.17), residues: 2643 helix: 0.96 (0.12), residues: 1876 sheet: None (None), residues: 0 loop : -1.39 (0.23), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 511 TYR 0.019 0.001 TYR B 445 PHE 0.022 0.001 PHE C 335 TRP 0.031 0.001 TRP D 326 HIS 0.009 0.001 HIS C 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (22178) covalent geometry : angle 0.59332 / 0.29 (30089) hydrogen bonds : bond 0.03137 / 2.15 ( 1168) hydrogen bonds : angle 3.70813 / 2.65 ( 3417) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 244 time to evaluate : 0.820 Fit side-chains REVERT: A 314 TRP cc_start: 0.8693 (OUTLIER) cc_final: 0.7741 (t60) REVERT: A 535 ASN cc_start: 0.8622 (t0) cc_final: 0.8258 (t0) REVERT: E 140 GLU cc_start: 0.6614 (tp30) cc_final: 0.6280 (tp30) REVERT: B 568 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8729 (mm) REVERT: D 339 MET cc_start: 0.6935 (mmt) cc_final: 0.6560 (mmm) outliers start: 41 outliers final: 33 residues processed: 274 average time/residue: 0.1290 time to fit residues: 57.0581 Evaluate side-chains 273 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 238 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 314 TRP Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 630 HIS Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 644 MET Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain D residue 200 TYR Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 704 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 64 optimal weight: 0.8980 chunk 117 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 237 optimal weight: 3.9990 chunk 243 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 245 optimal weight: 4.9990 chunk 239 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 262 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.115261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.096540 restraints weight = 42407.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.098934 restraints weight = 23718.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.100511 restraints weight = 16293.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.101549 restraints weight = 12777.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.102131 restraints weight = 10895.148| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22178 Z= 0.135 Angle : 0.598 13.683 30089 Z= 0.296 Chirality : 0.041 0.160 3402 Planarity : 0.004 0.046 3748 Dihedral : 6.294 59.149 2977 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.87 % Allowed : 19.89 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.17), residues: 2643 helix: 0.95 (0.12), residues: 1876 sheet: None (None), residues: 0 loop : -1.38 (0.23), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 511 TYR 0.017 0.001 TYR B 445 PHE 0.031 0.001 PHE C 335 TRP 0.031 0.001 TRP D 326 HIS 0.004 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 (22178) covalent geometry : angle 0.59832 / 0.30 (30089) hydrogen bonds : bond 0.03167 / 2.16 ( 1168) hydrogen bonds : angle 3.73686 / 2.66 ( 3417) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3126.29 seconds wall clock time: 55 minutes 3.91 seconds (3303.91 seconds total)