Starting phenix.real_space_refine on Mon Oct 13 09:42:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wqc_37739/10_2025/8wqc_37739_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wqc_37739/10_2025/8wqc_37739.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wqc_37739/10_2025/8wqc_37739_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wqc_37739/10_2025/8wqc_37739_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wqc_37739/10_2025/8wqc_37739.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wqc_37739/10_2025/8wqc_37739.map" } resolution = 3.54 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7312 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 6 6.06 5 S 180 5.16 5 C 16949 2.51 5 N 4677 2.21 5 O 5020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.18s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26832 Number of models: 1 Model: "" Number of chains: 14 Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 735 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 7, 'TRANS': 85} Chain breaks: 1 Chain: "F" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 693 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 83} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "C" Number of atoms: 5902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5902 Classifications: {'peptide': 720} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 701} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 679 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 5902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5902 Classifications: {'peptide': 720} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 701} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 402 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 4, 'ARG:plan': 3, 'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 96 Chain: "H" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "I" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 735 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 7, 'TRANS': 85} Chain breaks: 1 Chain: "K" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 400 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 203 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 4, 'ARG:plan': 3, 'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 96 Chain: "A" Number of atoms: 4929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4929 Classifications: {'peptide': 627} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 4929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4929 Classifications: {'peptide': 627} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1009 SG CYS F 53 83.163 16.600 139.550 1.00 56.59 S ATOM 1032 SG CYS F 56 83.599 15.919 143.338 1.00 58.73 S ATOM 923 SG CYS F 42 79.533 21.810 136.879 1.00 32.96 S ATOM 942 SG CYS F 45 78.341 18.200 137.144 1.00 36.98 S ATOM 1237 SG CYS F 83 82.052 18.933 137.256 1.00 37.25 S ATOM 1166 SG CYS F 75 79.851 33.024 132.919 1.00 24.57 S ATOM 1329 SG CYS F 94 81.387 30.362 132.167 1.00 14.88 S ATOM 8353 SG CYS J 53 58.854 17.381 121.383 1.00 55.28 S ATOM 8376 SG CYS J 56 56.420 15.582 119.080 1.00 53.64 S ATOM 8460 SG CYS J 68 58.632 18.364 117.678 1.00 50.39 S ATOM 8267 SG CYS J 42 62.038 22.603 125.673 1.00 38.07 S ATOM 8286 SG CYS J 45 62.953 18.891 125.860 1.00 36.56 S ATOM 8578 SG CYS J 83 59.289 19.968 125.613 1.00 36.78 S ATOM 8510 SG CYS J 75 61.688 35.551 128.984 1.00 26.58 S ATOM 8670 SG CYS J 94 62.014 31.482 130.201 1.00 17.25 S Time building chain proxies: 6.08, per 1000 atoms: 0.23 Number of scatterers: 26832 At special positions: 0 Unit cell: (139.4, 132.02, 264.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 6 29.99 S 180 16.00 O 5020 8.00 N 4677 7.00 C 16949 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: 2.25 Conformation dependent library (CDL) restraints added in 999.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN F 200 " pdb="ZN ZN F 200 " - pdb=" ND1 HIS F 82 " pdb="ZN ZN F 200 " - pdb=" SG CYS F 56 " pdb="ZN ZN F 200 " - pdb=" SG CYS F 53 " pdb=" ZN F 201 " pdb="ZN ZN F 201 " - pdb=" ND1 HIS F 80 " pdb="ZN ZN F 201 " - pdb=" SG CYS F 45 " pdb="ZN ZN F 201 " - pdb=" SG CYS F 83 " pdb="ZN ZN F 201 " - pdb=" SG CYS F 42 " pdb=" ZN F 202 " pdb="ZN ZN F 202 " - pdb=" SG CYS F 75 " pdb="ZN ZN F 202 " - pdb=" ND1 HIS F 77 " pdb="ZN ZN F 202 " - pdb=" SG CYS F 94 " pdb=" ZN J 200 " pdb="ZN ZN J 200 " - pdb=" NE2 HIS J 82 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 56 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 53 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 68 " pdb=" ZN J 201 " pdb="ZN ZN J 201 " - pdb=" ND1 HIS J 80 " pdb="ZN ZN J 201 " - pdb=" SG CYS J 42 " pdb="ZN ZN J 201 " - pdb=" SG CYS J 83 " pdb="ZN ZN J 201 " - pdb=" SG CYS J 45 " pdb=" ZN J 202 " pdb="ZN ZN J 202 " - pdb=" ND1 HIS J 77 " pdb="ZN ZN J 202 " - pdb=" SG CYS J 94 " pdb="ZN ZN J 202 " - pdb=" SG CYS J 75 " Number of angles added : 9 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6510 Finding SS restraints... Secondary structure from input PDB file: 153 helices and 17 sheets defined 58.1% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'D' and resid 23 through 36 removed outlier: 3.577A pdb=" N LEU D 27 " --> pdb=" O THR D 23 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY D 33 " --> pdb=" O ARG D 29 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE D 34 " --> pdb=" O ILE D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 40 No H-bonds generated for 'chain 'D' and resid 38 through 40' Processing helix chain 'F' and resid 59 through 64 removed outlier: 4.455A pdb=" N ALA F 63 " --> pdb=" O ASN F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 88 Processing helix chain 'B' and resid 33 through 37 Processing helix chain 'B' and resid 40 through 46 removed outlier: 3.541A pdb=" N ALA B 44 " --> pdb=" O GLY B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 84 Processing helix chain 'B' and resid 99 through 110 Processing helix chain 'C' and resid 9 through 25 removed outlier: 4.274A pdb=" N THR C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR C 20 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA C 23 " --> pdb=" O THR C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 47 removed outlier: 3.749A pdb=" N PHE C 39 " --> pdb=" O TRP C 35 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER C 40 " --> pdb=" O ASN C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 79 removed outlier: 3.610A pdb=" N GLU C 78 " --> pdb=" O LYS C 74 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER C 79 " --> pdb=" O ARG C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 91 through 105 removed outlier: 4.076A pdb=" N LYS C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 112 Processing helix chain 'C' and resid 138 through 150 removed outlier: 4.085A pdb=" N LEU C 144 " --> pdb=" O GLY C 140 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 150 " --> pdb=" O MET C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 173 removed outlier: 3.685A pdb=" N MET C 162 " --> pdb=" O ILE C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 186 removed outlier: 3.683A pdb=" N ASN C 186 " --> pdb=" O HIS C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 195 removed outlier: 4.531A pdb=" N TYR C 194 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS C 195 " --> pdb=" O GLU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 207 removed outlier: 3.534A pdb=" N PHE C 207 " --> pdb=" O TYR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 230 removed outlier: 3.849A pdb=" N GLN C 228 " --> pdb=" O SER C 224 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 252 removed outlier: 3.562A pdb=" N MET C 236 " --> pdb=" O CYS C 232 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU C 237 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS C 252 " --> pdb=" O ILE C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 260 removed outlier: 4.287A pdb=" N THR C 260 " --> pdb=" O SER C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 271 Processing helix chain 'C' and resid 274 through 288 removed outlier: 3.611A pdb=" N GLU C 281 " --> pdb=" O PHE C 277 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N HIS C 283 " --> pdb=" O HIS C 279 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASN C 284 " --> pdb=" O ALA C 280 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE C 286 " --> pdb=" O CYS C 282 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN C 288 " --> pdb=" O ASN C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 303 removed outlier: 4.255A pdb=" N ALA C 303 " --> pdb=" O VAL C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 327 removed outlier: 4.016A pdb=" N MET C 311 " --> pdb=" O GLY C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 358 removed outlier: 3.573A pdb=" N ASN C 355 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C 357 " --> pdb=" O LEU C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 377 Processing helix chain 'C' and resid 386 through 400 Processing helix chain 'C' and resid 407 through 423 removed outlier: 4.368A pdb=" N THR C 420 " --> pdb=" O THR C 416 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL C 421 " --> pdb=" O SER C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 445 removed outlier: 3.575A pdb=" N PHE C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS C 433 " --> pdb=" O ASP C 429 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS C 441 " --> pdb=" O ARG C 437 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG C 442 " --> pdb=" O MET C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 466 removed outlier: 3.697A pdb=" N GLU C 454 " --> pdb=" O SER C 450 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU C 455 " --> pdb=" O MET C 451 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA C 456 " --> pdb=" O ASP C 452 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYS C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA C 464 " --> pdb=" O LYS C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 471 removed outlier: 3.883A pdb=" N SER C 471 " --> pdb=" O GLU C 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 468 through 471' Processing helix chain 'C' and resid 472 through 489 removed outlier: 3.596A pdb=" N ASP C 479 " --> pdb=" O ARG C 475 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N MET C 480 " --> pdb=" O MET C 476 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA C 484 " --> pdb=" O MET C 480 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ASP C 485 " --> pdb=" O SER C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 490 through 496 Processing helix chain 'C' and resid 533 through 547 removed outlier: 3.678A pdb=" N VAL C 537 " --> pdb=" O LEU C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 584 removed outlier: 3.885A pdb=" N VAL C 584 " --> pdb=" O TYR C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 603 removed outlier: 3.634A pdb=" N ASP C 601 " --> pdb=" O LYS C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 620 removed outlier: 3.554A pdb=" N VAL C 620 " --> pdb=" O SER C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 692 removed outlier: 3.532A pdb=" N ARG C 669 " --> pdb=" O MET C 665 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER C 670 " --> pdb=" O GLU C 666 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL C 685 " --> pdb=" O GLN C 681 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG C 686 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ILE C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N MET C 688 " --> pdb=" O ILE C 684 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ALA C 690 " --> pdb=" O ARG C 686 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG C 691 " --> pdb=" O ILE C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 695 through 707 removed outlier: 4.131A pdb=" N GLN C 701 " --> pdb=" O ASN C 697 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER C 705 " --> pdb=" O GLN C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 723 removed outlier: 3.876A pdb=" N LYS C 720 " --> pdb=" O SER C 716 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU C 723 " --> pdb=" O LYS C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 728 removed outlier: 4.104A pdb=" N ASP C 727 " --> pdb=" O GLU C 723 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 58 Processing helix chain 'J' and resid 80 through 91 removed outlier: 3.710A pdb=" N THR J 90 " --> pdb=" O ARG J 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 26 removed outlier: 4.245A pdb=" N ASN E 15 " --> pdb=" O ASP E 11 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR E 19 " --> pdb=" O ASN E 15 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N THR E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS E 22 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ALA E 23 " --> pdb=" O THR E 19 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL E 24 " --> pdb=" O THR E 20 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL E 25 " --> pdb=" O ILE E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 48 removed outlier: 3.515A pdb=" N ARG E 38 " --> pdb=" O THR E 34 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE E 39 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER E 40 " --> pdb=" O ASN E 36 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA E 44 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU E 45 " --> pdb=" O ASP E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 79 removed outlier: 4.023A pdb=" N SER E 79 " --> pdb=" O ARG E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 105 removed outlier: 3.738A pdb=" N GLU E 93 " --> pdb=" O ARG E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 110 Processing helix chain 'E' and resid 111 through 116 Processing helix chain 'E' and resid 138 through 149 removed outlier: 3.935A pdb=" N LEU E 144 " --> pdb=" O GLY E 140 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP E 147 " --> pdb=" O ALA E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 172 removed outlier: 3.519A pdb=" N GLY E 172 " --> pdb=" O LYS E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 187 Processing helix chain 'E' and resid 188 through 189 No H-bonds generated for 'chain 'E' and resid 188 through 189' Processing helix chain 'E' and resid 190 through 194 removed outlier: 4.474A pdb=" N TYR E 194 " --> pdb=" O VAL E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 230 removed outlier: 4.186A pdb=" N GLN E 228 " --> pdb=" O SER E 224 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU E 229 " --> pdb=" O ASN E 225 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER E 230 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 254 removed outlier: 4.305A pdb=" N GLU E 237 " --> pdb=" O SER E 233 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS E 238 " --> pdb=" O GLN E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 259 Processing helix chain 'E' and resid 260 through 271 removed outlier: 3.510A pdb=" N ARG E 269 " --> pdb=" O GLU E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 288 removed outlier: 3.637A pdb=" N GLU E 281 " --> pdb=" O PHE E 277 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N HIS E 283 " --> pdb=" O HIS E 279 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ASN E 284 " --> pdb=" O ALA E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 304 removed outlier: 3.794A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASN E 296 " --> pdb=" O ASN E 292 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA E 303 " --> pdb=" O VAL E 299 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL E 304 " --> pdb=" O LEU E 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 327 removed outlier: 4.685A pdb=" N HIS E 310 " --> pdb=" O THR E 306 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET E 311 " --> pdb=" O GLY E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 357 Processing helix chain 'E' and resid 361 through 377 removed outlier: 3.594A pdb=" N SER E 374 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN E 377 " --> pdb=" O THR E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 400 Processing helix chain 'E' and resid 407 through 423 removed outlier: 4.194A pdb=" N THR E 420 " --> pdb=" O THR E 416 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL E 421 " --> pdb=" O SER E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 436 removed outlier: 3.509A pdb=" N PHE E 431 " --> pdb=" O ASP E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 445 removed outlier: 3.551A pdb=" N HIS E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 463 Processing helix chain 'E' and resid 471 through 495 removed outlier: 3.631A pdb=" N TYR E 477 " --> pdb=" O LEU E 473 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL E 482 " --> pdb=" O THR E 478 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA E 484 " --> pdb=" O MET E 480 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP E 485 " --> pdb=" O SER E 481 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS E 495 " --> pdb=" O ASN E 491 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 547 removed outlier: 3.587A pdb=" N LEU E 542 " --> pdb=" O GLN E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 579 through 584 removed outlier: 4.242A pdb=" N VAL E 584 " --> pdb=" O TYR E 580 " (cutoff:3.500A) Processing helix chain 'E' and resid 586 through 591 removed outlier: 4.212A pdb=" N ASN E 590 " --> pdb=" O LEU E 586 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER E 591 " --> pdb=" O ALA E 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 586 through 591' Processing helix chain 'E' and resid 597 through 602 Processing helix chain 'E' and resid 606 through 621 removed outlier: 4.542A pdb=" N LYS E 612 " --> pdb=" O LYS E 608 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL E 620 " --> pdb=" O SER E 616 " (cutoff:3.500A) Processing helix chain 'E' and resid 664 through 689 removed outlier: 3.961A pdb=" N VAL E 685 " --> pdb=" O GLN E 681 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ARG E 686 " --> pdb=" O ALA E 682 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE E 687 " --> pdb=" O ALA E 683 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET E 688 " --> pdb=" O ILE E 684 " (cutoff:3.500A) Processing helix chain 'E' and resid 697 through 707 removed outlier: 4.244A pdb=" N GLN E 701 " --> pdb=" O ASN E 697 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU E 702 " --> pdb=" O ALA E 698 " (cutoff:3.500A) Processing helix chain 'E' and resid 714 through 728 removed outlier: 3.547A pdb=" N VAL E 724 " --> pdb=" O LYS E 720 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 35 removed outlier: 3.834A pdb=" N LYS N 27 " --> pdb=" O VAL N 23 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N GLU N 28 " --> pdb=" O GLU N 24 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS N 33 " --> pdb=" O ARG N 29 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU N 34 " --> pdb=" O VAL N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 41 removed outlier: 3.738A pdb=" N GLN N 41 " --> pdb=" O PRO N 38 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 60 removed outlier: 3.500A pdb=" N LYS N 60 " --> pdb=" O ALA N 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 37 Processing helix chain 'H' and resid 39 through 46 Processing helix chain 'H' and resid 66 through 84 removed outlier: 4.369A pdb=" N LYS H 72 " --> pdb=" O HIS H 68 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR H 78 " --> pdb=" O CYS H 74 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR H 79 " --> pdb=" O MET H 75 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ARG H 82 " --> pdb=" O THR H 78 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR H 83 " --> pdb=" O TYR H 79 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR H 84 " --> pdb=" O LYS H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 36 removed outlier: 3.903A pdb=" N LEU I 27 " --> pdb=" O THR I 23 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS I 28 " --> pdb=" O VAL I 24 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL I 31 " --> pdb=" O LEU I 27 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY I 33 " --> pdb=" O ARG I 29 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 40 No H-bonds generated for 'chain 'I' and resid 38 through 40' Processing helix chain 'K' and resid 22 through 31 removed outlier: 4.162A pdb=" N GLU K 31 " --> pdb=" O LYS K 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 15 removed outlier: 3.699A pdb=" N GLY A 6 " --> pdb=" O GLU A 2 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR A 7 " --> pdb=" O GLY A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 25 Processing helix chain 'A' and resid 28 through 36 Processing helix chain 'A' and resid 48 through 56 Processing helix chain 'A' and resid 58 through 68 Processing helix chain 'A' and resid 90 through 98 Processing helix chain 'A' and resid 100 through 111 removed outlier: 4.493A pdb=" N LEU A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 132 Processing helix chain 'A' and resid 133 through 143 Processing helix chain 'A' and resid 156 through 164 Processing helix chain 'A' and resid 166 through 176 removed outlier: 3.598A pdb=" N VAL A 170 " --> pdb=" O HIS A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 198 Processing helix chain 'A' and resid 199 through 209 Processing helix chain 'A' and resid 221 through 229 Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.631A pdb=" N GLU A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 262 removed outlier: 3.543A pdb=" N GLY A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 284 removed outlier: 3.776A pdb=" N TYR A 273 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU A 276 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 279 " --> pdb=" O TYR A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 303 Processing helix chain 'A' and resid 310 through 317 removed outlier: 3.676A pdb=" N LEU A 314 " --> pdb=" O ASN A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 337 removed outlier: 3.608A pdb=" N LEU A 329 " --> pdb=" O HIS A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 357 removed outlier: 4.068A pdb=" N ILE A 347 " --> pdb=" O VAL A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 376 removed outlier: 4.017A pdb=" N CYS A 363 " --> pdb=" O GLU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 398 Processing helix chain 'A' and resid 403 through 428 removed outlier: 3.553A pdb=" N LEU A 416 " --> pdb=" O ARG A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 455 Processing helix chain 'A' and resid 460 through 477 Processing helix chain 'A' and resid 486 through 492 Processing helix chain 'A' and resid 511 through 521 Processing helix chain 'A' and resid 534 through 540 Processing helix chain 'A' and resid 549 through 560 removed outlier: 4.427A pdb=" N ILE A 555 " --> pdb=" O THR A 551 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A 558 " --> pdb=" O SER A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 593 Processing helix chain 'A' and resid 596 through 607 Processing helix chain 'A' and resid 617 through 627 removed outlier: 4.014A pdb=" N GLU A 622 " --> pdb=" O ARG A 618 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE A 623 " --> pdb=" O THR A 619 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 15 removed outlier: 3.552A pdb=" N GLY G 6 " --> pdb=" O GLU G 2 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR G 7 " --> pdb=" O GLY G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 24 Processing helix chain 'G' and resid 28 through 36 Processing helix chain 'G' and resid 48 through 56 Processing helix chain 'G' and resid 58 through 68 Processing helix chain 'G' and resid 90 through 98 Processing helix chain 'G' and resid 100 through 111 removed outlier: 4.453A pdb=" N LEU G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 132 Processing helix chain 'G' and resid 133 through 143 Processing helix chain 'G' and resid 156 through 164 Processing helix chain 'G' and resid 166 through 176 removed outlier: 3.634A pdb=" N VAL G 170 " --> pdb=" O HIS G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 198 removed outlier: 3.542A pdb=" N PHE G 193 " --> pdb=" O THR G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 199 through 209 Processing helix chain 'G' and resid 221 through 229 removed outlier: 3.621A pdb=" N ALA G 227 " --> pdb=" O LEU G 223 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 236 Processing helix chain 'G' and resid 246 through 262 Processing helix chain 'G' and resid 268 through 284 removed outlier: 3.568A pdb=" N THR G 272 " --> pdb=" O ASP G 268 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR G 273 " --> pdb=" O ILE G 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 310 through 317 removed outlier: 3.730A pdb=" N LEU G 314 " --> pdb=" O ASN G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 337 Processing helix chain 'G' and resid 343 through 357 removed outlier: 4.033A pdb=" N ILE G 347 " --> pdb=" O VAL G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 377 removed outlier: 3.665A pdb=" N LYS G 365 " --> pdb=" O GLU G 361 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY G 377 " --> pdb=" O LEU G 373 " (cutoff:3.500A) Processing helix chain 'G' and resid 382 through 398 Processing helix chain 'G' and resid 403 through 428 removed outlier: 3.583A pdb=" N LYS G 426 " --> pdb=" O MET G 422 " (cutoff:3.500A) Processing helix chain 'G' and resid 432 through 455 Processing helix chain 'G' and resid 460 through 477 Processing helix chain 'G' and resid 486 through 492 Processing helix chain 'G' and resid 511 through 521 removed outlier: 3.520A pdb=" N THR G 515 " --> pdb=" O ASN G 511 " (cutoff:3.500A) Processing helix chain 'G' and resid 534 through 540 Processing helix chain 'G' and resid 549 through 560 removed outlier: 4.505A pdb=" N ILE G 555 " --> pdb=" O THR G 551 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE G 556 " --> pdb=" O LEU G 552 " (cutoff:3.500A) Processing helix chain 'G' and resid 582 through 593 removed outlier: 3.639A pdb=" N LYS G 590 " --> pdb=" O GLU G 586 " (cutoff:3.500A) Processing helix chain 'G' and resid 596 through 609 Processing helix chain 'G' and resid 617 through 627 removed outlier: 3.535A pdb=" N GLU G 622 " --> pdb=" O ARG G 618 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE G 623 " --> pdb=" O THR G 619 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS G 627 " --> pdb=" O PHE G 623 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 42 through 43 removed outlier: 3.582A pdb=" N ARG D 43 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA D 78 " --> pdb=" O ARG D 43 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA D 73 " --> pdb=" O PHE D 4 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET D 6 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 30 " --> pdb=" O THR D 13 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LYS B 32 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 10.091A pdb=" N ASP D 17 " --> pdb=" O LYS B 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 45 through 46 Processing sheet with id=AA3, first strand: chain 'F' and resid 24 through 27 removed outlier: 6.462A pdb=" N GLU E 563 " --> pdb=" O LYS F 25 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE E 651 " --> pdb=" O VAL E 574 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET E 576 " --> pdb=" O PHE E 651 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 510 through 513 removed outlier: 3.659A pdb=" N ALA F 31 " --> pdb=" O TYR E 510 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 70 through 72 Processing sheet with id=AA6, first strand: chain 'C' and resid 508 through 513 removed outlier: 4.098A pdb=" N ALA J 31 " --> pdb=" O TYR C 510 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 650 through 652 Processing sheet with id=AA8, first strand: chain 'C' and resid 593 through 594 Processing sheet with id=AA9, first strand: chain 'E' and resid 594 through 595 Processing sheet with id=AB1, first strand: chain 'E' and resid 731 through 733 Processing sheet with id=AB2, first strand: chain 'N' and resid 42 through 43 Processing sheet with id=AB3, first strand: chain 'H' and resid 60 through 61 removed outlier: 5.853A pdb=" N GLU H 28 " --> pdb=" O THR I 13 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N PHE I 15 " --> pdb=" O GLU H 28 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE H 30 " --> pdb=" O PHE I 15 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ASP I 17 " --> pdb=" O ILE H 30 " (cutoff:3.500A) removed outlier: 9.489A pdb=" N LYS H 32 " --> pdb=" O ASP I 17 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR I 16 " --> pdb=" O LEU I 5 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU I 5 " --> pdb=" O THR I 16 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N PHE I 4 " --> pdb=" O ALA I 73 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N VAL I 75 " --> pdb=" O PHE I 4 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N MET I 6 " --> pdb=" O VAL I 75 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU I 77 " --> pdb=" O MET I 6 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR I 45 " --> pdb=" O GLY I 76 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA I 78 " --> pdb=" O ARG I 43 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU I 44 " --> pdb=" O LEU I 51 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 44 through 45 Processing sheet with id=AB5, first strand: chain 'A' and resid 40 through 42 removed outlier: 3.520A pdb=" N SER A 47 " --> pdb=" O SER A 40 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 77 through 80 removed outlier: 4.855A pdb=" N GLY A 77 " --> pdb=" O GLY A 88 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 40 through 42 Processing sheet with id=AB8, first strand: chain 'G' and resid 77 through 80 removed outlier: 4.327A pdb=" N GLY G 77 " --> pdb=" O GLY G 88 " (cutoff:3.500A) 1276 hydrogen bonds defined for protein. 3732 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.80 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8943 1.34 - 1.46: 5484 1.46 - 1.58: 12624 1.58 - 1.70: 0 1.70 - 1.81: 280 Bond restraints: 27331 Sorted by residual: bond pdb=" C MET E 335 " pdb=" N PRO E 336 " ideal model delta sigma weight residual 1.335 1.362 -0.026 1.30e-02 5.92e+03 4.12e+00 bond pdb=" CA ARG D 68 " pdb=" C ARG D 68 " ideal model delta sigma weight residual 1.528 1.507 0.020 1.26e-02 6.30e+03 2.61e+00 bond pdb=" N PRO D 69 " pdb=" CA PRO D 69 " ideal model delta sigma weight residual 1.470 1.489 -0.019 1.33e-02 5.65e+03 2.10e+00 bond pdb=" CB ASP C 498 " pdb=" CG ASP C 498 " ideal model delta sigma weight residual 1.516 1.552 -0.036 2.50e-02 1.60e+03 2.05e+00 bond pdb=" C MET C 335 " pdb=" N PRO C 336 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.73e+00 ... (remaining 27326 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 36810 3.16 - 6.33: 136 6.33 - 9.49: 13 9.49 - 12.66: 1 12.66 - 15.82: 3 Bond angle restraints: 36963 Sorted by residual: angle pdb=" C SER G 122 " pdb=" N THR G 123 " pdb=" CA THR G 123 " ideal model delta sigma weight residual 120.69 134.45 -13.76 2.95e+00 1.15e-01 2.18e+01 angle pdb=" CA LEU E 443 " pdb=" CB LEU E 443 " pdb=" CG LEU E 443 " ideal model delta sigma weight residual 116.30 132.12 -15.82 3.50e+00 8.16e-02 2.04e+01 angle pdb=" C LYS G 574 " pdb=" N THR G 575 " pdb=" CA THR G 575 " ideal model delta sigma weight residual 120.69 132.00 -11.31 2.95e+00 1.15e-01 1.47e+01 angle pdb=" N VAL G 103 " pdb=" CA VAL G 103 " pdb=" C VAL G 103 " ideal model delta sigma weight residual 112.96 109.20 3.76 1.00e+00 1.00e+00 1.41e+01 angle pdb=" C LEU G 559 " pdb=" N VAL G 560 " pdb=" CA VAL G 560 " ideal model delta sigma weight residual 121.65 118.14 3.51 9.40e-01 1.13e+00 1.39e+01 ... (remaining 36958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 14818 17.96 - 35.93: 1463 35.93 - 53.89: 249 53.89 - 71.85: 41 71.85 - 89.82: 26 Dihedral angle restraints: 16597 sinusoidal: 6586 harmonic: 10011 Sorted by residual: dihedral pdb=" CA ILE H 90 " pdb=" C ILE H 90 " pdb=" N PRO H 91 " pdb=" CA PRO H 91 " ideal model delta harmonic sigma weight residual 180.00 -154.61 -25.39 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA MET E 438 " pdb=" C MET E 438 " pdb=" N LEU E 439 " pdb=" CA LEU E 439 " ideal model delta harmonic sigma weight residual 180.00 156.58 23.42 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA LYS D 46 " pdb=" C LYS D 46 " pdb=" N ASP D 47 " pdb=" CA ASP D 47 " ideal model delta harmonic sigma weight residual 180.00 -160.62 -19.38 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 16594 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3361 0.050 - 0.100: 709 0.100 - 0.150: 100 0.150 - 0.200: 7 0.200 - 0.250: 2 Chirality restraints: 4179 Sorted by residual: chirality pdb=" CG LEU E 443 " pdb=" CB LEU E 443 " pdb=" CD1 LEU E 443 " pdb=" CD2 LEU E 443 " both_signs ideal model delta sigma weight residual False -2.59 -2.84 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB ILE H 90 " pdb=" CA ILE H 90 " pdb=" CG1 ILE H 90 " pdb=" CG2 ILE H 90 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB ILE E 501 " pdb=" CA ILE E 501 " pdb=" CG1 ILE E 501 " pdb=" CG2 ILE E 501 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.26e-01 ... (remaining 4176 not shown) Planarity restraints: 4762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 68 " -0.042 5.00e-02 4.00e+02 6.30e-02 6.34e+00 pdb=" N PRO D 69 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO D 69 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 69 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 616 " 0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO A 617 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 617 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 617 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 65 " 0.035 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO B 66 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 66 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 66 " 0.030 5.00e-02 4.00e+02 ... (remaining 4759 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 457 2.69 - 3.24: 27319 3.24 - 3.79: 43478 3.79 - 4.35: 57818 4.35 - 4.90: 91715 Nonbonded interactions: 220787 Sorted by model distance: nonbonded pdb=" OD1 ASP F 97 " pdb="ZN ZN F 202 " model vdw 2.135 2.230 nonbonded pdb=" NE2 GLN G 390 " pdb=" OD2 ASP G 499 " model vdw 2.167 3.120 nonbonded pdb=" NZ LYS E 689 " pdb=" O GLY N 76 " model vdw 2.172 3.120 nonbonded pdb=" OD1 ASP A 384 " pdb=" NH1 ARG A 387 " model vdw 2.199 3.120 nonbonded pdb=" OG SER A 28 " pdb=" OD2 ASP A 31 " model vdw 2.201 3.040 ... (remaining 220782 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' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'I' } ncs_group { reference = (chain 'F' and (resid 22 through 75 or (resid 76 and (name N or name CA or name \ C or name O or name CB )) or resid 77 through 202)) selection = chain 'J' } ncs_group { reference = chain 'K' selection = (chain 'N' and (resid 1 through 37 or (resid 38 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 76)) } 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: 11.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 28.490 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.100 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 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 : 0.003 0.037 27352 Z= 0.123 Angle : 0.583 15.822 36972 Z= 0.299 Chirality : 0.041 0.250 4179 Planarity : 0.004 0.063 4762 Dihedral : 14.707 89.817 10087 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.07 % Allowed : 0.42 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: -1.33 (0.14), residues: 3357 helix: -0.57 (0.12), residues: 1876 sheet: -3.49 (0.54), residues: 66 loop : -1.00 (0.17), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 8 TYR 0.021 0.001 TYR C 580 PHE 0.012 0.001 PHE E 339 TRP 0.015 0.001 TRP F 33 HIS 0.004 0.001 HIS E 71 Details of bonding type rmsd covalent geometry : bond 0.00262 (27331) covalent geometry : angle 0.58244 (36963) hydrogen bonds : bond 0.22712 ( 1276) hydrogen bonds : angle 7.50232 ( 3732) metal coordination : bond 0.00414 ( 21) metal coordination : angle 1.30345 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 427 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 29 ARG cc_start: 0.6167 (mmp-170) cc_final: 0.5840 (mmp-170) REVERT: C 248 ILE cc_start: 0.8629 (tp) cc_final: 0.8423 (mt) REVERT: C 409 ASN cc_start: 0.7957 (t0) cc_final: 0.7696 (t0) REVERT: C 476 MET cc_start: 0.8991 (mtm) cc_final: 0.8791 (mtm) REVERT: C 729 GLN cc_start: 0.8081 (mp10) cc_final: 0.7854 (mp10) REVERT: E 63 ILE cc_start: 0.8739 (mm) cc_final: 0.8469 (mt) REVERT: E 160 ILE cc_start: 0.7917 (mm) cc_final: 0.7566 (mt) REVERT: E 329 ASN cc_start: 0.7403 (p0) cc_final: 0.7115 (p0) REVERT: E 476 MET cc_start: 0.8436 (mtt) cc_final: 0.8124 (mtt) REVERT: H 105 MET cc_start: 0.8589 (tmm) cc_final: 0.8137 (tmm) REVERT: A 1 MET cc_start: 0.1560 (tpt) cc_final: 0.0661 (mmm) REVERT: A 110 HIS cc_start: 0.3762 (t-90) cc_final: 0.2669 (m90) REVERT: A 368 LEU cc_start: 0.8804 (mt) cc_final: 0.8509 (pp) REVERT: G 1 MET cc_start: 0.3337 (tpt) cc_final: 0.3134 (ptp) REVERT: G 7 TYR cc_start: 0.4255 (m-80) cc_final: 0.4054 (m-80) REVERT: G 300 HIS cc_start: 0.8528 (t70) cc_final: 0.8115 (p90) REVERT: G 349 TYR cc_start: 0.5003 (t80) cc_final: 0.4728 (t80) REVERT: G 357 ASN cc_start: 0.8439 (t0) cc_final: 0.8121 (t0) REVERT: G 364 ILE cc_start: 0.8626 (mm) cc_final: 0.8385 (tt) REVERT: G 368 LEU cc_start: 0.8990 (mt) cc_final: 0.8701 (pp) REVERT: G 385 LEU cc_start: 0.7728 (mm) cc_final: 0.7462 (mt) REVERT: G 440 TYR cc_start: 0.5591 (t80) cc_final: 0.4998 (t80) outliers start: 2 outliers final: 1 residues processed: 428 average time/residue: 0.1765 time to fit residues: 119.8638 Evaluate side-chains 285 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 284 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 231 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 0.1980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 40.0000 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.0370 chunk 298 optimal weight: 20.0000 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 HIS ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 HIS ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 65 GLN A 274 HIS A 443 ASN G 274 HIS ** G 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 476 HIS G 502 HIS G 526 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.181236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.143148 restraints weight = 50444.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.133940 restraints weight = 63403.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.129495 restraints weight = 52705.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.128927 restraints weight = 46207.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.129272 restraints weight = 40438.719| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27352 Z= 0.150 Angle : 0.591 12.066 36972 Z= 0.311 Chirality : 0.041 0.166 4179 Planarity : 0.004 0.062 4762 Dihedral : 4.671 83.462 3676 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.63 % Allowed : 8.02 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: -0.89 (0.14), residues: 3357 helix: -0.09 (0.12), residues: 1933 sheet: -3.31 (0.58), residues: 60 loop : -1.06 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG I 37 TYR 0.024 0.002 TYR G 472 PHE 0.019 0.001 PHE I 79 TRP 0.016 0.001 TRP J 27 HIS 0.007 0.001 HIS I 10 Details of bonding type rmsd covalent geometry : bond 0.00335 (27331) covalent geometry : angle 0.59005 (36963) hydrogen bonds : bond 0.05110 ( 1276) hydrogen bonds : angle 5.30084 ( 3732) metal coordination : bond 0.00307 ( 21) metal coordination : angle 1.74510 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 317 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 409 ASN cc_start: 0.7969 (t0) cc_final: 0.7756 (t0) REVERT: C 729 GLN cc_start: 0.8101 (mp10) cc_final: 0.7764 (mp10) REVERT: E 63 ILE cc_start: 0.8757 (mm) cc_final: 0.8494 (mt) REVERT: E 160 ILE cc_start: 0.7877 (mm) cc_final: 0.7568 (mt) REVERT: E 177 ASN cc_start: 0.7587 (t0) cc_final: 0.7331 (t0) REVERT: E 329 ASN cc_start: 0.7511 (p0) cc_final: 0.7274 (p0) REVERT: E 476 MET cc_start: 0.8626 (mtt) cc_final: 0.8370 (mtt) REVERT: E 717 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7084 (ppp) REVERT: A 1 MET cc_start: -0.0067 (tpt) cc_final: -0.0384 (mmt) REVERT: A 110 HIS cc_start: 0.3924 (t-90) cc_final: 0.2820 (m90) REVERT: A 368 LEU cc_start: 0.8937 (mt) cc_final: 0.8645 (pp) REVERT: A 455 THR cc_start: 0.8045 (p) cc_final: 0.7782 (t) REVERT: G 357 ASN cc_start: 0.8097 (t0) cc_final: 0.7794 (t0) REVERT: G 385 LEU cc_start: 0.7582 (mm) cc_final: 0.7265 (mt) outliers start: 18 outliers final: 11 residues processed: 325 average time/residue: 0.1563 time to fit residues: 83.8532 Evaluate side-chains 290 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 278 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain C residue 221 GLN Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain E residue 717 MET Chi-restraints excluded: chain H residue 17 MET Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain A residue 274 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 45 optimal weight: 0.5980 chunk 221 optimal weight: 50.0000 chunk 140 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 197 optimal weight: 0.7980 chunk 192 optimal weight: 0.9980 chunk 222 optimal weight: 30.0000 chunk 62 optimal weight: 3.9990 chunk 259 optimal weight: 6.9990 chunk 107 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 HIS E 190 HIS ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 541 GLN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.180765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 129)---------------| | r_work = 0.3894 r_free = 0.3894 target = 0.130358 restraints weight = 50251.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.124822 restraints weight = 40246.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.124609 restraints weight = 39578.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.125059 restraints weight = 39163.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.125058 restraints weight = 37793.819| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27352 Z= 0.141 Angle : 0.560 12.567 36972 Z= 0.291 Chirality : 0.040 0.228 4179 Planarity : 0.004 0.063 4762 Dihedral : 4.559 84.092 3674 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.08 % Allowed : 10.91 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: -0.73 (0.15), residues: 3357 helix: 0.07 (0.12), residues: 1940 sheet: -3.33 (0.56), residues: 61 loop : -1.03 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 37 TYR 0.021 0.001 TYR C 510 PHE 0.023 0.001 PHE C 112 TRP 0.015 0.001 TRP J 27 HIS 0.006 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00318 (27331) covalent geometry : angle 0.55948 (36963) hydrogen bonds : bond 0.04249 ( 1276) hydrogen bonds : angle 4.92534 ( 3732) metal coordination : bond 0.00332 ( 21) metal coordination : angle 1.76905 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 298 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 729 GLN cc_start: 0.7907 (mp10) cc_final: 0.7582 (mp10) REVERT: E 160 ILE cc_start: 0.8016 (mm) cc_final: 0.7683 (mt) REVERT: E 717 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.7047 (ppp) REVERT: E 728 LYS cc_start: 0.7718 (mttp) cc_final: 0.7489 (mttp) REVERT: A 1 MET cc_start: 0.0849 (tpt) cc_final: 0.0239 (mmt) REVERT: A 110 HIS cc_start: 0.3903 (t-90) cc_final: 0.2883 (m90) REVERT: A 368 LEU cc_start: 0.9063 (mt) cc_final: 0.8780 (pp) REVERT: G 357 ASN cc_start: 0.8380 (t0) cc_final: 0.8024 (t0) outliers start: 31 outliers final: 17 residues processed: 315 average time/residue: 0.1642 time to fit residues: 84.9309 Evaluate side-chains 289 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 271 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 221 GLN Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 717 MET Chi-restraints excluded: chain H residue 17 MET Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain G residue 364 ILE Chi-restraints excluded: chain G residue 475 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 202 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 240 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 188 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 241 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 71 HIS E 111 GLN E 190 HIS E 329 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 HIS ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 GLN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 380 ASN ** G 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 434 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.178035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.139658 restraints weight = 49854.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.129127 restraints weight = 63441.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.125212 restraints weight = 57199.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.124560 restraints weight = 50359.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.125127 restraints weight = 46443.412| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 27352 Z= 0.229 Angle : 0.610 11.312 36972 Z= 0.314 Chirality : 0.043 0.177 4179 Planarity : 0.004 0.069 4762 Dihedral : 4.673 88.467 3674 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.70 % Allowed : 13.30 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: -0.76 (0.15), residues: 3357 helix: 0.04 (0.12), residues: 1945 sheet: -3.36 (0.58), residues: 61 loop : -1.04 (0.18), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 63 TYR 0.025 0.002 TYR C 544 PHE 0.030 0.002 PHE B 77 TRP 0.022 0.002 TRP E 147 HIS 0.008 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00539 (27331) covalent geometry : angle 0.60877 (36963) hydrogen bonds : bond 0.04049 ( 1276) hydrogen bonds : angle 4.86077 ( 3732) metal coordination : bond 0.00828 ( 21) metal coordination : angle 2.41534 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 289 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 85 SER cc_start: 0.8707 (m) cc_final: 0.8492 (p) REVERT: C 45 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8448 (mp) REVERT: C 510 TYR cc_start: 0.8334 (OUTLIER) cc_final: 0.7043 (t80) REVERT: C 729 GLN cc_start: 0.8129 (mp10) cc_final: 0.7718 (mp10) REVERT: E 164 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7605 (mm) REVERT: E 717 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.7263 (ppp) REVERT: A 1 MET cc_start: -0.0260 (tpt) cc_final: -0.0586 (mmt) REVERT: A 110 HIS cc_start: 0.3815 (t-90) cc_final: 0.2926 (m90) REVERT: A 368 LEU cc_start: 0.8896 (mt) cc_final: 0.8625 (pp) REVERT: G 357 ASN cc_start: 0.8102 (t0) cc_final: 0.7809 (t0) REVERT: G 472 TYR cc_start: 0.8553 (t80) cc_final: 0.8291 (t80) outliers start: 49 outliers final: 25 residues processed: 317 average time/residue: 0.1569 time to fit residues: 82.3470 Evaluate side-chains 301 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 272 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 221 GLN Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 510 TYR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 532 GLU Chi-restraints excluded: chain E residue 605 MET Chi-restraints excluded: chain E residue 717 MET Chi-restraints excluded: chain E residue 721 CYS Chi-restraints excluded: chain H residue 17 MET Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain A residue 93 TRP Chi-restraints excluded: chain G residue 364 ILE Chi-restraints excluded: chain G residue 475 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 149 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 296 optimal weight: 20.0000 chunk 146 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 306 optimal weight: 20.0000 chunk 90 optimal weight: 8.9990 chunk 134 optimal weight: 0.8980 chunk 298 optimal weight: 9.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 ASN B 68 HIS E 190 HIS E 329 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 49 GLN A 166 HIS A 443 ASN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 526 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.178457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 129)---------------| | r_work = 0.3868 r_free = 0.3868 target = 0.126783 restraints weight = 49779.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.121084 restraints weight = 42575.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.121272 restraints weight = 39592.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.121754 restraints weight = 39621.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.121929 restraints weight = 36838.656| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27352 Z= 0.185 Angle : 0.592 11.666 36972 Z= 0.303 Chirality : 0.042 0.235 4179 Planarity : 0.004 0.072 4762 Dihedral : 4.657 88.564 3674 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.67 % Allowed : 15.04 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: -0.69 (0.15), residues: 3357 helix: 0.13 (0.12), residues: 1937 sheet: -3.53 (0.61), residues: 56 loop : -1.07 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 63 TYR 0.024 0.002 TYR E 510 PHE 0.044 0.002 PHE B 77 TRP 0.019 0.002 TRP E 147 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00433 (27331) covalent geometry : angle 0.59064 (36963) hydrogen bonds : bond 0.03846 ( 1276) hydrogen bonds : angle 4.73612 ( 3732) metal coordination : bond 0.00628 ( 21) metal coordination : angle 2.14352 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 282 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 85 SER cc_start: 0.8749 (m) cc_final: 0.8525 (p) REVERT: B 56 GLU cc_start: 0.6345 (pm20) cc_final: 0.6010 (pm20) REVERT: C 45 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8382 (mp) REVERT: C 53 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8405 (pp) REVERT: C 510 TYR cc_start: 0.8361 (OUTLIER) cc_final: 0.7052 (t80) REVERT: C 729 GLN cc_start: 0.8039 (mp10) cc_final: 0.7641 (mp10) REVERT: E 160 ILE cc_start: 0.8115 (mm) cc_final: 0.7707 (mt) REVERT: E 164 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7752 (mm) REVERT: E 717 MET cc_start: 0.7563 (OUTLIER) cc_final: 0.7186 (ppp) REVERT: H 80 LYS cc_start: 0.8219 (tttm) cc_final: 0.8010 (tttp) REVERT: A 1 MET cc_start: 0.0557 (tpt) cc_final: -0.0086 (mmt) REVERT: A 110 HIS cc_start: 0.3991 (t-90) cc_final: 0.2956 (m90) REVERT: A 368 LEU cc_start: 0.9027 (mt) cc_final: 0.8720 (pp) REVERT: G 357 ASN cc_start: 0.8273 (t0) cc_final: 0.7952 (t0) REVERT: G 568 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7766 (tpp) outliers start: 48 outliers final: 29 residues processed: 310 average time/residue: 0.1526 time to fit residues: 78.8592 Evaluate side-chains 305 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 270 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 25 PHE Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 221 GLN Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 510 TYR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain E residue 532 GLU Chi-restraints excluded: chain E residue 605 MET Chi-restraints excluded: chain E residue 685 VAL Chi-restraints excluded: chain E residue 717 MET Chi-restraints excluded: chain E residue 721 CYS Chi-restraints excluded: chain H residue 17 MET Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain G residue 364 ILE Chi-restraints excluded: chain G residue 568 MET Chi-restraints excluded: chain G residue 595 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 287 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 chunk 204 optimal weight: 50.0000 chunk 6 optimal weight: 0.2980 chunk 306 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 199 optimal weight: 0.6980 chunk 254 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 192 optimal weight: 0.0170 overall best weight: 1.0022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 71 HIS E 190 HIS E 329 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 49 GLN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 375 GLN G 382 HIS G 526 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.178972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.137548 restraints weight = 49794.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.130716 restraints weight = 66161.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.125655 restraints weight = 43599.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.124894 restraints weight = 49842.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.125838 restraints weight = 47416.505| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 27352 Z= 0.165 Angle : 0.575 10.996 36972 Z= 0.295 Chirality : 0.041 0.193 4179 Planarity : 0.004 0.071 4762 Dihedral : 4.595 88.405 3674 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.12 % Allowed : 15.28 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: -0.58 (0.15), residues: 3357 helix: 0.25 (0.12), residues: 1937 sheet: -3.54 (0.61), residues: 56 loop : -1.07 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 63 TYR 0.024 0.002 TYR C 510 PHE 0.035 0.001 PHE B 77 TRP 0.016 0.002 TRP E 147 HIS 0.004 0.001 HIS I 10 Details of bonding type rmsd covalent geometry : bond 0.00382 (27331) covalent geometry : angle 0.57382 (36963) hydrogen bonds : bond 0.03614 ( 1276) hydrogen bonds : angle 4.61148 ( 3732) metal coordination : bond 0.00519 ( 21) metal coordination : angle 2.00912 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 282 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8403 (mp) REVERT: C 53 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8403 (pp) REVERT: C 269 ARG cc_start: 0.8269 (mmp80) cc_final: 0.8032 (mmp80) REVERT: C 480 MET cc_start: 0.8573 (mmt) cc_final: 0.7909 (mmt) REVERT: C 510 TYR cc_start: 0.8331 (OUTLIER) cc_final: 0.7145 (t80) REVERT: C 729 GLN cc_start: 0.8119 (mp10) cc_final: 0.7700 (mp10) REVERT: E 160 ILE cc_start: 0.7918 (mm) cc_final: 0.7684 (mt) REVERT: E 717 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.7170 (ppp) REVERT: I 45 TYR cc_start: 0.6042 (m-80) cc_final: 0.5814 (m-80) REVERT: A 1 MET cc_start: 0.0044 (tpt) cc_final: -0.0523 (mmt) REVERT: A 110 HIS cc_start: 0.3987 (t-90) cc_final: 0.2935 (m90) REVERT: A 368 LEU cc_start: 0.8896 (mt) cc_final: 0.8603 (pp) REVERT: A 388 PHE cc_start: 0.7097 (OUTLIER) cc_final: 0.6051 (m-80) REVERT: G 357 ASN cc_start: 0.8138 (t0) cc_final: 0.7862 (t0) REVERT: G 375 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8132 (mm110) REVERT: G 568 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7687 (tpp) outliers start: 61 outliers final: 34 residues processed: 317 average time/residue: 0.1519 time to fit residues: 79.7812 Evaluate side-chains 310 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 269 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 25 PHE Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 221 GLN Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 510 TYR Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain E residue 532 GLU Chi-restraints excluded: chain E residue 576 MET Chi-restraints excluded: chain E residue 717 MET Chi-restraints excluded: chain E residue 721 CYS Chi-restraints excluded: chain H residue 17 MET Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain A residue 93 TRP Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 388 PHE Chi-restraints excluded: chain G residue 364 ILE Chi-restraints excluded: chain G residue 375 GLN Chi-restraints excluded: chain G residue 568 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 109 optimal weight: 1.9990 chunk 273 optimal weight: 6.9990 chunk 298 optimal weight: 7.9990 chunk 147 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 90 optimal weight: 20.0000 chunk 246 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 chunk 157 optimal weight: 1.9990 chunk 108 optimal weight: 0.4980 chunk 15 optimal weight: 0.3980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 73 HIS E 190 HIS E 329 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.179269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.141205 restraints weight = 49852.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.130445 restraints weight = 63411.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.126726 restraints weight = 54310.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.126368 restraints weight = 50893.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.126941 restraints weight = 44988.176| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 27352 Z= 0.153 Angle : 0.579 11.328 36972 Z= 0.296 Chirality : 0.041 0.223 4179 Planarity : 0.004 0.071 4762 Dihedral : 4.556 88.249 3674 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 1.81 % Allowed : 16.26 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: -0.51 (0.15), residues: 3357 helix: 0.32 (0.12), residues: 1937 sheet: -3.54 (0.60), residues: 56 loop : -1.08 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 63 TYR 0.025 0.001 TYR C 510 PHE 0.038 0.001 PHE B 77 TRP 0.015 0.002 TRP E 147 HIS 0.009 0.001 HIS E 71 Details of bonding type rmsd covalent geometry : bond 0.00356 (27331) covalent geometry : angle 0.57875 (36963) hydrogen bonds : bond 0.03528 ( 1276) hydrogen bonds : angle 4.52588 ( 3732) metal coordination : bond 0.00497 ( 21) metal coordination : angle 1.94518 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 277 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 GLU cc_start: 0.6187 (pm20) cc_final: 0.5925 (pm20) REVERT: C 45 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8342 (mp) REVERT: C 53 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8382 (pp) REVERT: C 293 ASP cc_start: 0.6287 (t0) cc_final: 0.5844 (t0) REVERT: C 480 MET cc_start: 0.8515 (mmt) cc_final: 0.7844 (mmt) REVERT: C 510 TYR cc_start: 0.8290 (OUTLIER) cc_final: 0.7147 (t80) REVERT: C 559 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8987 (tt) REVERT: C 729 GLN cc_start: 0.8205 (mp10) cc_final: 0.7777 (mp10) REVERT: E 160 ILE cc_start: 0.7897 (mm) cc_final: 0.7541 (mt) REVERT: E 164 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7694 (mm) REVERT: E 717 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.7262 (ppp) REVERT: I 5 LEU cc_start: 0.7796 (mm) cc_final: 0.7527 (mm) REVERT: I 45 TYR cc_start: 0.6081 (m-80) cc_final: 0.5870 (m-80) REVERT: A 1 MET cc_start: -0.0371 (tpt) cc_final: -0.0826 (mmt) REVERT: A 110 HIS cc_start: 0.3853 (t-90) cc_final: 0.2832 (m90) REVERT: A 368 LEU cc_start: 0.8816 (mt) cc_final: 0.8540 (pp) REVERT: A 388 PHE cc_start: 0.6877 (OUTLIER) cc_final: 0.5884 (m-80) REVERT: G 357 ASN cc_start: 0.7994 (t0) cc_final: 0.7755 (t0) REVERT: G 568 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7778 (tpp) outliers start: 52 outliers final: 33 residues processed: 309 average time/residue: 0.1487 time to fit residues: 77.1820 Evaluate side-chains 309 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 268 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 221 GLN Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 510 TYR Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain E residue 532 GLU Chi-restraints excluded: chain E residue 576 MET Chi-restraints excluded: chain E residue 717 MET Chi-restraints excluded: chain E residue 721 CYS Chi-restraints excluded: chain H residue 17 MET Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain A residue 93 TRP Chi-restraints excluded: chain A residue 388 PHE Chi-restraints excluded: chain G residue 364 ILE Chi-restraints excluded: chain G residue 568 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 9 optimal weight: 1.9990 chunk 301 optimal weight: 4.9990 chunk 233 optimal weight: 0.9980 chunk 310 optimal weight: 6.9990 chunk 114 optimal weight: 0.9990 chunk 294 optimal weight: 8.9990 chunk 127 optimal weight: 0.6980 chunk 260 optimal weight: 7.9990 chunk 276 optimal weight: 30.0000 chunk 174 optimal weight: 0.9980 chunk 322 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 71 HIS E 190 HIS E 329 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.178528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.138368 restraints weight = 50013.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.129733 restraints weight = 66522.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.125242 restraints weight = 49649.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.124424 restraints weight = 50833.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.124944 restraints weight = 45802.244| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 27352 Z= 0.178 Angle : 0.600 11.651 36972 Z= 0.305 Chirality : 0.041 0.206 4179 Planarity : 0.004 0.068 4762 Dihedral : 4.594 89.453 3674 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 1.98 % Allowed : 16.60 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: -0.50 (0.15), residues: 3357 helix: 0.35 (0.12), residues: 1947 sheet: -3.48 (0.62), residues: 56 loop : -1.11 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 63 TYR 0.027 0.002 TYR C 510 PHE 0.039 0.002 PHE B 77 TRP 0.018 0.002 TRP E 147 HIS 0.008 0.001 HIS E 190 Details of bonding type rmsd covalent geometry : bond 0.00417 (27331) covalent geometry : angle 0.59872 (36963) hydrogen bonds : bond 0.03490 ( 1276) hydrogen bonds : angle 4.51494 ( 3732) metal coordination : bond 0.00619 ( 21) metal coordination : angle 2.26119 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 271 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 GLU cc_start: 0.6191 (pm20) cc_final: 0.5816 (pm20) REVERT: C 45 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8432 (mp) REVERT: C 53 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8378 (pp) REVERT: C 269 ARG cc_start: 0.8272 (mmp80) cc_final: 0.8034 (mmp80) REVERT: C 480 MET cc_start: 0.8436 (mmt) cc_final: 0.7815 (mmt) REVERT: C 510 TYR cc_start: 0.8312 (OUTLIER) cc_final: 0.7314 (t80) REVERT: C 559 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9023 (tt) REVERT: C 729 GLN cc_start: 0.8182 (mp10) cc_final: 0.7771 (mp10) REVERT: E 160 ILE cc_start: 0.8008 (mm) cc_final: 0.7643 (mt) REVERT: E 164 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7626 (mm) REVERT: E 717 MET cc_start: 0.7562 (OUTLIER) cc_final: 0.7241 (ppp) REVERT: E 728 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7646 (mttp) REVERT: I 45 TYR cc_start: 0.6058 (m-80) cc_final: 0.5841 (m-80) REVERT: A 1 MET cc_start: -0.0255 (tpt) cc_final: -0.0815 (mmt) REVERT: A 110 HIS cc_start: 0.3762 (t-90) cc_final: 0.2803 (m90) REVERT: A 388 PHE cc_start: 0.7033 (OUTLIER) cc_final: 0.5988 (m-80) REVERT: G 220 MET cc_start: 0.5875 (ttp) cc_final: 0.4376 (mmt) REVERT: G 357 ASN cc_start: 0.8092 (t0) cc_final: 0.7817 (t0) REVERT: G 568 MET cc_start: 0.8085 (tpp) cc_final: 0.7777 (tpp) outliers start: 57 outliers final: 37 residues processed: 306 average time/residue: 0.1556 time to fit residues: 79.3553 Evaluate side-chains 311 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 266 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 25 PHE Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 221 GLN Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 510 TYR Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain E residue 532 GLU Chi-restraints excluded: chain E residue 576 MET Chi-restraints excluded: chain E residue 717 MET Chi-restraints excluded: chain E residue 721 CYS Chi-restraints excluded: chain E residue 728 LYS Chi-restraints excluded: chain H residue 17 MET Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain A residue 93 TRP Chi-restraints excluded: chain A residue 388 PHE Chi-restraints excluded: chain G residue 364 ILE Chi-restraints excluded: chain G residue 475 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 287 optimal weight: 20.0000 chunk 255 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 137 optimal weight: 0.0170 chunk 288 optimal weight: 8.9990 chunk 224 optimal weight: 7.9990 chunk 144 optimal weight: 0.6980 chunk 125 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 293 optimal weight: 30.0000 chunk 232 optimal weight: 3.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 329 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 HIS G 274 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.180168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3889 r_free = 0.3889 target = 0.128888 restraints weight = 50240.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.123927 restraints weight = 43498.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.124063 restraints weight = 38586.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.124488 restraints weight = 36463.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.124608 restraints weight = 34511.904| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27352 Z= 0.126 Angle : 0.573 11.207 36972 Z= 0.291 Chirality : 0.040 0.195 4179 Planarity : 0.003 0.070 4762 Dihedral : 4.502 88.132 3674 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.70 % Allowed : 16.85 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: -0.41 (0.15), residues: 3357 helix: 0.46 (0.12), residues: 1948 sheet: -3.47 (0.60), residues: 56 loop : -1.13 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 29 TYR 0.026 0.001 TYR C 510 PHE 0.039 0.001 PHE B 77 TRP 0.016 0.001 TRP A 209 HIS 0.009 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00290 (27331) covalent geometry : angle 0.57223 (36963) hydrogen bonds : bond 0.03348 ( 1276) hydrogen bonds : angle 4.41120 ( 3732) metal coordination : bond 0.00422 ( 21) metal coordination : angle 1.80615 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 285 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 GLU cc_start: 0.6220 (pm20) cc_final: 0.5886 (pm20) REVERT: C 45 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8348 (mp) REVERT: C 53 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8301 (pp) REVERT: C 269 ARG cc_start: 0.8244 (mmp80) cc_final: 0.7865 (mmp80) REVERT: C 480 MET cc_start: 0.8350 (mmt) cc_final: 0.7690 (mmt) REVERT: C 510 TYR cc_start: 0.8152 (OUTLIER) cc_final: 0.7073 (t80) REVERT: C 559 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9015 (tt) REVERT: C 665 MET cc_start: 0.2268 (tpp) cc_final: 0.1614 (mtp) REVERT: C 729 GLN cc_start: 0.8069 (mp10) cc_final: 0.7664 (mp10) REVERT: E 101 MET cc_start: 0.8650 (tpp) cc_final: 0.8315 (tpp) REVERT: E 160 ILE cc_start: 0.7995 (mm) cc_final: 0.7652 (mt) REVERT: E 164 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7819 (mm) REVERT: E 566 MET cc_start: 0.4123 (mmm) cc_final: 0.3769 (mmt) REVERT: E 608 LYS cc_start: 0.8119 (tptp) cc_final: 0.7881 (tptp) REVERT: E 689 LYS cc_start: 0.7858 (tttt) cc_final: 0.7537 (tppt) REVERT: E 717 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.7219 (ppp) REVERT: E 728 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7572 (mtmm) REVERT: I 45 TYR cc_start: 0.6064 (m-80) cc_final: 0.5825 (m-80) REVERT: A 1 MET cc_start: 0.0248 (tpt) cc_final: -0.0509 (mmt) REVERT: A 110 HIS cc_start: 0.3826 (t-90) cc_final: 0.2792 (m90) REVERT: A 388 PHE cc_start: 0.7279 (OUTLIER) cc_final: 0.6149 (m-80) REVERT: A 565 HIS cc_start: 0.8155 (OUTLIER) cc_final: 0.5393 (m170) REVERT: G 220 MET cc_start: 0.6209 (ttp) cc_final: 0.4577 (mmt) REVERT: G 357 ASN cc_start: 0.8270 (t0) cc_final: 0.7958 (t0) REVERT: G 477 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8319 (mm) REVERT: G 568 MET cc_start: 0.8056 (tpp) cc_final: 0.7672 (tpp) outliers start: 49 outliers final: 33 residues processed: 317 average time/residue: 0.1678 time to fit residues: 87.7854 Evaluate side-chains 312 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 269 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 25 PHE Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 221 GLN Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 510 TYR Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain E residue 532 GLU Chi-restraints excluded: chain E residue 576 MET Chi-restraints excluded: chain E residue 717 MET Chi-restraints excluded: chain E residue 721 CYS Chi-restraints excluded: chain E residue 728 LYS Chi-restraints excluded: chain H residue 17 MET Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain A residue 93 TRP Chi-restraints excluded: chain A residue 388 PHE Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain G residue 274 HIS Chi-restraints excluded: chain G residue 364 ILE Chi-restraints excluded: chain G residue 477 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 261 optimal weight: 0.0470 chunk 293 optimal weight: 40.0000 chunk 5 optimal weight: 5.9990 chunk 314 optimal weight: 2.9990 chunk 233 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 221 optimal weight: 0.0980 chunk 236 optimal weight: 8.9990 chunk 271 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 152 optimal weight: 1.9990 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 71 HIS E 329 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 116 HIS G 274 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.180526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.143199 restraints weight = 50338.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.133098 restraints weight = 65167.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.129266 restraints weight = 53499.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.130263 restraints weight = 43944.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.129443 restraints weight = 39103.436| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27352 Z= 0.127 Angle : 0.582 11.168 36972 Z= 0.295 Chirality : 0.041 0.281 4179 Planarity : 0.003 0.060 4762 Dihedral : 4.469 87.602 3674 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.63 % Allowed : 17.02 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: -0.35 (0.15), residues: 3357 helix: 0.50 (0.12), residues: 1944 sheet: -3.40 (0.61), residues: 56 loop : -1.10 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 29 TYR 0.027 0.001 TYR G 275 PHE 0.040 0.001 PHE B 77 TRP 0.016 0.002 TRP A 209 HIS 0.010 0.001 HIS G 274 Details of bonding type rmsd covalent geometry : bond 0.00292 (27331) covalent geometry : angle 0.58156 (36963) hydrogen bonds : bond 0.03303 ( 1276) hydrogen bonds : angle 4.37926 ( 3732) metal coordination : bond 0.00377 ( 21) metal coordination : angle 1.73159 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 280 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 GLU cc_start: 0.6102 (pm20) cc_final: 0.5790 (pm20) REVERT: B 85 ASN cc_start: 0.8008 (p0) cc_final: 0.7690 (p0) REVERT: C 45 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8306 (mp) REVERT: C 53 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8274 (pp) REVERT: C 269 ARG cc_start: 0.8224 (mmp80) cc_final: 0.7855 (mmp80) REVERT: C 510 TYR cc_start: 0.8221 (OUTLIER) cc_final: 0.6931 (t80) REVERT: C 559 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8983 (tt) REVERT: C 665 MET cc_start: 0.2664 (tpp) cc_final: 0.1930 (mtp) REVERT: C 729 GLN cc_start: 0.8231 (mp10) cc_final: 0.7784 (mp10) REVERT: E 160 ILE cc_start: 0.7855 (mm) cc_final: 0.7551 (mt) REVERT: E 164 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7671 (mm) REVERT: E 566 MET cc_start: 0.4409 (mmm) cc_final: 0.4014 (mmt) REVERT: E 717 MET cc_start: 0.7630 (OUTLIER) cc_final: 0.7369 (ppp) REVERT: E 728 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7752 (mtmm) REVERT: I 45 TYR cc_start: 0.6080 (m-80) cc_final: 0.5868 (m-80) REVERT: A 1 MET cc_start: -0.0494 (tpt) cc_final: -0.0974 (mmt) REVERT: A 110 HIS cc_start: 0.3687 (t-90) cc_final: 0.2770 (m90) REVERT: A 384 ASP cc_start: 0.7655 (t0) cc_final: 0.7359 (t0) REVERT: A 388 PHE cc_start: 0.6811 (OUTLIER) cc_final: 0.5764 (m-80) REVERT: A 565 HIS cc_start: 0.8169 (OUTLIER) cc_final: 0.5380 (m170) REVERT: G 220 MET cc_start: 0.5655 (ttp) cc_final: 0.4293 (mmt) REVERT: G 357 ASN cc_start: 0.7936 (t0) cc_final: 0.7703 (t0) REVERT: G 568 MET cc_start: 0.8012 (tpp) cc_final: 0.7710 (tpp) outliers start: 47 outliers final: 31 residues processed: 311 average time/residue: 0.1664 time to fit residues: 86.2189 Evaluate side-chains 310 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 270 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 25 PHE Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 221 GLN Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 510 TYR Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain E residue 532 GLU Chi-restraints excluded: chain E residue 576 MET Chi-restraints excluded: chain E residue 717 MET Chi-restraints excluded: chain E residue 728 LYS Chi-restraints excluded: chain H residue 17 MET Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain A residue 388 PHE Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain G residue 93 TRP Chi-restraints excluded: chain G residue 274 HIS Chi-restraints excluded: chain G residue 364 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 100 optimal weight: 2.9990 chunk 203 optimal weight: 50.0000 chunk 219 optimal weight: 9.9990 chunk 138 optimal weight: 1.9990 chunk 299 optimal weight: 20.0000 chunk 183 optimal weight: 20.0000 chunk 1 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 chunk 230 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 264 HIS ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.177700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.140072 restraints weight = 49840.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.127119 restraints weight = 67852.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.123429 restraints weight = 59423.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.123652 restraints weight = 48173.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.123589 restraints weight = 45761.226| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 27352 Z= 0.246 Angle : 0.654 12.674 36972 Z= 0.332 Chirality : 0.044 0.266 4179 Planarity : 0.004 0.057 4762 Dihedral : 4.634 88.338 3674 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 1.74 % Allowed : 17.12 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: -0.54 (0.15), residues: 3357 helix: 0.33 (0.12), residues: 1932 sheet: -3.41 (0.64), residues: 56 loop : -1.13 (0.17), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 29 TYR 0.028 0.002 TYR C 510 PHE 0.042 0.002 PHE B 77 TRP 0.042 0.003 TRP A 93 HIS 0.008 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00582 (27331) covalent geometry : angle 0.65264 (36963) hydrogen bonds : bond 0.03554 ( 1276) hydrogen bonds : angle 4.55855 ( 3732) metal coordination : bond 0.00928 ( 21) metal coordination : angle 2.62474 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5346.97 seconds wall clock time: 93 minutes 13.10 seconds (5593.10 seconds total)