Starting phenix.real_space_refine on Thu May 29 20:44:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wqc_37739/05_2025/8wqc_37739_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wqc_37739/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wqc_37739/05_2025/8wqc_37739.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wqc_37739/05_2025/8wqc_37739.map" model { file = "/net/cci-nas-00/data/ceres_data/8wqc_37739/05_2025/8wqc_37739_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wqc_37739/05_2025/8wqc_37739_neut.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLU:plan': 1, 'ASN:plan1': 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: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4, 'GLU:plan': 9, 'ARG:plan': 3} 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: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4, 'GLU:plan': 9, 'ARG:plan': 3} 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: 15.21, per 1000 atoms: 0.57 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: 6.98 Conformation dependent library (CDL) restraints added in 3.7 seconds 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: 2.68 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: 10.07 Time building geometry restraints manager: 8.17 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 105 or resid 200 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: 5.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.020 Extract box with map and model: 0.980 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 66.560 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.150 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.000 ------------------------------------------------------------------------------- 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 : 9.58 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (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 TRP 0.015 0.001 TRP F 33 HIS 0.004 0.001 HIS E 71 PHE 0.012 0.001 PHE E 339 TYR 0.021 0.001 TYR C 580 ARG 0.005 0.000 ARG D 8 Details of bonding type rmsd hydrogen bonds : bond 0.22712 ( 1276) hydrogen bonds : angle 7.50232 ( 3732) metal coordination : bond 0.00414 ( 21) metal coordination : angle 1.30345 ( 9) covalent geometry : bond 0.00262 (27331) covalent geometry : angle 0.58244 (36963) *********************** 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 : 2.988 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: 0.8790 (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: 0.7567 (mt) REVERT: E 329 ASN cc_start: 0.7403 (p0) cc_final: 0.7113 (p0) REVERT: E 476 MET cc_start: 0.8436 (mtt) cc_final: 0.8125 (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: 0.0659 (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: 0.8508 (pp) REVERT: G 1 MET cc_start: 0.3337 (tpt) cc_final: 0.3133 (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: 0.8116 (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: 0.3791 time to fit residues: 255.7757 Evaluate side-chains 287 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 286 time to evaluate : 3.158 ------------------------------------------------------------------------------- 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 282 optimal weight: 3.9990 chunk 253 optimal weight: 7.9990 chunk 140 optimal weight: 0.6980 chunk 86 optimal weight: 10.0000 chunk 170 optimal weight: 1.9990 chunk 135 optimal weight: 0.5980 chunk 261 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 159 optimal weight: 1.9990 chunk 194 optimal weight: 0.2980 chunk 303 optimal weight: 0.0370 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 HIS ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 HIS E 231 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 65 GLN A 166 HIS A 274 HIS G 274 HIS ** G 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 476 HIS G 526 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.181726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.141936 restraints weight = 50151.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.133729 restraints weight = 60968.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.130042 restraints weight = 45113.117| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27352 Z= 0.140 Angle : 0.587 11.927 36972 Z= 0.308 Chirality : 0.041 0.164 4179 Planarity : 0.004 0.061 4762 Dihedral : 4.669 83.069 3676 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.66 % Allowed : 7.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.14), residues: 3357 helix: -0.09 (0.12), residues: 1943 sheet: -3.30 (0.58), residues: 60 loop : -1.03 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 27 HIS 0.007 0.001 HIS I 10 PHE 0.021 0.001 PHE C 10 TYR 0.024 0.002 TYR G 472 ARG 0.005 0.000 ARG I 37 Details of bonding type rmsd hydrogen bonds : bond 0.04663 ( 1276) hydrogen bonds : angle 5.21357 ( 3732) metal coordination : bond 0.00311 ( 21) metal coordination : angle 1.62948 ( 9) covalent geometry : bond 0.00308 (27331) covalent geometry : angle 0.58605 (36963) *********************** 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 342 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 323 time to evaluate : 3.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 729 GLN cc_start: 0.8073 (mp10) cc_final: 0.7781 (mp10) REVERT: E 63 ILE cc_start: 0.8757 (mm) cc_final: 0.8501 (mt) REVERT: E 160 ILE cc_start: 0.7892 (mm) cc_final: 0.7584 (mt) REVERT: E 177 ASN cc_start: 0.7513 (t0) cc_final: 0.7259 (t0) REVERT: E 329 ASN cc_start: 0.7398 (p0) cc_final: 0.7182 (p0) REVERT: E 476 MET cc_start: 0.8640 (mtt) cc_final: 0.8352 (mtt) REVERT: E 717 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.7122 (ppp) REVERT: E 728 LYS cc_start: 0.7946 (mttp) cc_final: 0.7664 (mttp) REVERT: A 1 MET cc_start: 0.0098 (tpt) cc_final: -0.0284 (mmt) REVERT: A 110 HIS cc_start: 0.3949 (t-90) cc_final: 0.2762 (m90) REVERT: A 368 LEU cc_start: 0.8964 (mt) cc_final: 0.8663 (pp) REVERT: A 437 MET cc_start: 0.8121 (tpp) cc_final: 0.7898 (tpp) REVERT: A 455 THR cc_start: 0.8108 (p) cc_final: 0.7836 (t) REVERT: G 357 ASN cc_start: 0.8183 (t0) cc_final: 0.7853 (t0) REVERT: G 568 MET cc_start: 0.7631 (tmm) cc_final: 0.7359 (ttt) outliers start: 19 outliers final: 10 residues processed: 332 average time/residue: 0.3523 time to fit residues: 189.4486 Evaluate side-chains 293 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 282 time to evaluate : 2.868 ------------------------------------------------------------------------------- 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 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 33 optimal weight: 3.9990 chunk 229 optimal weight: 20.0000 chunk 278 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 208 optimal weight: 20.0000 chunk 125 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 153 optimal weight: 0.5980 chunk 250 optimal weight: 3.9990 chunk 223 optimal weight: 10.0000 chunk 31 optimal weight: 0.0050 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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 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 375 GLN ** G 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 434 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.181271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.142266 restraints weight = 50072.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.133511 restraints weight = 64732.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.131913 restraints weight = 47001.776| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27352 Z= 0.140 Angle : 0.559 12.243 36972 Z= 0.290 Chirality : 0.040 0.254 4179 Planarity : 0.004 0.065 4762 Dihedral : 4.554 83.757 3674 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.08 % Allowed : 10.80 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.15), residues: 3357 helix: 0.08 (0.12), residues: 1945 sheet: -3.36 (0.58), residues: 60 loop : -1.03 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 27 HIS 0.010 0.001 HIS A 274 PHE 0.027 0.001 PHE C 112 TYR 0.021 0.001 TYR C 510 ARG 0.006 0.000 ARG B 63 Details of bonding type rmsd hydrogen bonds : bond 0.04201 ( 1276) hydrogen bonds : angle 4.86233 ( 3732) metal coordination : bond 0.00328 ( 21) metal coordination : angle 1.72348 ( 9) covalent geometry : bond 0.00312 (27331) covalent geometry : angle 0.55842 (36963) *********************** 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 335 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 304 time to evaluate : 3.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 729 GLN cc_start: 0.8054 (mp10) cc_final: 0.7687 (mp10) REVERT: E 63 ILE cc_start: 0.8756 (mm) cc_final: 0.8490 (mt) REVERT: E 160 ILE cc_start: 0.7905 (mm) cc_final: 0.7579 (mt) REVERT: E 476 MET cc_start: 0.8766 (mtt) cc_final: 0.8558 (mtt) REVERT: E 608 LYS cc_start: 0.7922 (tptp) cc_final: 0.7691 (tptp) REVERT: E 717 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7134 (ppp) REVERT: A 1 MET cc_start: 0.0136 (tpt) cc_final: -0.0249 (mmt) REVERT: A 110 HIS cc_start: 0.3856 (t-90) cc_final: 0.2923 (m90) REVERT: A 368 LEU cc_start: 0.8982 (mt) cc_final: 0.8674 (pp) REVERT: A 437 MET cc_start: 0.8183 (tpp) cc_final: 0.7959 (tpp) REVERT: G 357 ASN cc_start: 0.8186 (t0) cc_final: 0.7869 (t0) REVERT: G 375 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8153 (mm110) outliers start: 31 outliers final: 14 residues processed: 324 average time/residue: 0.3662 time to fit residues: 193.5885 Evaluate side-chains 290 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 274 time to evaluate : 2.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 375 GLN 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 162 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 289 optimal weight: 7.9990 chunk 142 optimal weight: 0.5980 chunk 258 optimal weight: 0.0980 chunk 16 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 141 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 HIS E 111 GLN E 190 HIS E 329 ASN ** E 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 49 GLN A 199 HIS ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.181711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.140166 restraints weight = 50445.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.135901 restraints weight = 63606.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.137239 restraints weight = 56270.072| |-----------------------------------------------------------------------------| r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27352 Z= 0.127 Angle : 0.546 11.723 36972 Z= 0.281 Chirality : 0.040 0.203 4179 Planarity : 0.003 0.063 4762 Dihedral : 4.470 83.909 3674 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.49 % Allowed : 12.85 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.15), residues: 3357 helix: 0.24 (0.12), residues: 1942 sheet: -3.33 (0.68), residues: 50 loop : -1.01 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 27 HIS 0.011 0.001 HIS A 274 PHE 0.028 0.001 PHE C 112 TYR 0.021 0.001 TYR C 510 ARG 0.006 0.000 ARG B 63 Details of bonding type rmsd hydrogen bonds : bond 0.03758 ( 1276) hydrogen bonds : angle 4.67239 ( 3732) metal coordination : bond 0.00323 ( 21) metal coordination : angle 1.54573 ( 9) covalent geometry : bond 0.00285 (27331) covalent geometry : angle 0.54543 (36963) *********************** 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 334 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 291 time to evaluate : 3.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 46 ARG cc_start: 0.7466 (mpp80) cc_final: 0.7186 (mpp80) REVERT: B 56 GLU cc_start: 0.6051 (pm20) cc_final: 0.5638 (pm20) REVERT: C 510 TYR cc_start: 0.8097 (OUTLIER) cc_final: 0.6476 (t80) REVERT: C 729 GLN cc_start: 0.8169 (mp10) cc_final: 0.7825 (mp10) REVERT: E 101 MET cc_start: 0.8640 (tpp) cc_final: 0.8410 (tpp) REVERT: E 160 ILE cc_start: 0.8019 (mm) cc_final: 0.7686 (mt) REVERT: E 476 MET cc_start: 0.8665 (mtt) cc_final: 0.8428 (mtt) REVERT: E 597 LYS cc_start: 0.8594 (mptt) cc_final: 0.8384 (mptt) REVERT: A 110 HIS cc_start: 0.3511 (t-90) cc_final: 0.2860 (m90) outliers start: 43 outliers final: 21 residues processed: 318 average time/residue: 0.3670 time to fit residues: 190.9273 Evaluate side-chains 293 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 271 time to evaluate : 3.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 306 THR Chi-restraints excluded: chain C residue 510 TYR 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 532 GLU 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 I residue 23 THR Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain A residue 93 TRP Chi-restraints excluded: chain G residue 364 ILE Chi-restraints excluded: chain G residue 595 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 92 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 262 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 122 optimal weight: 0.0870 chunk 8 optimal weight: 7.9990 chunk 195 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 310 optimal weight: 8.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- 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** E 71 HIS ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 369 HIS ** G 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 526 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.181074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.144174 restraints weight = 50118.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.131620 restraints weight = 65431.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.129820 restraints weight = 54639.436| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2098 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= 0.137 Angle : 0.556 12.363 36972 Z= 0.284 Chirality : 0.040 0.173 4179 Planarity : 0.003 0.063 4762 Dihedral : 4.446 85.249 3674 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.49 % Allowed : 14.24 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.15), residues: 3357 helix: 0.35 (0.12), residues: 1945 sheet: -3.34 (0.67), residues: 50 loop : -0.99 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 147 HIS 0.011 0.001 HIS A 274 PHE 0.032 0.001 PHE C 112 TYR 0.030 0.001 TYR G 472 ARG 0.007 0.000 ARG B 63 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 1276) hydrogen bonds : angle 4.52622 ( 3732) metal coordination : bond 0.00400 ( 21) metal coordination : angle 1.65613 ( 9) covalent geometry : bond 0.00314 (27331) covalent geometry : angle 0.55500 (36963) *********************** 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 329 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 286 time to evaluate : 3.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 53 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8266 (pp) REVERT: C 510 TYR cc_start: 0.8134 (OUTLIER) cc_final: 0.6581 (t80) REVERT: C 729 GLN cc_start: 0.8207 (mp10) cc_final: 0.7761 (mp10) REVERT: E 160 ILE cc_start: 0.7916 (mm) cc_final: 0.7530 (mt) REVERT: E 164 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7560 (mm) REVERT: E 597 LYS cc_start: 0.8764 (mptt) cc_final: 0.8514 (mptt) REVERT: H 105 MET cc_start: 0.8496 (tmm) cc_final: 0.8283 (tmm) REVERT: I 5 LEU cc_start: 0.7689 (mm) cc_final: 0.7440 (mm) REVERT: A 1 MET cc_start: 0.1584 (mmt) cc_final: 0.1245 (tpt) REVERT: A 110 HIS cc_start: 0.3766 (t-90) cc_final: 0.2819 (m90) REVERT: A 565 HIS cc_start: 0.8117 (OUTLIER) cc_final: 0.5112 (m-70) REVERT: G 568 MET cc_start: 0.8145 (tpt) cc_final: 0.7857 (tpp) outliers start: 43 outliers final: 28 residues processed: 311 average time/residue: 0.3525 time to fit residues: 179.8113 Evaluate side-chains 297 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 265 time to evaluate : 3.024 ------------------------------------------------------------------------------- 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 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 8 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 137 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 306 THR Chi-restraints excluded: chain C residue 510 TYR 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 164 LEU Chi-restraints excluded: chain E residue 257 SER 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 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 K residue 73 LEU Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain G residue 364 ILE Chi-restraints excluded: chain G residue 475 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 333 optimal weight: 2.9990 chunk 246 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 313 optimal weight: 8.9990 chunk 173 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 285 optimal weight: 20.0000 chunk 316 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 71 HIS ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 GLN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 375 GLN ** G 382 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 = 0.4478 r_free = 0.4478 target = 0.178532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.140021 restraints weight = 49752.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.126964 restraints weight = 62577.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.123439 restraints weight = 60547.057| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 27352 Z= 0.204 Angle : 0.597 9.767 36972 Z= 0.305 Chirality : 0.042 0.237 4179 Planarity : 0.004 0.067 4762 Dihedral : 4.542 88.928 3674 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 1.70 % Allowed : 15.21 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.15), residues: 3357 helix: 0.32 (0.12), residues: 1943 sheet: -3.40 (0.68), residues: 50 loop : -1.03 (0.18), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 147 HIS 0.009 0.001 HIS A 274 PHE 0.019 0.002 PHE C 10 TYR 0.024 0.002 TYR C 510 ARG 0.008 0.000 ARG B 63 Details of bonding type rmsd hydrogen bonds : bond 0.03650 ( 1276) hydrogen bonds : angle 4.55739 ( 3732) metal coordination : bond 0.00803 ( 21) metal coordination : angle 2.18387 ( 9) covalent geometry : bond 0.00481 (27331) covalent geometry : angle 0.59567 (36963) *********************** 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 322 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 273 time to evaluate : 3.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 GLU cc_start: 0.6408 (pm20) cc_final: 0.6035 (pm20) REVERT: C 45 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8382 (mp) REVERT: C 53 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8386 (pp) REVERT: C 510 TYR cc_start: 0.8373 (OUTLIER) cc_final: 0.7191 (t80) REVERT: C 729 GLN cc_start: 0.8089 (mp10) cc_final: 0.7660 (mp10) REVERT: E 101 MET cc_start: 0.8857 (tpp) cc_final: 0.8570 (tpp) REVERT: E 160 ILE cc_start: 0.8037 (mm) cc_final: 0.7646 (mt) REVERT: E 164 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7653 (mm) REVERT: E 429 ASP cc_start: 0.6813 (t0) cc_final: 0.6474 (t0) REVERT: E 597 LYS cc_start: 0.8802 (mptt) cc_final: 0.8549 (mptt) REVERT: H 105 MET cc_start: 0.8575 (tmm) cc_final: 0.8348 (tmm) REVERT: I 45 TYR cc_start: 0.6055 (m-80) cc_final: 0.5832 (m-80) REVERT: A 1 MET cc_start: 0.1661 (mmt) cc_final: 0.1355 (tpt) REVERT: A 110 HIS cc_start: 0.3916 (t-90) cc_final: 0.2887 (m90) REVERT: A 388 PHE cc_start: 0.7217 (OUTLIER) cc_final: 0.6111 (m-80) REVERT: G 220 MET cc_start: 0.5876 (ttp) cc_final: 0.4424 (mmt) REVERT: G 568 MET cc_start: 0.8258 (tpt) cc_final: 0.8029 (tpp) outliers start: 49 outliers final: 32 residues processed: 301 average time/residue: 0.3468 time to fit residues: 172.3154 Evaluate side-chains 302 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 265 time to evaluate : 2.956 ------------------------------------------------------------------------------- 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 D residue 94 SER Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 137 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 306 THR Chi-restraints excluded: chain C residue 510 TYR Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 25 VAL 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 505 ILE Chi-restraints excluded: chain E residue 532 GLU Chi-restraints excluded: chain E residue 685 VAL 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 K residue 73 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 0 optimal weight: 7.9990 chunk 99 optimal weight: 0.7980 chunk 124 optimal weight: 0.1980 chunk 49 optimal weight: 0.6980 chunk 226 optimal weight: 8.9990 chunk 309 optimal weight: 10.0000 chunk 194 optimal weight: 0.4980 chunk 155 optimal weight: 0.2980 chunk 329 optimal weight: 0.0570 chunk 330 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 HIS G 382 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.181175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.136620 restraints weight = 49972.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.132223 restraints weight = 52913.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.132748 restraints weight = 44691.858| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 27352 Z= 0.113 Angle : 0.550 16.368 36972 Z= 0.279 Chirality : 0.039 0.229 4179 Planarity : 0.003 0.066 4762 Dihedral : 4.412 86.418 3674 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.53 % Allowed : 15.94 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.15), residues: 3357 helix: 0.48 (0.12), residues: 1944 sheet: -3.27 (0.68), residues: 50 loop : -1.06 (0.17), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 33 HIS 0.010 0.001 HIS A 274 PHE 0.021 0.001 PHE C 10 TYR 0.026 0.001 TYR C 510 ARG 0.007 0.000 ARG B 63 Details of bonding type rmsd hydrogen bonds : bond 0.03362 ( 1276) hydrogen bonds : angle 4.38238 ( 3732) metal coordination : bond 0.00415 ( 21) metal coordination : angle 1.45000 ( 9) covalent geometry : bond 0.00250 (27331) covalent geometry : angle 0.54982 (36963) *********************** 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 327 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 283 time to evaluate : 3.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 GLU cc_start: 0.6286 (pm20) cc_final: 0.5968 (pm20) REVERT: C 45 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8274 (mp) REVERT: C 269 ARG cc_start: 0.8133 (mmp80) cc_final: 0.7794 (mmp80) REVERT: C 293 ASP cc_start: 0.6238 (t0) cc_final: 0.5910 (t0) REVERT: C 510 TYR cc_start: 0.8090 (OUTLIER) cc_final: 0.6523 (t80) REVERT: C 614 ILE cc_start: 0.7891 (mm) cc_final: 0.7420 (mt) REVERT: C 667 GLN cc_start: 0.1844 (OUTLIER) cc_final: 0.1489 (pm20) REVERT: C 729 GLN cc_start: 0.8243 (mp10) cc_final: 0.7793 (mp10) REVERT: E 160 ILE cc_start: 0.7897 (mm) cc_final: 0.7536 (mt) REVERT: E 164 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7655 (mm) REVERT: E 429 ASP cc_start: 0.6826 (t0) cc_final: 0.6467 (t0) REVERT: E 597 LYS cc_start: 0.8686 (mptt) cc_final: 0.8440 (mptt) REVERT: I 5 LEU cc_start: 0.7681 (mm) cc_final: 0.7449 (mm) REVERT: I 45 TYR cc_start: 0.6150 (m-80) cc_final: 0.5931 (m-80) REVERT: A 1 MET cc_start: 0.1323 (mmt) cc_final: 0.1037 (tpt) REVERT: A 110 HIS cc_start: 0.3570 (t-90) cc_final: 0.2758 (m90) REVERT: A 388 PHE cc_start: 0.6571 (OUTLIER) cc_final: 0.5610 (m-80) REVERT: A 565 HIS cc_start: 0.8140 (OUTLIER) cc_final: 0.5350 (m170) REVERT: G 220 MET cc_start: 0.5385 (ttp) cc_final: 0.4189 (mmt) outliers start: 44 outliers final: 30 residues processed: 312 average time/residue: 0.3515 time to fit residues: 181.6100 Evaluate side-chains 300 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 264 time to evaluate : 3.231 ------------------------------------------------------------------------------- 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 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 137 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 667 GLN Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 25 VAL 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 344 LEU 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 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 K residue 73 LEU 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 364 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 33 optimal weight: 3.9990 chunk 322 optimal weight: 10.0000 chunk 295 optimal weight: 8.9990 chunk 130 optimal weight: 0.6980 chunk 250 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 234 optimal weight: 20.0000 chunk 158 optimal weight: 0.8980 chunk 251 optimal weight: 0.9990 chunk 244 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 ASN ** E 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4489 r_free = 0.4489 target = 0.179437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.141189 restraints weight = 49992.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.133729 restraints weight = 67096.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.129704 restraints weight = 48100.666| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 27352 Z= 0.169 Angle : 0.590 12.378 36972 Z= 0.298 Chirality : 0.041 0.252 4179 Planarity : 0.003 0.058 4762 Dihedral : 4.486 88.435 3674 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.49 % Allowed : 16.22 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.15), residues: 3357 helix: 0.47 (0.12), residues: 1940 sheet: -3.43 (0.63), residues: 56 loop : -1.04 (0.17), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 147 HIS 0.006 0.001 HIS E 71 PHE 0.024 0.001 PHE C 10 TYR 0.034 0.002 TYR A 472 ARG 0.008 0.000 ARG B 63 Details of bonding type rmsd hydrogen bonds : bond 0.03429 ( 1276) hydrogen bonds : angle 4.38409 ( 3732) metal coordination : bond 0.00585 ( 21) metal coordination : angle 1.94551 ( 9) covalent geometry : bond 0.00397 (27331) covalent geometry : angle 0.58969 (36963) *********************** 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 319 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 276 time to evaluate : 2.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 ASN cc_start: 0.8096 (p0) cc_final: 0.7767 (p0) REVERT: C 45 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8399 (mp) REVERT: C 53 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8296 (pp) REVERT: C 510 TYR cc_start: 0.8256 (OUTLIER) cc_final: 0.6977 (t80) REVERT: C 667 GLN cc_start: 0.1631 (OUTLIER) cc_final: 0.1308 (pm20) REVERT: C 729 GLN cc_start: 0.8132 (mp10) cc_final: 0.7701 (mp10) REVERT: E 160 ILE cc_start: 0.8063 (mm) cc_final: 0.7676 (mt) REVERT: E 164 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7670 (mm) REVERT: E 429 ASP cc_start: 0.6874 (t0) cc_final: 0.6583 (t0) REVERT: E 597 LYS cc_start: 0.8805 (mptt) cc_final: 0.8538 (mptt) REVERT: I 45 TYR cc_start: 0.6108 (m-80) cc_final: 0.5878 (m-80) REVERT: A 1 MET cc_start: 0.1606 (mmt) cc_final: 0.1328 (tpt) REVERT: A 110 HIS cc_start: 0.3573 (t-90) cc_final: 0.2783 (m90) REVERT: A 388 PHE cc_start: 0.7059 (OUTLIER) cc_final: 0.5989 (m-80) REVERT: G 220 MET cc_start: 0.6048 (ttp) cc_final: 0.4571 (mmt) outliers start: 43 outliers final: 32 residues processed: 303 average time/residue: 0.3463 time to fit residues: 173.5422 Evaluate side-chains 304 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 266 time to evaluate : 2.986 ------------------------------------------------------------------------------- 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 137 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 306 THR Chi-restraints excluded: chain C residue 510 TYR Chi-restraints excluded: chain C residue 667 GLN Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 25 VAL 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 505 ILE Chi-restraints excluded: chain E residue 532 GLU Chi-restraints excluded: chain E residue 576 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 A residue 388 PHE Chi-restraints excluded: chain G residue 274 HIS 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 294 optimal weight: 5.9990 chunk 290 optimal weight: 30.0000 chunk 3 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 208 optimal weight: 30.0000 chunk 139 optimal weight: 0.6980 chunk 76 optimal weight: 0.0050 chunk 177 optimal weight: 10.0000 chunk 130 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 71 HIS ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 116 HIS G 274 HIS G 443 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.180591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.142933 restraints weight = 50102.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.127312 restraints weight = 60456.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.127219 restraints weight = 55288.205| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27352 Z= 0.127 Angle : 0.575 11.868 36972 Z= 0.290 Chirality : 0.040 0.204 4179 Planarity : 0.003 0.059 4762 Dihedral : 4.436 87.546 3674 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.46 % Allowed : 16.53 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.15), residues: 3357 helix: 0.53 (0.12), residues: 1942 sheet: -3.32 (0.64), residues: 56 loop : -1.07 (0.17), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 209 HIS 0.009 0.001 HIS A 274 PHE 0.030 0.001 PHE C 10 TYR 0.029 0.001 TYR A 472 ARG 0.008 0.000 ARG B 63 Details of bonding type rmsd hydrogen bonds : bond 0.03289 ( 1276) hydrogen bonds : angle 4.33617 ( 3732) metal coordination : bond 0.00382 ( 21) metal coordination : angle 1.62532 ( 9) covalent geometry : bond 0.00291 (27331) covalent geometry : angle 0.57416 (36963) *********************** 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 315 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 273 time to evaluate : 3.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 GLU cc_start: 0.6324 (pm20) cc_final: 0.6101 (pm20) REVERT: B 85 ASN cc_start: 0.8002 (p0) cc_final: 0.7711 (p0) REVERT: C 45 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8357 (mp) REVERT: C 53 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8225 (pp) REVERT: C 269 ARG cc_start: 0.8187 (mmp80) cc_final: 0.7864 (mmp80) REVERT: C 480 MET cc_start: 0.8432 (mmt) cc_final: 0.7431 (mmt) REVERT: C 510 TYR cc_start: 0.8227 (OUTLIER) cc_final: 0.6826 (t80) REVERT: C 582 MET cc_start: 0.6860 (ttt) cc_final: 0.6629 (ttt) REVERT: C 665 MET cc_start: 0.2460 (tpp) cc_final: 0.1598 (mtp) REVERT: C 667 GLN cc_start: 0.1672 (OUTLIER) cc_final: 0.1370 (pm20) REVERT: C 729 GLN cc_start: 0.8147 (mp10) cc_final: 0.7713 (mp10) REVERT: E 160 ILE cc_start: 0.7897 (mm) cc_final: 0.7523 (mt) REVERT: E 164 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7765 (mm) REVERT: E 429 ASP cc_start: 0.6662 (t0) cc_final: 0.6322 (t0) REVERT: E 597 LYS cc_start: 0.8830 (mptt) cc_final: 0.8553 (mptt) REVERT: I 45 TYR cc_start: 0.6123 (m-80) cc_final: 0.5898 (m-80) REVERT: A 1 MET cc_start: 0.1517 (mmt) cc_final: 0.1264 (tpt) REVERT: A 110 HIS cc_start: 0.3640 (t-90) cc_final: 0.2838 (m90) REVERT: A 388 PHE cc_start: 0.7086 (OUTLIER) cc_final: 0.6015 (m-80) REVERT: G 220 MET cc_start: 0.5938 (ttp) cc_final: 0.4491 (mmt) REVERT: G 395 MET cc_start: 0.8428 (ptp) cc_final: 0.8017 (ptp) outliers start: 42 outliers final: 30 residues processed: 298 average time/residue: 0.3423 time to fit residues: 169.1198 Evaluate side-chains 305 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 269 time to evaluate : 2.995 ------------------------------------------------------------------------------- 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 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 236 MET Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 510 TYR Chi-restraints excluded: chain C residue 667 GLN Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 25 VAL 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 505 ILE Chi-restraints excluded: chain E residue 532 GLU Chi-restraints excluded: chain E residue 576 MET 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 A residue 388 PHE Chi-restraints excluded: chain G residue 93 TRP Chi-restraints excluded: chain G residue 364 ILE Chi-restraints excluded: chain G residue 475 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 306 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 323 optimal weight: 5.9990 chunk 277 optimal weight: 20.0000 chunk 207 optimal weight: 6.9990 chunk 211 optimal weight: 7.9990 chunk 215 optimal weight: 8.9990 chunk 309 optimal weight: 0.8980 chunk 278 optimal weight: 2.9990 chunk 173 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 264 HIS C 581 GLN E 71 HIS ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 264 HIS ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 443 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.176154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.137400 restraints weight = 49716.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.125472 restraints weight = 65740.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.122104 restraints weight = 53669.969| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 27352 Z= 0.318 Angle : 0.717 12.310 36972 Z= 0.363 Chirality : 0.046 0.198 4179 Planarity : 0.004 0.064 4762 Dihedral : 4.796 85.131 3674 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 1.49 % Allowed : 16.53 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.15), residues: 3357 helix: 0.17 (0.12), residues: 1945 sheet: -3.40 (0.66), residues: 56 loop : -1.20 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP E 147 HIS 0.014 0.001 HIS E 71 PHE 0.030 0.002 PHE C 10 TYR 0.042 0.002 TYR G 349 ARG 0.006 0.001 ARG E 251 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 1276) hydrogen bonds : angle 4.68870 ( 3732) metal coordination : bond 0.01554 ( 21) metal coordination : angle 3.29247 ( 9) covalent geometry : bond 0.00750 (27331) covalent geometry : angle 0.71569 (36963) ********************** 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 311 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 268 time to evaluate : 3.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 GLU cc_start: 0.6308 (pm20) cc_final: 0.5766 (pm20) REVERT: C 45 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8683 (mp) REVERT: C 53 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8583 (pp) REVERT: C 510 TYR cc_start: 0.8419 (OUTLIER) cc_final: 0.7581 (t80) REVERT: C 665 MET cc_start: 0.2525 (tpp) cc_final: 0.1758 (mtp) REVERT: C 729 GLN cc_start: 0.8146 (mp10) cc_final: 0.7678 (mp10) REVERT: E 164 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7554 (mm) REVERT: E 429 ASP cc_start: 0.7361 (t0) cc_final: 0.6836 (t0) REVERT: E 597 LYS cc_start: 0.8779 (mptt) cc_final: 0.8541 (mptt) REVERT: I 45 TYR cc_start: 0.6144 (m-80) cc_final: 0.5926 (m-80) REVERT: A 1 MET cc_start: 0.1569 (mmt) cc_final: 0.1283 (tpt) REVERT: A 110 HIS cc_start: 0.3553 (t-90) cc_final: 0.2848 (m90) REVERT: A 388 PHE cc_start: 0.7237 (OUTLIER) cc_final: 0.6187 (m-80) REVERT: G 220 MET cc_start: 0.6019 (ttp) cc_final: 0.4519 (mmt) REVERT: G 395 MET cc_start: 0.8451 (ptp) cc_final: 0.8061 (ptp) outliers start: 43 outliers final: 29 residues processed: 292 average time/residue: 0.3375 time to fit residues: 162.5265 Evaluate side-chains 293 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 259 time to evaluate : 2.982 ------------------------------------------------------------------------------- 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 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 F residue 76 ASN 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 306 THR Chi-restraints excluded: chain C residue 510 TYR Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 49 TYR 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 505 ILE Chi-restraints excluded: chain E residue 532 GLU 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 388 PHE Chi-restraints excluded: chain G residue 93 TRP 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 0 optimal weight: 6.9990 chunk 147 optimal weight: 0.5980 chunk 124 optimal weight: 0.0970 chunk 300 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 271 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 26 optimal weight: 0.0170 chunk 50 optimal weight: 0.7980 chunk 216 optimal weight: 5.9990 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 ASN ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 581 GLN E 73 HIS ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 ASN G 443 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.180632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3967 r_free = 0.3967 target = 0.133970 restraints weight = 50018.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.127228 restraints weight = 48890.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.128279 restraints weight = 42845.324| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27352 Z= 0.124 Angle : 0.595 11.297 36972 Z= 0.301 Chirality : 0.040 0.200 4179 Planarity : 0.003 0.059 4762 Dihedral : 4.572 89.288 3674 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.11 % Allowed : 17.09 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.15), residues: 3357 helix: 0.43 (0.12), residues: 1945 sheet: -3.37 (0.64), residues: 56 loop : -1.09 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 93 HIS 0.009 0.001 HIS A 274 PHE 0.021 0.001 PHE C 112 TYR 0.039 0.001 TYR G 349 ARG 0.007 0.000 ARG D 29 Details of bonding type rmsd hydrogen bonds : bond 0.03292 ( 1276) hydrogen bonds : angle 4.40651 ( 3732) metal coordination : bond 0.00676 ( 21) metal coordination : angle 1.94574 ( 9) covalent geometry : bond 0.00282 (27331) covalent geometry : angle 0.59477 (36963) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9136.94 seconds wall clock time: 161 minutes 10.72 seconds (9670.72 seconds total)