Starting phenix.real_space_refine on Thu May 16 15:30:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqc_37739/05_2024/8wqc_37739_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqc_37739/05_2024/8wqc_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqc_37739/05_2024/8wqc_37739.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqc_37739/05_2024/8wqc_37739.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqc_37739/05_2024/8wqc_37739_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqc_37739/05_2024/8wqc_37739_neut.pdb" } 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 Residue "E PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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: 11.62, per 1000 atoms: 0.43 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.77 Conformation dependent library (CDL) restraints added in 4.9 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: 3.00 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: 10.34 Time building geometry restraints manager: 11.62 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: 96.85 - 104.37: 325 104.37 - 111.89: 13076 111.89 - 119.41: 9934 119.41 - 126.93: 13336 126.93 - 134.45: 292 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 2.520 nonbonded pdb=" NZ LYS E 689 " pdb=" O GLY N 76 " model vdw 2.172 2.520 nonbonded pdb=" OD1 ASP A 384 " pdb=" NH1 ARG A 387 " model vdw 2.199 2.520 nonbonded pdb=" OG SER A 28 " pdb=" OD2 ASP A 31 " model vdw 2.201 2.440 ... (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 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.220 Construct map_model_manager: 0.020 Extract box with map and model: 42.140 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 71.960 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.280 ------------------------------------------------------------------------------- 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 27331 Z= 0.173 Angle : 0.582 15.822 36963 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 *********************** 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 fitting. rotamer outliers: 2 poor density : 427 time to evaluate : 2.876 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: 0.3981 time to fit residues: 268.9503 Evaluate side-chains 287 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 286 time to evaluate : 3.106 ------------------------------------------------------------------------------- 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: 20.0000 chunk 253 optimal weight: 8.9990 chunk 140 optimal weight: 0.5980 chunk 86 optimal weight: 0.0270 chunk 170 optimal weight: 4.9990 chunk 135 optimal weight: 0.5980 chunk 261 optimal weight: 0.6980 chunk 101 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 194 optimal weight: 0.7980 chunk 303 optimal weight: 6.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 HIS ** E 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 65 GLN A 166 HIS A 274 HIS G 274 HIS G 375 GLN G 476 HIS G 502 HIS ** G 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27331 Z= 0.205 Angle : 0.569 12.142 36963 Z= 0.298 Chirality : 0.040 0.175 4179 Planarity : 0.004 0.059 4762 Dihedral : 4.699 83.111 3676 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.69 % Allowed : 8.16 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.15), residues: 3357 helix: -0.04 (0.12), residues: 1937 sheet: -3.27 (0.68), residues: 50 loop : -1.02 (0.17), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 27 HIS 0.007 0.001 HIS I 10 PHE 0.020 0.001 PHE C 10 TYR 0.021 0.002 TYR G 472 ARG 0.008 0.000 ARG I 37 *********************** 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 339 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 319 time to evaluate : 3.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 729 GLN cc_start: 0.8103 (mp10) cc_final: 0.7876 (mp10) REVERT: E 63 ILE cc_start: 0.8739 (mm) cc_final: 0.8468 (mt) REVERT: E 160 ILE cc_start: 0.7932 (mm) cc_final: 0.7600 (mt) REVERT: E 177 ASN cc_start: 0.7509 (t0) cc_final: 0.7271 (t0) REVERT: E 329 ASN cc_start: 0.7372 (p0) cc_final: 0.7093 (p0) REVERT: E 476 MET cc_start: 0.8361 (mtt) cc_final: 0.8067 (mtt) REVERT: A 1 MET cc_start: 0.1564 (tpt) cc_final: 0.0669 (mmm) REVERT: A 110 HIS cc_start: 0.3978 (t-90) cc_final: 0.2800 (m90) REVERT: A 368 LEU cc_start: 0.8781 (mt) cc_final: 0.8520 (pp) REVERT: G 300 HIS cc_start: 0.8530 (t70) cc_final: 0.8077 (p-80) REVERT: G 357 ASN cc_start: 0.8455 (t0) cc_final: 0.8129 (t0) REVERT: G 385 LEU cc_start: 0.7627 (mm) cc_final: 0.7336 (mt) REVERT: G 587 ILE cc_start: 0.8084 (tp) cc_final: 0.7849 (tp) outliers start: 20 outliers final: 10 residues processed: 328 average time/residue: 0.3812 time to fit residues: 203.9921 Evaluate side-chains 286 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 276 time to evaluate : 3.337 ------------------------------------------------------------------------------- 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 231 ASN Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain G residue 375 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 168 optimal weight: 7.9990 chunk 94 optimal weight: 0.0030 chunk 252 optimal weight: 9.9990 chunk 206 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 303 optimal weight: 20.0000 chunk 328 optimal weight: 1.9990 chunk 270 optimal weight: 3.9990 chunk 301 optimal weight: 0.0370 chunk 103 optimal weight: 3.9990 chunk 243 optimal weight: 10.0000 overall best weight: 1.8074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 HIS ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 HIS E 111 GLN E 190 HIS ** E 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 526 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 27331 Z= 0.392 Angle : 0.631 11.844 36963 Z= 0.326 Chirality : 0.043 0.234 4179 Planarity : 0.004 0.056 4762 Dihedral : 4.826 88.938 3676 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 1.60 % Allowed : 12.26 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.84 (0.15), residues: 3357 helix: -0.03 (0.12), residues: 1933 sheet: -3.55 (0.63), residues: 56 loop : -1.06 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 147 HIS 0.016 0.001 HIS A 274 PHE 0.026 0.002 PHE C 112 TYR 0.027 0.002 TYR C 544 ARG 0.006 0.000 ARG B 63 *********************** 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 fitting. rotamer outliers: 46 poor density : 289 time to evaluate : 3.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 510 TYR cc_start: 0.8499 (OUTLIER) cc_final: 0.7214 (t80) REVERT: C 729 GLN cc_start: 0.8041 (mp10) cc_final: 0.7732 (mp10) REVERT: E 63 ILE cc_start: 0.8804 (mm) cc_final: 0.8554 (mt) REVERT: E 329 ASN cc_start: 0.7437 (p0) cc_final: 0.7148 (p0) REVERT: E 480 MET cc_start: 0.7565 (mmm) cc_final: 0.7326 (mmm) REVERT: A 1 MET cc_start: 0.1544 (tpt) cc_final: 0.0634 (mmm) REVERT: A 110 HIS cc_start: 0.3954 (t-90) cc_final: 0.2902 (m90) REVERT: A 209 TRP cc_start: 0.5954 (t-100) cc_final: 0.5673 (t-100) REVERT: A 368 LEU cc_start: 0.8804 (mt) cc_final: 0.8544 (pp) REVERT: G 300 HIS cc_start: 0.8502 (t70) cc_final: 0.8116 (p-80) REVERT: G 357 ASN cc_start: 0.8455 (t0) cc_final: 0.8108 (t0) REVERT: G 385 LEU cc_start: 0.7656 (mm) cc_final: 0.7368 (mt) REVERT: G 587 ILE cc_start: 0.8169 (tp) cc_final: 0.7938 (tp) outliers start: 46 outliers final: 26 residues processed: 319 average time/residue: 0.3717 time to fit residues: 194.1159 Evaluate side-chains 293 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 266 time to evaluate : 3.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 76 ASN 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 496 ASN Chi-restraints excluded: chain C residue 510 TYR Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain E residue 17 LEU 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 478 THR Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain E residue 532 GLU Chi-restraints excluded: chain E residue 605 MET Chi-restraints excluded: chain E residue 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 I residue 34 ILE Chi-restraints excluded: chain G residue 364 ILE Chi-restraints excluded: chain G residue 475 ILE Chi-restraints excluded: chain G residue 591 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 300 optimal weight: 0.6980 chunk 228 optimal weight: 30.0000 chunk 157 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 145 optimal weight: 0.9980 chunk 204 optimal weight: 40.0000 chunk 304 optimal weight: 2.9990 chunk 322 optimal weight: 10.0000 chunk 159 optimal weight: 0.5980 chunk 289 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** E 190 HIS ** E 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 HIS A 375 GLN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27331 Z= 0.211 Angle : 0.547 11.912 36963 Z= 0.281 Chirality : 0.040 0.173 4179 Planarity : 0.003 0.061 4762 Dihedral : 4.604 87.235 3674 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 1.63 % Allowed : 14.31 % Favored : 84.06 % 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: -0.64 (0.15), residues: 3357 helix: 0.17 (0.12), residues: 1939 sheet: -3.53 (0.63), residues: 56 loop : -1.04 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 33 HIS 0.006 0.001 HIS I 10 PHE 0.037 0.001 PHE B 77 TYR 0.022 0.001 TYR C 510 ARG 0.006 0.000 ARG N 74 *********************** 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 339 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 292 time to evaluate : 2.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 GLU cc_start: 0.6010 (pm20) cc_final: 0.5607 (pm20) REVERT: C 45 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8400 (mp) REVERT: C 510 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.6895 (t80) REVERT: C 614 ILE cc_start: 0.7929 (mm) cc_final: 0.7564 (mt) REVERT: C 729 GLN cc_start: 0.8043 (mp10) cc_final: 0.7742 (mp10) REVERT: E 160 ILE cc_start: 0.7949 (mm) cc_final: 0.7563 (mt) REVERT: E 164 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7704 (mm) REVERT: E 329 ASN cc_start: 0.7340 (p0) cc_final: 0.7061 (p0) REVERT: E 344 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9141 (tt) REVERT: A 1 MET cc_start: 0.1568 (tpt) cc_final: 0.0607 (mmm) REVERT: A 110 HIS cc_start: 0.4070 (t-90) cc_final: 0.2971 (m90) REVERT: A 209 TRP cc_start: 0.6105 (t-100) cc_final: 0.5878 (t-100) REVERT: A 368 LEU cc_start: 0.8761 (mt) cc_final: 0.8536 (pp) REVERT: G 300 HIS cc_start: 0.8471 (t70) cc_final: 0.8088 (p-80) REVERT: G 357 ASN cc_start: 0.8415 (t0) cc_final: 0.8082 (t0) REVERT: G 385 LEU cc_start: 0.7650 (mm) cc_final: 0.7361 (mt) REVERT: G 587 ILE cc_start: 0.8119 (tp) cc_final: 0.7897 (tp) outliers start: 47 outliers final: 23 residues processed: 323 average time/residue: 0.3628 time to fit residues: 192.2859 Evaluate side-chains 299 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 272 time to evaluate : 3.320 ------------------------------------------------------------------------------- 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 45 LEU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 496 ASN Chi-restraints excluded: chain C residue 510 TYR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 187 SER 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 532 GLU Chi-restraints excluded: chain E residue 576 MET Chi-restraints excluded: chain E residue 605 MET Chi-restraints excluded: chain E residue 721 CYS Chi-restraints excluded: chain H residue 17 MET Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain A residue 93 TRP Chi-restraints excluded: chain G residue 364 ILE Chi-restraints excluded: chain G residue 475 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 268 optimal weight: 0.7980 chunk 183 optimal weight: 10.0000 chunk 4 optimal weight: 0.6980 chunk 240 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 chunk 275 optimal weight: 40.0000 chunk 223 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 164 optimal weight: 0.5980 chunk 289 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 E 190 HIS ** E 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 434 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27331 Z= 0.284 Angle : 0.578 13.974 36963 Z= 0.294 Chirality : 0.041 0.211 4179 Planarity : 0.003 0.059 4762 Dihedral : 4.633 88.524 3674 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.84 % Allowed : 15.32 % Favored : 82.84 % 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: -0.60 (0.15), residues: 3357 helix: 0.23 (0.12), residues: 1936 sheet: -3.55 (0.64), residues: 56 loop : -1.08 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 147 HIS 0.012 0.001 HIS A 274 PHE 0.042 0.002 PHE B 77 TYR 0.027 0.002 TYR G 472 ARG 0.008 0.000 ARG E 676 *********************** 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 342 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 289 time to evaluate : 3.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 29 ARG cc_start: 0.6214 (mmp-170) cc_final: 0.5804 (mmp-170) REVERT: B 98 GLU cc_start: 0.7121 (pm20) cc_final: 0.6893 (pm20) REVERT: C 45 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8480 (mp) REVERT: C 53 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8436 (pp) REVERT: C 510 TYR cc_start: 0.8449 (OUTLIER) cc_final: 0.7197 (t80) REVERT: C 559 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9098 (tt) REVERT: C 665 MET cc_start: 0.2753 (tpp) cc_final: 0.1856 (mtt) REVERT: C 729 GLN cc_start: 0.8069 (mp10) cc_final: 0.7769 (mp10) REVERT: E 160 ILE cc_start: 0.8073 (mm) cc_final: 0.7689 (mt) REVERT: E 164 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7643 (mm) REVERT: E 329 ASN cc_start: 0.7341 (p0) cc_final: 0.7044 (p0) REVERT: H 105 MET cc_start: 0.8626 (tmm) cc_final: 0.8339 (tmm) REVERT: A 1 MET cc_start: 0.1606 (tpt) cc_final: 0.0783 (mmt) REVERT: A 110 HIS cc_start: 0.3942 (t-90) cc_final: 0.2876 (m90) REVERT: A 368 LEU cc_start: 0.8757 (mt) cc_final: 0.8469 (pp) REVERT: A 388 PHE cc_start: 0.6149 (OUTLIER) cc_final: 0.5407 (m-80) REVERT: A 595 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7510 (ptt) REVERT: G 300 HIS cc_start: 0.8437 (t70) cc_final: 0.8067 (p-80) REVERT: G 357 ASN cc_start: 0.8409 (t0) cc_final: 0.8098 (t0) REVERT: G 385 LEU cc_start: 0.7681 (mm) cc_final: 0.7374 (mt) REVERT: G 587 ILE cc_start: 0.8136 (tp) cc_final: 0.7922 (tp) outliers start: 53 outliers final: 32 residues processed: 321 average time/residue: 0.3558 time to fit residues: 189.0689 Evaluate side-chains 310 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 271 time to evaluate : 3.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 221 GLN Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 496 ASN Chi-restraints excluded: chain C residue 510 TYR Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 262 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 605 MET Chi-restraints excluded: chain E residue 721 CYS Chi-restraints excluded: chain H residue 17 MET Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain A residue 388 PHE Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 364 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 108 optimal weight: 1.9990 chunk 290 optimal weight: 5.9990 chunk 63 optimal weight: 0.5980 chunk 189 optimal weight: 0.5980 chunk 79 optimal weight: 0.4980 chunk 323 optimal weight: 7.9990 chunk 268 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 26 optimal weight: 0.0070 chunk 106 optimal weight: 0.2980 chunk 169 optimal weight: 3.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- 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** E 71 HIS E 73 HIS ** E 735 GLN ** 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 375 GLN G 382 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 27331 Z= 0.165 Angle : 0.533 10.729 36963 Z= 0.272 Chirality : 0.039 0.192 4179 Planarity : 0.003 0.061 4762 Dihedral : 4.476 85.977 3674 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.77 % Allowed : 16.19 % Favored : 82.04 % 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: 0.47 (0.12), residues: 1930 sheet: -3.46 (0.66), residues: 50 loop : -1.02 (0.17), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 33 HIS 0.006 0.001 HIS E 71 PHE 0.034 0.001 PHE B 77 TYR 0.023 0.001 TYR C 510 ARG 0.003 0.000 ARG B 63 *********************** 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 351 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 300 time to evaluate : 3.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8376 (mp) REVERT: C 53 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8287 (pp) REVERT: C 269 ARG cc_start: 0.8159 (mmp80) cc_final: 0.7761 (mmp80) REVERT: C 480 MET cc_start: 0.8540 (mmt) cc_final: 0.7298 (mmt) REVERT: C 510 TYR cc_start: 0.8280 (OUTLIER) cc_final: 0.6785 (t80) REVERT: C 614 ILE cc_start: 0.7824 (mm) cc_final: 0.7446 (mt) REVERT: E 160 ILE cc_start: 0.7933 (mm) cc_final: 0.7552 (mt) REVERT: E 164 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7651 (mm) REVERT: E 329 ASN cc_start: 0.7290 (p0) cc_final: 0.7014 (p0) REVERT: E 468 GLU cc_start: 0.8133 (tp30) cc_final: 0.7738 (tp30) REVERT: H 79 TYR cc_start: 0.8237 (t80) cc_final: 0.7921 (t80) REVERT: H 105 MET cc_start: 0.8596 (tmm) cc_final: 0.8365 (tmm) REVERT: A 1 MET cc_start: 0.1553 (tpt) cc_final: 0.0715 (mmt) REVERT: A 110 HIS cc_start: 0.3883 (t-90) cc_final: 0.2796 (m90) REVERT: A 368 LEU cc_start: 0.8733 (mt) cc_final: 0.8470 (pp) REVERT: A 388 PHE cc_start: 0.6011 (OUTLIER) cc_final: 0.5210 (m-80) REVERT: G 220 MET cc_start: 0.7041 (ttp) cc_final: 0.5793 (mmt) REVERT: G 300 HIS cc_start: 0.8490 (t70) cc_final: 0.8101 (p-80) REVERT: G 357 ASN cc_start: 0.8399 (t0) cc_final: 0.8065 (t0) REVERT: G 385 LEU cc_start: 0.7661 (mm) cc_final: 0.7363 (mt) REVERT: G 587 ILE cc_start: 0.8150 (tp) cc_final: 0.7938 (tp) outliers start: 51 outliers final: 36 residues processed: 336 average time/residue: 0.3669 time to fit residues: 204.4134 Evaluate side-chains 319 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 278 time to evaluate : 3.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 221 GLN Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 496 ASN Chi-restraints excluded: chain C residue 506 SER 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 262 VAL Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 470 THR 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 88 THR Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain A residue 93 TRP Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 388 PHE Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 364 ILE Chi-restraints excluded: chain G residue 371 LEU 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 311 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 184 optimal weight: 30.0000 chunk 235 optimal weight: 9.9990 chunk 182 optimal weight: 10.0000 chunk 272 optimal weight: 20.0000 chunk 180 optimal weight: 10.0000 chunk 321 optimal weight: 7.9990 chunk 201 optimal weight: 6.9990 chunk 196 optimal weight: 6.9990 chunk 148 optimal weight: 0.1980 overall best weight: 4.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 GLN ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 HIS ** C 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 HIS E 264 HIS E 320 HIS E 521 GLN ** E 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 526 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.119 27331 Z= 0.925 Angle : 0.953 16.296 36963 Z= 0.488 Chirality : 0.056 0.228 4179 Planarity : 0.006 0.085 4762 Dihedral : 5.436 83.533 3674 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 22.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.43 % Favored : 91.42 % Rotamer: Outliers : 2.95 % Allowed : 16.57 % Favored : 80.48 % 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: -1.40 (0.14), residues: 3357 helix: -0.44 (0.12), residues: 1930 sheet: -3.88 (0.72), residues: 46 loop : -1.41 (0.17), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.005 TRP E 147 HIS 0.013 0.002 HIS H 35 PHE 0.042 0.004 PHE E 469 TYR 0.056 0.003 TYR B 79 ARG 0.011 0.001 ARG B 33 *********************** 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 357 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 272 time to evaluate : 3.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7532 (tp30) REVERT: B 111 ASP cc_start: 0.7986 (m-30) cc_final: 0.7630 (t0) REVERT: C 45 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8836 (mp) REVERT: C 53 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8753 (pp) REVERT: C 429 ASP cc_start: 0.7800 (t70) cc_final: 0.7396 (t0) REVERT: C 510 TYR cc_start: 0.8761 (OUTLIER) cc_final: 0.7901 (t80) REVERT: C 665 MET cc_start: 0.2714 (tpp) cc_final: 0.2210 (mtp) REVERT: C 729 GLN cc_start: 0.8126 (mp10) cc_final: 0.7817 (mp10) REVERT: E 67 ASN cc_start: 0.7930 (m-40) cc_final: 0.7670 (t0) REVERT: E 164 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7613 (mm) REVERT: E 329 ASN cc_start: 0.7742 (p0) cc_final: 0.7450 (p0) REVERT: E 468 GLU cc_start: 0.8295 (tp30) cc_final: 0.8053 (tp30) REVERT: E 554 THR cc_start: 0.8816 (t) cc_final: 0.8479 (t) REVERT: E 689 LYS cc_start: 0.7366 (tttt) cc_final: 0.6738 (tppt) REVERT: H 79 TYR cc_start: 0.8586 (t80) cc_final: 0.8292 (t80) REVERT: I 77 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6724 (mp) REVERT: A 1 MET cc_start: 0.1389 (tpt) cc_final: 0.0452 (mmt) REVERT: A 110 HIS cc_start: 0.4060 (t-90) cc_final: 0.3022 (m90) REVERT: A 388 PHE cc_start: 0.6565 (OUTLIER) cc_final: 0.5941 (m-80) REVERT: G 220 MET cc_start: 0.7173 (ttp) cc_final: 0.6098 (mmt) REVERT: G 300 HIS cc_start: 0.8437 (t70) cc_final: 0.8115 (p-80) REVERT: G 357 ASN cc_start: 0.8513 (t0) cc_final: 0.8207 (t0) REVERT: G 385 LEU cc_start: 0.7791 (mm) cc_final: 0.7463 (mt) REVERT: G 568 MET cc_start: 0.8587 (tpt) cc_final: 0.8345 (tpp) outliers start: 85 outliers final: 58 residues processed: 329 average time/residue: 0.3554 time to fit residues: 192.1551 Evaluate side-chains 320 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 255 time to evaluate : 3.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 221 GLN Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 496 ASN Chi-restraints excluded: chain C residue 510 TYR Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 623 ILE Chi-restraints excluded: chain J residue 27 TRP Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 443 LEU 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 N residue 70 VAL Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain H residue 17 MET Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain A residue 93 TRP Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 300 HIS Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 388 PHE Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 364 ILE Chi-restraints excluded: chain G residue 371 LEU Chi-restraints excluded: chain G residue 475 ILE Chi-restraints excluded: chain G residue 551 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 199 optimal weight: 0.3980 chunk 128 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 204 optimal weight: 50.0000 chunk 219 optimal weight: 30.0000 chunk 159 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 253 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 ASN C 432 GLN ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 HIS ** E 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27331 Z= 0.231 Angle : 0.608 13.733 36963 Z= 0.309 Chirality : 0.041 0.189 4179 Planarity : 0.004 0.058 4762 Dihedral : 4.907 88.498 3674 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.98 % Allowed : 17.92 % Favored : 80.10 % 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: -0.79 (0.15), residues: 3357 helix: 0.11 (0.12), residues: 1922 sheet: -3.59 (0.65), residues: 56 loop : -1.21 (0.17), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 27 HIS 0.013 0.001 HIS A 274 PHE 0.035 0.002 PHE B 77 TYR 0.026 0.002 TYR C 510 ARG 0.005 0.000 ARG I 29 *********************** 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 336 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 279 time to evaluate : 3.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 53 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8486 (pp) REVERT: C 510 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.7141 (t80) REVERT: C 559 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9135 (tt) REVERT: C 665 MET cc_start: 0.2609 (tpp) cc_final: 0.1771 (mtt) REVERT: E 164 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7656 (mm) REVERT: E 329 ASN cc_start: 0.7559 (p0) cc_final: 0.7291 (p0) REVERT: E 468 GLU cc_start: 0.8197 (tp30) cc_final: 0.7876 (tp30) REVERT: E 566 MET cc_start: 0.4339 (mmt) cc_final: 0.3917 (mmt) REVERT: E 689 LYS cc_start: 0.7150 (tttt) cc_final: 0.6562 (tppt) REVERT: H 105 MET cc_start: 0.8642 (tmm) cc_final: 0.8397 (tmm) REVERT: A 1 MET cc_start: 0.1387 (tpt) cc_final: 0.0486 (mmt) REVERT: A 110 HIS cc_start: 0.3833 (t-90) cc_final: 0.2975 (m90) REVERT: A 388 PHE cc_start: 0.6182 (OUTLIER) cc_final: 0.5341 (m-80) REVERT: G 220 MET cc_start: 0.7165 (ttp) cc_final: 0.6055 (mmt) REVERT: G 300 HIS cc_start: 0.8435 (t70) cc_final: 0.8112 (p-80) REVERT: G 357 ASN cc_start: 0.8459 (t0) cc_final: 0.8146 (t0) REVERT: G 385 LEU cc_start: 0.7646 (mm) cc_final: 0.7330 (mt) outliers start: 57 outliers final: 39 residues processed: 321 average time/residue: 0.3692 time to fit residues: 193.8387 Evaluate side-chains 306 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 262 time to evaluate : 2.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 221 GLN Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 496 ASN Chi-restraints excluded: chain C residue 510 TYR Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 40 ASP 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 187 SER Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain E residue 532 GLU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain H residue 17 MET Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain A residue 93 TRP Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 388 PHE Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 159 MET Chi-restraints excluded: chain G residue 364 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 292 optimal weight: 10.0000 chunk 308 optimal weight: 0.0070 chunk 281 optimal weight: 9.9990 chunk 299 optimal weight: 20.0000 chunk 180 optimal weight: 0.0370 chunk 130 optimal weight: 0.9980 chunk 235 optimal weight: 9.9990 chunk 92 optimal weight: 0.0060 chunk 271 optimal weight: 0.8980 chunk 283 optimal weight: 20.0000 chunk 298 optimal weight: 8.9990 overall best weight: 0.3892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 GLN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 HIS ** E 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27331 Z= 0.185 Angle : 0.581 13.433 36963 Z= 0.294 Chirality : 0.040 0.300 4179 Planarity : 0.003 0.057 4762 Dihedral : 4.691 88.672 3674 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.81 % Allowed : 17.89 % Favored : 80.31 % 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: -0.49 (0.15), residues: 3357 helix: 0.37 (0.12), residues: 1926 sheet: -3.51 (0.65), residues: 56 loop : -1.11 (0.17), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 93 HIS 0.012 0.001 HIS A 274 PHE 0.031 0.001 PHE B 77 TYR 0.036 0.001 TYR G 349 ARG 0.013 0.000 ARG D 29 *********************** 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 337 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 285 time to evaluate : 3.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 53 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8249 (pp) REVERT: C 269 ARG cc_start: 0.8299 (mmp80) cc_final: 0.8008 (mmp80) REVERT: C 510 TYR cc_start: 0.8324 (OUTLIER) cc_final: 0.6857 (t80) REVERT: C 559 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9103 (tt) REVERT: C 665 MET cc_start: 0.2643 (tpp) cc_final: 0.1763 (mtt) REVERT: E 151 MET cc_start: 0.8549 (tpp) cc_final: 0.8081 (tpp) REVERT: E 160 ILE cc_start: 0.7951 (mm) cc_final: 0.7566 (mt) REVERT: E 164 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7636 (mm) REVERT: E 329 ASN cc_start: 0.7426 (p0) cc_final: 0.7178 (p0) REVERT: E 429 ASP cc_start: 0.6607 (t0) cc_final: 0.6347 (t0) REVERT: E 468 GLU cc_start: 0.8244 (tp30) cc_final: 0.7852 (tp30) REVERT: E 689 LYS cc_start: 0.7112 (tttt) cc_final: 0.6541 (tppt) REVERT: E 728 LYS cc_start: 0.8013 (mtmm) cc_final: 0.7591 (mttp) REVERT: A 1 MET cc_start: 0.1285 (tpt) cc_final: 0.0371 (mmt) REVERT: A 110 HIS cc_start: 0.3834 (t-90) cc_final: 0.2972 (m90) REVERT: A 388 PHE cc_start: 0.6073 (OUTLIER) cc_final: 0.5234 (m-80) REVERT: G 220 MET cc_start: 0.7214 (ttp) cc_final: 0.5990 (mmt) REVERT: G 300 HIS cc_start: 0.8479 (t70) cc_final: 0.8131 (p-80) REVERT: G 357 ASN cc_start: 0.8449 (t0) cc_final: 0.8151 (t0) REVERT: G 385 LEU cc_start: 0.7587 (mm) cc_final: 0.7278 (mt) outliers start: 52 outliers final: 35 residues processed: 320 average time/residue: 0.3618 time to fit residues: 190.3413 Evaluate side-chains 312 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 272 time to evaluate : 3.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 496 ASN Chi-restraints excluded: chain C residue 510 TYR Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain J residue 39 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 71 HIS Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 443 LEU 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 N residue 73 LEU Chi-restraints excluded: chain H residue 17 MET Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 388 PHE Chi-restraints excluded: chain G residue 93 TRP Chi-restraints excluded: chain G residue 159 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 196 optimal weight: 0.9980 chunk 317 optimal weight: 0.0470 chunk 193 optimal weight: 0.5980 chunk 150 optimal weight: 0.9980 chunk 220 optimal weight: 20.0000 chunk 332 optimal weight: 2.9990 chunk 306 optimal weight: 20.0000 chunk 264 optimal weight: 7.9990 chunk 27 optimal weight: 0.4980 chunk 204 optimal weight: 40.0000 chunk 162 optimal weight: 2.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 GLN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 HIS ** E 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 27331 Z= 0.204 Angle : 0.596 11.616 36963 Z= 0.299 Chirality : 0.041 0.261 4179 Planarity : 0.003 0.059 4762 Dihedral : 4.629 87.949 3674 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.70 % Allowed : 18.20 % Favored : 80.10 % 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: -0.41 (0.15), residues: 3357 helix: 0.44 (0.12), residues: 1926 sheet: -3.49 (0.68), residues: 50 loop : -1.10 (0.17), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 93 HIS 0.012 0.001 HIS A 274 PHE 0.039 0.001 PHE B 77 TYR 0.035 0.001 TYR G 349 ARG 0.004 0.000 ARG F 21 ********************** 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 322 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 273 time to evaluate : 3.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 53 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8311 (pp) REVERT: C 269 ARG cc_start: 0.8307 (mmp80) cc_final: 0.8007 (mmp80) REVERT: C 510 TYR cc_start: 0.8382 (OUTLIER) cc_final: 0.6990 (t80) REVERT: C 559 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9114 (tt) REVERT: C 665 MET cc_start: 0.2508 (tpp) cc_final: 0.1507 (mtp) REVERT: E 160 ILE cc_start: 0.7982 (mm) cc_final: 0.7601 (mt) REVERT: E 164 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7618 (mm) REVERT: E 329 ASN cc_start: 0.7413 (p0) cc_final: 0.7161 (p0) REVERT: E 429 ASP cc_start: 0.6756 (t0) cc_final: 0.6475 (t0) REVERT: E 468 GLU cc_start: 0.8257 (tp30) cc_final: 0.7853 (tp30) REVERT: E 566 MET cc_start: 0.4438 (mmt) cc_final: 0.4031 (mmt) REVERT: E 689 LYS cc_start: 0.7093 (tttt) cc_final: 0.6506 (tppt) REVERT: E 728 LYS cc_start: 0.8029 (mtmm) cc_final: 0.7645 (mttp) REVERT: A 1 MET cc_start: 0.1283 (tpt) cc_final: 0.0359 (mmt) REVERT: A 110 HIS cc_start: 0.3808 (t-90) cc_final: 0.2922 (m90) REVERT: A 388 PHE cc_start: 0.6074 (OUTLIER) cc_final: 0.5231 (m-80) REVERT: G 220 MET cc_start: 0.7162 (ttp) cc_final: 0.5981 (mmt) REVERT: G 300 HIS cc_start: 0.8456 (t70) cc_final: 0.8119 (p-80) REVERT: G 357 ASN cc_start: 0.8444 (t0) cc_final: 0.8148 (t0) REVERT: G 385 LEU cc_start: 0.7573 (mm) cc_final: 0.7199 (mp) outliers start: 49 outliers final: 36 residues processed: 303 average time/residue: 0.3699 time to fit residues: 184.8705 Evaluate side-chains 309 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 268 time to evaluate : 3.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 221 GLN Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 496 ASN Chi-restraints excluded: chain C residue 510 TYR Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain J residue 39 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 71 HIS Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 443 LEU 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 N residue 73 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain A residue 93 TRP Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 388 PHE Chi-restraints excluded: chain G residue 93 TRP Chi-restraints excluded: chain G residue 159 MET Chi-restraints excluded: chain G residue 274 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 210 optimal weight: 8.9990 chunk 282 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 244 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 265 optimal weight: 3.9990 chunk 111 optimal weight: 0.2980 chunk 272 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.177285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.136727 restraints weight = 49736.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.127895 restraints weight = 67609.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.124798 restraints weight = 51793.520| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 27331 Z= 0.288 Angle : 0.623 12.667 36963 Z= 0.313 Chirality : 0.042 0.250 4179 Planarity : 0.004 0.057 4762 Dihedral : 4.664 89.140 3674 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.77 % Allowed : 18.17 % Favored : 80.06 % 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: -0.47 (0.15), residues: 3357 helix: 0.40 (0.12), residues: 1927 sheet: -3.52 (0.68), residues: 50 loop : -1.13 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 93 HIS 0.012 0.001 HIS A 274 PHE 0.040 0.002 PHE B 77 TYR 0.036 0.002 TYR G 275 ARG 0.008 0.000 ARG B 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5475.95 seconds wall clock time: 102 minutes 31.42 seconds (6151.42 seconds total)