Starting phenix.real_space_refine on Tue Aug 26 02:39:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wqg_37744/08_2025/8wqg_37744_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wqg_37744/08_2025/8wqg_37744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wqg_37744/08_2025/8wqg_37744_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wqg_37744/08_2025/8wqg_37744_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wqg_37744/08_2025/8wqg_37744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wqg_37744/08_2025/8wqg_37744.map" } resolution = 4.09 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7312 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 6 6.06 5 S 180 5.16 5 C 16949 2.51 5 N 4677 2.21 5 O 5020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26832 Number of models: 1 Model: "" Number of chains: 14 Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 735 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 7, 'TRANS': 85} Chain breaks: 1 Chain: "F" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 693 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 83} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "C" Number of atoms: 5902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5902 Classifications: {'peptide': 720} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 701} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 679 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 5902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5902 Classifications: {'peptide': 720} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 701} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 402 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 4, 'ARG:plan': 3, 'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 96 Chain: "H" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "I" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 735 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 7, 'TRANS': 85} Chain breaks: 1 Chain: "K" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 400 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 203 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 4, 'ARG:plan': 3, 'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 96 Chain: "A" Number of atoms: 4929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4929 Classifications: {'peptide': 627} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 4929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4929 Classifications: {'peptide': 627} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1009 SG CYS F 53 82.496 16.118 141.942 1.00128.53 S ATOM 1032 SG CYS F 56 82.735 15.286 145.724 1.00129.23 S ATOM 923 SG CYS F 42 80.086 21.002 138.718 1.00 88.33 S ATOM 942 SG CYS F 45 78.237 17.715 139.209 1.00 99.20 S ATOM 1237 SG CYS F 83 82.101 17.823 138.970 1.00 89.64 S ATOM 1166 SG CYS F 75 81.596 31.478 134.346 1.00 80.46 S ATOM 1329 SG CYS F 94 82.866 29.113 133.535 1.00 55.06 S ATOM 8353 SG CYS J 53 60.167 17.085 121.922 1.00136.80 S ATOM 8376 SG CYS J 56 57.834 15.374 119.569 1.00136.58 S ATOM 8460 SG CYS J 68 60.458 17.812 118.179 1.00146.43 S ATOM 8267 SG CYS J 42 63.831 22.037 125.579 1.00119.47 S ATOM 8286 SG CYS J 45 64.056 18.293 126.044 1.00114.32 S ATOM 8578 SG CYS J 83 60.602 19.949 125.669 1.00102.86 S ATOM 8510 SG CYS J 75 63.961 34.583 128.937 1.00106.72 S ATOM 8670 SG CYS J 94 64.204 31.224 129.785 1.00 83.97 S Time building chain proxies: 6.04, per 1000 atoms: 0.23 Number of scatterers: 26832 At special positions: 0 Unit cell: (145.14, 132.02, 263.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 6 29.99 S 180 16.00 O 5020 8.00 N 4677 7.00 C 16949 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN F 200 " pdb="ZN ZN F 200 " - pdb=" SG CYS F 56 " pdb="ZN ZN F 200 " - pdb=" ND1 HIS F 82 " 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 42 " pdb="ZN ZN F 201 " - pdb=" SG CYS F 45 " pdb="ZN ZN F 201 " - pdb=" SG CYS F 83 " 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 53 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 56 " 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 45 " pdb="ZN ZN J 201 " - pdb=" SG CYS J 83 " pdb=" ZN J 202 " pdb="ZN ZN J 202 " - pdb=" SG CYS J 94 " pdb="ZN ZN J 202 " - pdb=" SG CYS J 75 " pdb="ZN ZN J 202 " - pdb=" ND1 HIS J 77 " 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: 150 helices and 15 sheets defined 58.9% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'D' and resid 23 through 36 removed outlier: 3.603A pdb=" N LEU D 27 " --> pdb=" O THR D 23 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE D 34 " --> pdb=" O ILE D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 42 Processing helix chain 'F' and resid 81 through 88 Processing helix chain 'B' and resid 33 through 37 Processing helix chain 'B' and resid 39 through 47 Processing helix chain 'B' and resid 66 through 83 removed outlier: 3.636A pdb=" N LEU B 70 " --> pdb=" O PRO B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 110 removed outlier: 4.348A pdb=" N LEU B 101 " --> pdb=" O PRO B 97 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU B 102 " --> pdb=" O GLU B 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 26 removed outlier: 4.492A pdb=" N THR C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA C 23 " --> pdb=" O THR C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 47 removed outlier: 3.639A pdb=" N PHE C 39 " --> pdb=" O TRP C 35 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER C 40 " --> pdb=" O ASN C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 79 removed outlier: 3.598A pdb=" N SER C 79 " --> pdb=" O ARG C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 105 removed outlier: 3.927A pdb=" N LYS C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) removed outlier: 3.704A 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 151 Processing helix chain 'C' and resid 156 through 173 Processing helix chain 'C' and resid 177 through 190 removed outlier: 3.530A pdb=" N PHE C 188 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL C 189 " --> pdb=" O ILE C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 207 removed outlier: 3.659A pdb=" N GLU C 205 " --> pdb=" O LYS C 201 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE C 207 " --> pdb=" O TYR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 230 removed outlier: 4.070A pdb=" N GLN C 228 " --> pdb=" O SER C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 252 removed outlier: 3.793A pdb=" N MET C 236 " --> pdb=" O CYS C 232 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU C 237 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG C 251 " --> pdb=" O GLU C 247 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS C 252 " --> pdb=" O ILE C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 257 No H-bonds generated for 'chain 'C' and resid 255 through 257' Processing helix chain 'C' and resid 258 through 271 removed outlier: 3.758A pdb=" N VAL C 262 " --> pdb=" O SER C 258 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE C 263 " --> pdb=" O TYR C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 288 removed outlier: 3.812A pdb=" N GLU C 281 " --> pdb=" O PHE C 277 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N HIS C 283 " --> pdb=" O HIS C 279 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASN C 284 " --> pdb=" O ALA C 280 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE C 286 " --> pdb=" O CYS C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 304 removed outlier: 3.812A pdb=" N ALA C 303 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 327 removed outlier: 4.091A pdb=" N MET C 311 " --> pdb=" O GLY C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 333 No H-bonds generated for 'chain 'C' and resid 331 through 333' Processing helix chain 'C' and resid 334 through 359 removed outlier: 3.560A pdb=" N LEU C 338 " --> pdb=" O ASN C 334 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN C 355 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 3.603A 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: 4.282A pdb=" N THR C 420 " --> pdb=" O THR C 416 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL C 421 " --> pdb=" O SER C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 426 No H-bonds generated for 'chain 'C' and resid 424 through 426' Processing helix chain 'C' and resid 427 through 445 removed outlier: 3.784A pdb=" N PHE C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS C 441 " --> pdb=" O ARG C 437 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS C 445 " --> pdb=" O LYS C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 466 removed outlier: 4.029A pdb=" N LYS C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN C 463 " --> pdb=" O ASN C 459 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA C 464 " --> pdb=" O LYS C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 496 removed outlier: 3.525A pdb=" N ASP C 479 " --> pdb=" O ARG C 475 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET C 480 " --> pdb=" O MET C 476 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER C 481 " --> pdb=" O TYR C 477 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ASP C 485 " --> pdb=" O SER C 481 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN C 492 " --> pdb=" O ASN C 488 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N PHE C 493 " --> pdb=" O LYS C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 548 removed outlier: 3.792A pdb=" N VAL C 537 " --> pdb=" O LEU C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 587 removed outlier: 3.894A pdb=" N VAL C 584 " --> pdb=" O TYR C 580 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LEU C 585 " --> pdb=" O GLN C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 590 No H-bonds generated for 'chain 'C' and resid 588 through 590' Processing helix chain 'C' and resid 595 through 603 removed outlier: 3.672A pdb=" N ASP C 601 " --> pdb=" O LYS C 597 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER C 602 " --> pdb=" O GLU C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 620 Processing helix chain 'C' and resid 664 through 692 removed outlier: 3.598A pdb=" N THR C 668 " --> pdb=" O GLU C 664 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG C 669 " --> pdb=" O MET C 665 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N SER C 670 " --> pdb=" O GLU C 666 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL C 685 " --> pdb=" O GLN C 681 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ARG C 686 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N MET C 688 " --> pdb=" O ILE C 684 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS C 689 " --> pdb=" O VAL C 685 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ALA C 690 " --> pdb=" O ARG C 686 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ARG C 691 " --> pdb=" O ILE C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 695 through 707 removed outlier: 3.559A pdb=" N ILE C 700 " --> pdb=" O HIS C 696 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLN C 701 " --> pdb=" O ASN C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 728 removed outlier: 3.772A pdb=" N GLU C 723 " --> pdb=" O LYS C 719 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 724 " --> pdb=" O LYS C 720 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 725 " --> pdb=" O CYS C 721 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP C 727 " --> pdb=" O GLU C 723 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS C 728 " --> pdb=" O VAL C 724 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 58 Processing helix chain 'J' and resid 80 through 91 removed outlier: 3.864A pdb=" N THR J 90 " --> pdb=" O ARG J 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 25 removed outlier: 3.667A pdb=" N THR E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ALA E 23 " --> pdb=" O THR E 19 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL E 25 " --> pdb=" O ILE E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 47 removed outlier: 3.500A pdb=" N ASP E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE E 39 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N SER E 40 " --> pdb=" O ASN E 36 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP E 41 " --> pdb=" O ASP E 37 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ALA E 44 " --> pdb=" O SER E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 79 Processing helix chain 'E' and resid 82 through 105 removed outlier: 4.212A pdb=" N GLU E 93 " --> pdb=" O ARG E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 112 removed outlier: 3.865A pdb=" N PHE E 112 " --> pdb=" O LEU E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 145 removed outlier: 3.565A pdb=" N LEU E 144 " --> pdb=" O GLY E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 173 Processing helix chain 'E' and resid 177 through 192 removed outlier: 3.552A pdb=" N ASN E 186 " --> pdb=" O HIS E 182 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL E 189 " --> pdb=" O ILE E 185 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU E 192 " --> pdb=" O PHE E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 206 Processing helix chain 'E' and resid 207 through 230 removed outlier: 4.040A pdb=" N GLN E 228 " --> pdb=" O SER E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 254 removed outlier: 4.102A pdb=" N MET E 236 " --> pdb=" O CYS E 232 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU E 237 " --> pdb=" O SER E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 257 No H-bonds generated for 'chain 'E' and resid 255 through 257' Processing helix chain 'E' and resid 258 through 271 removed outlier: 3.740A pdb=" N VAL E 262 " --> pdb=" O SER E 258 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE E 263 " --> pdb=" O TYR E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 288 removed outlier: 4.297A pdb=" N HIS E 283 " --> pdb=" O HIS E 279 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ASN E 284 " --> pdb=" O ALA E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 302 Processing helix chain 'E' and resid 307 through 327 removed outlier: 4.190A 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 376 Processing helix chain 'E' and resid 386 through 400 removed outlier: 3.963A pdb=" N LEU E 390 " --> pdb=" O LYS E 386 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS E 400 " --> pdb=" O ASP E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 423 Processing helix chain 'E' and resid 427 through 443 removed outlier: 3.608A pdb=" N PHE E 431 " --> pdb=" O ASP E 427 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS E 441 " --> pdb=" O ARG E 437 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG E 442 " --> pdb=" O MET E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 450 through 465 removed outlier: 3.791A pdb=" N GLN E 463 " --> pdb=" O ASN E 459 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA E 464 " --> pdb=" O LYS E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 495 removed outlier: 3.794A pdb=" N MET E 476 " --> pdb=" O LYS E 472 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR E 477 " --> pdb=" O LEU E 473 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP E 479 " --> pdb=" O ARG E 475 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N VAL E 482 " --> pdb=" O THR E 478 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA E 484 " --> pdb=" O MET E 480 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ASP E 485 " --> pdb=" O SER E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 547 Processing helix chain 'E' and resid 556 through 559 removed outlier: 3.955A pdb=" N LEU E 559 " --> pdb=" O LEU E 556 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 556 through 559' Processing helix chain 'E' and resid 579 through 591 removed outlier: 3.746A pdb=" N VAL E 584 " --> pdb=" O TYR E 580 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER E 591 " --> pdb=" O ALA E 587 " (cutoff:3.500A) Processing helix chain 'E' and resid 596 through 604 removed outlier: 3.978A pdb=" N ASP E 601 " --> pdb=" O LYS E 597 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER E 602 " --> pdb=" O GLU E 598 " (cutoff:3.500A) Processing helix chain 'E' and resid 606 through 620 removed outlier: 3.880A pdb=" N LYS E 612 " --> pdb=" O LYS E 608 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL E 620 " --> pdb=" O SER E 616 " (cutoff:3.500A) Processing helix chain 'E' and resid 664 through 689 removed outlier: 4.399A pdb=" N VAL E 685 " --> pdb=" O GLN E 681 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ARG E 686 " --> pdb=" O ALA E 682 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ILE E 687 " --> pdb=" O ALA E 683 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET E 688 " --> pdb=" O ILE E 684 " (cutoff:3.500A) Processing helix chain 'E' and resid 695 through 707 removed outlier: 3.981A pdb=" N ILE E 700 " --> pdb=" O HIS E 696 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN E 701 " --> pdb=" O ASN E 697 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU E 702 " --> pdb=" O ALA E 698 " (cutoff:3.500A) Processing helix chain 'E' and resid 714 through 723 removed outlier: 3.559A pdb=" N LYS E 719 " --> pdb=" O ILE E 715 " (cutoff:3.500A) Processing helix chain 'E' and resid 723 through 728 removed outlier: 3.506A pdb=" N ASP E 727 " --> pdb=" O GLU E 723 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 33 removed outlier: 4.489A pdb=" N GLU N 28 " --> pdb=" O GLU N 24 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG N 29 " --> pdb=" O ARG N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 41 removed outlier: 3.878A pdb=" N GLN N 41 " --> pdb=" O PRO N 38 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 59 Processing helix chain 'H' and resid 33 through 37 Processing helix chain 'H' and resid 39 through 47 removed outlier: 3.663A pdb=" N ALA H 44 " --> pdb=" O GLY H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 84 removed outlier: 3.746A pdb=" N LEU H 70 " --> pdb=" O PRO H 66 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER H 71 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS H 72 " --> pdb=" O HIS H 68 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG H 82 " --> pdb=" O THR H 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 28 removed outlier: 3.782A pdb=" N LEU I 27 " --> pdb=" O THR I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 36 removed outlier: 3.856A pdb=" N GLU I 32 " --> pdb=" O LYS I 28 " (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 'I' and resid 56 through 60 removed outlier: 3.518A pdb=" N GLU I 59 " --> pdb=" O THR I 56 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N CYS I 60 " --> pdb=" O LEU I 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 56 through 60' Processing helix chain 'K' and resid 22 through 31 removed outlier: 3.883A pdb=" N GLU K 31 " --> pdb=" O LYS K 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 15 removed outlier: 3.585A pdb=" N GLY A 6 " --> pdb=" O GLU A 2 " (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: 4.412A 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 removed outlier: 3.604A pdb=" N VAL A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 164 Processing helix chain 'A' and resid 166 through 176 removed outlier: 3.574A pdb=" N VAL A 170 " --> pdb=" O HIS A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 198 removed outlier: 3.509A pdb=" N GLU A 196 " --> pdb=" O HIS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 209 Processing helix chain 'A' and resid 221 through 229 removed outlier: 3.520A pdb=" N ALA A 226 " --> pdb=" O PRO A 222 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 239 removed outlier: 3.643A pdb=" N GLU A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 237 " --> pdb=" O ASP A 233 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU A 239 " --> pdb=" O VAL A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 262 removed outlier: 3.632A pdb=" N GLY A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 284 removed outlier: 3.738A pdb=" N TYR A 273 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 276 " --> pdb=" O THR A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 316 removed outlier: 3.769A pdb=" N LEU A 314 " --> pdb=" O ASN A 310 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 315 " --> pdb=" O PRO A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 337 removed outlier: 3.621A pdb=" N HIS A 325 " --> pdb=" O ARG A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 357 removed outlier: 4.056A pdb=" N ILE A 347 " --> pdb=" O VAL A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 377 Processing helix chain 'A' and resid 381 through 398 removed outlier: 3.734A pdb=" N LEU A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 428 removed outlier: 3.690A pdb=" N LEU A 416 " --> pdb=" O ARG A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 456 removed outlier: 3.698A pdb=" N LYS A 456 " --> pdb=" O CYS A 452 " (cutoff:3.500A) 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: 4.531A pdb=" N ILE A 555 " --> pdb=" O THR A 551 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 593 Processing helix chain 'A' and resid 596 through 609 Processing helix chain 'A' and resid 617 through 627 Processing helix chain 'G' and resid 2 through 15 removed outlier: 3.695A pdb=" N GLY G 6 " --> pdb=" O GLU G 2 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR G 7 " --> pdb=" O GLY G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 25 Processing helix chain 'G' and resid 28 through 36 Processing helix chain 'G' and resid 48 through 56 removed outlier: 3.564A pdb=" N ALA G 53 " --> pdb=" O PRO G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 68 removed outlier: 3.669A pdb=" N HIS G 68 " --> pdb=" O LEU G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 98 Processing helix chain 'G' and resid 100 through 111 removed outlier: 3.508A pdb=" N VAL G 104 " --> pdb=" O HIS G 100 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS G 105 " --> pdb=" O PHE G 101 " (cutoff:3.500A) removed outlier: 4.638A 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 removed outlier: 3.623A pdb=" N ILE G 160 " --> pdb=" O THR G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 176 Processing helix chain 'G' and resid 189 through 198 Processing helix chain 'G' and resid 199 through 209 Processing helix chain 'G' and resid 221 through 229 Processing helix chain 'G' and resid 231 through 239 removed outlier: 3.774A pdb=" N GLU G 236 " --> pdb=" O ALA G 232 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU G 237 " --> pdb=" O ASP G 233 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU G 238 " --> pdb=" O VAL G 234 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU G 239 " --> pdb=" O VAL G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 262 removed outlier: 3.591A pdb=" N ASN G 262 " --> pdb=" O ALA G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 284 removed outlier: 3.849A pdb=" N TYR G 273 " --> pdb=" O ILE G 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 310 through 317 removed outlier: 3.909A pdb=" N LEU G 314 " --> pdb=" O ASN G 310 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE G 317 " --> pdb=" O GLU G 313 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 337 removed outlier: 3.532A pdb=" N HIS G 325 " --> pdb=" O ARG G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 343 through 357 removed outlier: 4.093A pdb=" N ILE G 347 " --> pdb=" O VAL G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 377 Processing helix chain 'G' and resid 381 through 398 removed outlier: 3.861A pdb=" N LEU G 385 " --> pdb=" O THR G 381 " (cutoff:3.500A) Processing helix chain 'G' and resid 403 through 428 removed outlier: 3.584A pdb=" N GLU G 417 " --> pdb=" O CYS G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 429 through 457 removed outlier: 4.273A pdb=" N HIS G 434 " --> pdb=" O ASP G 430 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ASN G 435 " --> pdb=" O ALA G 431 " (cutoff:3.500A) Processing helix chain 'G' and resid 460 through 477 removed outlier: 3.708A pdb=" N LYS G 466 " --> pdb=" O GLU G 462 " (cutoff:3.500A) Processing helix chain 'G' and resid 486 through 492 Processing helix chain 'G' and resid 502 through 506 Processing helix chain 'G' and resid 511 through 521 removed outlier: 3.594A pdb=" N THR G 515 " --> pdb=" O ASN G 511 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS G 521 " --> pdb=" O LEU G 517 " (cutoff:3.500A) Processing helix chain 'G' and resid 535 through 540 removed outlier: 3.578A pdb=" N ILE G 539 " --> pdb=" O ALA G 535 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL G 540 " --> pdb=" O LEU G 536 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 535 through 540' Processing helix chain 'G' and resid 548 through 563 removed outlier: 3.559A pdb=" N SER G 558 " --> pdb=" O SER G 554 " (cutoff:3.500A) Processing helix chain 'G' and resid 582 through 593 removed outlier: 4.168A pdb=" N ILE G 587 " --> pdb=" O GLY G 583 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS G 590 " --> pdb=" O GLU G 586 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN G 592 " --> pdb=" O LEU G 588 " (cutoff:3.500A) Processing helix chain 'G' and resid 598 through 603 Processing helix chain 'G' and resid 617 through 627 removed outlier: 3.730A pdb=" N GLU G 622 " --> pdb=" O ARG G 618 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE G 623 " --> pdb=" O THR G 619 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 49 through 50 removed outlier: 3.749A pdb=" N ALA D 73 " --> pdb=" O PHE D 4 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LYS B 32 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 10.650A pdb=" N ASP D 17 " --> pdb=" O LYS B 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 24 through 28 removed outlier: 5.505A pdb=" N VAL F 24 " --> pdb=" O LYS E 565 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N LYS E 565 " --> pdb=" O VAL F 24 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR E 561 " --> pdb=" O ASN F 28 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 510 through 513 removed outlier: 6.052A pdb=" N ALA F 31 " --> pdb=" O LEU E 512 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 70 through 71 removed outlier: 3.558A pdb=" N PHE F 79 " --> pdb=" O ALA F 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 508 through 513 removed outlier: 4.203A pdb=" N GLN C 508 " --> pdb=" O TRP J 27 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA J 29 " --> pdb=" O GLN C 508 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA J 31 " --> pdb=" O TYR C 510 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 508 through 513 removed outlier: 4.203A pdb=" N GLN C 508 " --> pdb=" O TRP J 27 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA J 29 " --> pdb=" O GLN C 508 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA J 31 " --> pdb=" O TYR C 510 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N VAL J 24 " --> pdb=" O LYS C 565 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LYS C 565 " --> pdb=" O VAL J 24 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS J 26 " --> pdb=" O GLU C 563 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 593 through 594 Processing sheet with id=AA8, first strand: chain 'J' and resid 41 through 42 Processing sheet with id=AA9, first strand: chain 'E' and resid 594 through 595 removed outlier: 3.541A pdb=" N SER E 639 " --> pdb=" O ASN E 624 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 731 through 733 Processing sheet with id=AB2, first strand: chain 'H' and resid 59 through 61 removed outlier: 8.350A pdb=" N VAL H 60 " --> pdb=" O TYR H 18 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LYS H 20 " --> pdb=" O VAL H 60 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR I 13 " --> pdb=" O GLU H 28 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS H 32 " --> pdb=" O PHE I 15 " (cutoff:3.500A) removed outlier: 9.594A pdb=" N ASP I 17 " --> pdb=" O LYS H 32 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR I 16 " --> pdb=" O LEU I 5 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU I 5 " --> pdb=" O THR I 16 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA I 73 " --> pdb=" O PHE I 4 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 40 through 42 removed outlier: 3.634A pdb=" N SER A 47 " --> pdb=" O SER A 40 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 77 through 80 removed outlier: 3.986A pdb=" N GLY A 77 " --> pdb=" O GLY A 88 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 40 through 41 Processing sheet with id=AB6, first strand: chain 'G' and resid 77 through 81 removed outlier: 4.835A pdb=" N GLY G 77 " --> pdb=" O GLY G 88 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY G 88 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR G 84 " --> pdb=" O PHE G 81 " (cutoff:3.500A) 1317 hydrogen bonds defined for protein. 3882 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: 4.90 Time building geometry restraints manager: 3.03 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: 8942 1.34 - 1.46: 5875 1.46 - 1.58: 12234 1.58 - 1.70: 0 1.70 - 1.82: 280 Bond restraints: 27331 Sorted by residual: bond pdb=" C LEU E 308 " pdb=" N PRO E 309 " ideal model delta sigma weight residual 1.334 1.369 -0.035 1.51e-02 4.39e+03 5.33e+00 bond pdb=" C GLU C 153 " pdb=" N PRO C 154 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.30e-02 5.92e+03 2.62e+00 bond pdb=" CB ASP C 498 " pdb=" CG ASP C 498 " ideal model delta sigma weight residual 1.516 1.556 -0.040 2.50e-02 1.60e+03 2.55e+00 bond pdb=" C LYS E 571 " pdb=" N PRO E 572 " ideal model delta sigma weight residual 1.332 1.348 -0.016 1.12e-02 7.97e+03 1.99e+00 bond pdb=" N SER C 636 " pdb=" CA SER C 636 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.47e+00 ... (remaining 27326 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.46: 36848 3.46 - 6.93: 107 6.93 - 10.39: 4 10.39 - 13.86: 3 13.86 - 17.32: 1 Bond angle restraints: 36963 Sorted by residual: angle pdb=" N VAL E 376 " pdb=" CA VAL E 376 " pdb=" C VAL E 376 " ideal model delta sigma weight residual 111.91 108.03 3.88 8.90e-01 1.26e+00 1.90e+01 angle pdb=" C SER G 122 " pdb=" N THR G 123 " pdb=" CA THR G 123 " ideal model delta sigma weight residual 120.69 133.22 -12.53 2.95e+00 1.15e-01 1.80e+01 angle pdb=" C ASP A 245 " pdb=" CA ASP A 245 " pdb=" CB ASP A 245 " ideal model delta sigma weight residual 115.89 110.34 5.55 1.32e+00 5.74e-01 1.77e+01 angle pdb=" C HIS E 557 " pdb=" N TYR E 558 " pdb=" CA TYR E 558 " ideal model delta sigma weight residual 120.82 126.56 -5.74 1.50e+00 4.44e-01 1.46e+01 angle pdb=" C LEU A 477 " pdb=" N ASP A 478 " pdb=" CA ASP A 478 " ideal model delta sigma weight residual 121.80 130.50 -8.70 2.44e+00 1.68e-01 1.27e+01 ... (remaining 36958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 14730 17.66 - 35.31: 1541 35.31 - 52.97: 249 52.97 - 70.63: 46 70.63 - 88.28: 31 Dihedral angle restraints: 16597 sinusoidal: 6586 harmonic: 10011 Sorted by residual: dihedral pdb=" CA LEU E 142 " pdb=" C LEU E 142 " pdb=" N ALA E 143 " pdb=" CA ALA E 143 " ideal model delta harmonic sigma weight residual 180.00 152.78 27.22 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA VAL E 376 " pdb=" C VAL E 376 " pdb=" N ASN E 377 " pdb=" CA ASN E 377 " ideal model delta harmonic sigma weight residual 180.00 157.99 22.01 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA SER C 506 " pdb=" C SER C 506 " pdb=" N PHE C 507 " pdb=" CA PHE C 507 " ideal model delta harmonic sigma weight residual -180.00 -161.10 -18.90 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 16594 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3443 0.054 - 0.108: 661 0.108 - 0.162: 72 0.162 - 0.216: 1 0.216 - 0.270: 2 Chirality restraints: 4179 Sorted by residual: chirality pdb=" CB THR C 306 " pdb=" CA THR C 306 " pdb=" OG1 THR C 306 " pdb=" CG2 THR C 306 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.82e+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 2.39 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CB VAL E 271 " pdb=" CA VAL E 271 " pdb=" CG1 VAL E 271 " pdb=" CG2 VAL E 271 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.16 2.00e-01 2.50e+01 6.77e-01 ... (remaining 4176 not shown) Planarity restraints: 4762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 65 " 0.035 5.00e-02 4.00e+02 5.28e-02 4.47e+00 pdb=" N PRO B 66 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 66 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 66 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 255 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO C 256 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 256 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 256 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 308 " -0.030 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO E 309 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO E 309 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 309 " -0.026 5.00e-02 4.00e+02 ... (remaining 4759 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 362 2.65 - 3.21: 26049 3.21 - 3.77: 44267 3.77 - 4.34: 58291 4.34 - 4.90: 91660 Nonbonded interactions: 220629 Sorted by model distance: nonbonded pdb=" OD1 ASP J 97 " pdb="ZN ZN J 202 " model vdw 2.082 2.230 nonbonded pdb=" OH TYR G 542 " pdb=" OD2 ASP G 548 " model vdw 2.116 3.040 nonbonded pdb=" OH TYR B 79 " pdb=" O PRO B 91 " model vdw 2.151 3.040 nonbonded pdb=" OD2 ASP A 263 " pdb=" ND2 ASN A 266 " model vdw 2.155 3.120 nonbonded pdb=" OD1 ASP G 384 " pdb=" NH2 ARG G 387 " model vdw 2.177 3.120 ... (remaining 220624 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'I' } ncs_group { reference = (chain 'F' and (resid 22 through 75 or (resid 76 and (name N or name CA or name \ C or name O or name CB )) or resid 77 through 202)) selection = chain 'J' } ncs_group { reference = chain 'K' selection = (chain 'N' and (resid 1 through 37 or (resid 38 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 76)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 27.700 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 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 0.049 27352 Z= 0.142 Angle : 0.603 17.323 36972 Z= 0.318 Chirality : 0.042 0.270 4179 Planarity : 0.004 0.059 4762 Dihedral : 14.754 88.285 10087 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.03 % Allowed : 0.31 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.14), residues: 3357 helix: 0.07 (0.12), residues: 1802 sheet: -2.64 (0.57), residues: 61 loop : -1.22 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 68 TYR 0.019 0.001 TYR C 510 PHE 0.021 0.001 PHE E 202 TRP 0.018 0.002 TRP F 27 HIS 0.010 0.001 HIS G 537 Details of bonding type rmsd covalent geometry : bond 0.00305 (27331) covalent geometry : angle 0.60180 (36963) hydrogen bonds : bond 0.22986 ( 1314) hydrogen bonds : angle 7.40413 ( 3882) metal coordination : bond 0.00773 ( 21) metal coordination : angle 2.25703 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 558 time to evaluate : 1.055 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 43 ARG cc_start: 0.7997 (mpt90) cc_final: 0.7730 (mtm-85) REVERT: F 25 LYS cc_start: 0.7983 (mmtt) cc_final: 0.7684 (mmmt) REVERT: B 33 ARG cc_start: 0.8539 (ttm-80) cc_final: 0.8281 (ttm110) REVERT: B 42 ILE cc_start: 0.8830 (mm) cc_final: 0.8585 (mt) REVERT: B 43 LYS cc_start: 0.9164 (ttmt) cc_final: 0.8644 (tptt) REVERT: B 73 VAL cc_start: 0.9495 (p) cc_final: 0.9063 (p) REVERT: B 77 PHE cc_start: 0.8779 (m-10) cc_final: 0.8553 (m-80) REVERT: B 79 TYR cc_start: 0.8717 (t80) cc_final: 0.8117 (t80) REVERT: B 105 MET cc_start: 0.9123 (mtt) cc_final: 0.8842 (mtt) REVERT: C 99 ASP cc_start: 0.8393 (m-30) cc_final: 0.8091 (p0) REVERT: C 102 ASP cc_start: 0.7536 (t0) cc_final: 0.6507 (t70) REVERT: C 179 LYS cc_start: 0.9125 (ttpp) cc_final: 0.8908 (tppt) REVERT: C 390 LEU cc_start: 0.8765 (mt) cc_final: 0.8475 (mt) REVERT: C 465 CYS cc_start: 0.8450 (m) cc_final: 0.8231 (m) REVERT: C 642 MET cc_start: 0.6394 (tpt) cc_final: 0.6031 (mmm) REVERT: C 665 MET cc_start: 0.1000 (tpp) cc_final: -0.1065 (ptt) REVERT: C 708 ARG cc_start: 0.8035 (ppt170) cc_final: 0.7409 (tpp-160) REVERT: E 355 ASN cc_start: 0.8035 (t0) cc_final: 0.7482 (t0) REVERT: E 622 MET cc_start: 0.6863 (mmp) cc_final: 0.6597 (tpt) REVERT: H 28 GLU cc_start: 0.7568 (pm20) cc_final: 0.7077 (pm20) REVERT: H 37 LEU cc_start: 0.9016 (tp) cc_final: 0.8747 (tp) REVERT: H 67 SER cc_start: 0.6568 (m) cc_final: 0.6203 (t) REVERT: H 81 VAL cc_start: 0.8439 (m) cc_final: 0.8153 (p) REVERT: H 102 GLU cc_start: 0.8537 (tp30) cc_final: 0.7905 (mm-30) REVERT: I 65 GLN cc_start: 0.8389 (mm110) cc_final: 0.8168 (tp40) REVERT: A 310 ASN cc_start: 0.7744 (m110) cc_final: 0.7258 (m-40) REVERT: A 321 ARG cc_start: 0.5630 (ttt90) cc_final: 0.5356 (mtp85) REVERT: G 315 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7893 (pt0) REVERT: G 358 MET cc_start: 0.4892 (mmp) cc_final: 0.2925 (mtp) REVERT: G 430 ASP cc_start: 0.7693 (t0) cc_final: 0.6755 (p0) REVERT: G 536 LEU cc_start: 0.8687 (tp) cc_final: 0.8477 (tt) REVERT: G 569 THR cc_start: 0.8499 (m) cc_final: 0.8173 (p) outliers start: 1 outliers final: 0 residues processed: 559 average time/residue: 0.1970 time to fit residues: 169.3961 Evaluate side-chains 321 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 197 optimal weight: 0.1980 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 50.0000 chunk 298 optimal weight: 4.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 28 ASN F 48 HIS C 156 GLN C 182 HIS C 497 GLN C 581 GLN C 667 GLN E 36 ASN E 73 HIS E 178 GLN ** E 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 663 GLN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 ASN A 310 ASN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 325 HIS G 340 ASN ** G 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 423 ASN G 435 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.150868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.121482 restraints weight = 88121.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.121657 restraints weight = 123877.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.119754 restraints weight = 94417.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.118525 restraints weight = 83586.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.118905 restraints weight = 77229.089| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 27352 Z= 0.198 Angle : 0.649 14.279 36972 Z= 0.344 Chirality : 0.043 0.245 4179 Planarity : 0.005 0.139 4762 Dihedral : 4.908 80.380 3674 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.17 % Allowed : 6.18 % Favored : 93.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.14), residues: 3357 helix: 0.18 (0.12), residues: 1883 sheet: -2.12 (0.56), residues: 63 loop : -1.27 (0.17), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 9 TYR 0.027 0.002 TYR H 79 PHE 0.038 0.002 PHE A 485 TRP 0.034 0.002 TRP A 93 HIS 0.016 0.001 HIS N 68 Details of bonding type rmsd covalent geometry : bond 0.00434 (27331) covalent geometry : angle 0.64890 (36963) hydrogen bonds : bond 0.05344 ( 1314) hydrogen bonds : angle 5.31709 ( 3882) metal coordination : bond 0.01040 ( 21) metal coordination : angle 1.77920 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 434 time to evaluate : 1.087 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 25 LYS cc_start: 0.8366 (mmtt) cc_final: 0.8051 (mttp) REVERT: B 43 LYS cc_start: 0.9093 (ttmt) cc_final: 0.8716 (tptt) REVERT: B 73 VAL cc_start: 0.9056 (p) cc_final: 0.8690 (p) REVERT: C 103 CYS cc_start: 0.8559 (m) cc_final: 0.8252 (m) REVERT: C 390 LEU cc_start: 0.8680 (mt) cc_final: 0.8288 (mp) REVERT: C 566 MET cc_start: 0.2792 (mpp) cc_final: 0.2443 (mpp) REVERT: C 651 PHE cc_start: 0.5785 (p90) cc_final: 0.5539 (p90) REVERT: C 665 MET cc_start: 0.1828 (tpp) cc_final: -0.0603 (ptt) REVERT: C 667 GLN cc_start: 0.5168 (OUTLIER) cc_final: 0.4731 (pm20) REVERT: C 708 ARG cc_start: 0.7790 (ppt170) cc_final: 0.7512 (tpp-160) REVERT: E 78 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7644 (pt0) REVERT: E 355 ASN cc_start: 0.8264 (t0) cc_final: 0.7668 (t0) REVERT: E 487 ASN cc_start: 0.7847 (m-40) cc_final: 0.6191 (m110) REVERT: E 607 GLU cc_start: 0.8109 (mp0) cc_final: 0.7844 (mp0) REVERT: E 622 MET cc_start: 0.6467 (mmp) cc_final: 0.6207 (tpt) REVERT: H 28 GLU cc_start: 0.7545 (pm20) cc_final: 0.7291 (pm20) REVERT: H 37 LEU cc_start: 0.8948 (tp) cc_final: 0.8410 (tt) REVERT: H 39 SER cc_start: 0.9076 (t) cc_final: 0.8574 (p) REVERT: H 67 SER cc_start: 0.6406 (m) cc_final: 0.6158 (m) REVERT: H 68 HIS cc_start: 0.7862 (p-80) cc_final: 0.7593 (p90) REVERT: H 75 MET cc_start: 0.8023 (mtm) cc_final: 0.7816 (mtt) REVERT: H 90 ILE cc_start: 0.9271 (pt) cc_final: 0.9004 (pt) REVERT: H 102 GLU cc_start: 0.8469 (tp30) cc_final: 0.7721 (mm-30) REVERT: A 437 MET cc_start: 0.7543 (mmm) cc_final: 0.7231 (mmm) outliers start: 5 outliers final: 0 residues processed: 439 average time/residue: 0.1885 time to fit residues: 129.0387 Evaluate side-chains 309 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 308 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 45 optimal weight: 4.9990 chunk 221 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 19 optimal weight: 0.4980 chunk 197 optimal weight: 0.9980 chunk 192 optimal weight: 0.0980 chunk 222 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 259 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 10 HIS F 48 HIS B 58 ASN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN C 581 GLN E 36 ASN E 73 HIS E 111 GLN ** E 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 ASN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 611 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.152870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.127036 restraints weight = 88423.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.124423 restraints weight = 117752.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.121802 restraints weight = 87767.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.122195 restraints weight = 85489.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.121760 restraints weight = 66824.399| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27352 Z= 0.142 Angle : 0.613 13.193 36972 Z= 0.318 Chirality : 0.042 0.205 4179 Planarity : 0.005 0.136 4762 Dihedral : 4.776 79.456 3674 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.10 % Allowed : 4.38 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.14), residues: 3357 helix: 0.33 (0.12), residues: 1882 sheet: -2.41 (0.57), residues: 60 loop : -1.23 (0.17), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 32 TYR 0.034 0.002 TYR E 743 PHE 0.055 0.002 PHE B 77 TRP 0.030 0.002 TRP G 209 HIS 0.012 0.001 HIS N 68 Details of bonding type rmsd covalent geometry : bond 0.00308 (27331) covalent geometry : angle 0.61282 (36963) hydrogen bonds : bond 0.04730 ( 1314) hydrogen bonds : angle 4.93697 ( 3882) metal coordination : bond 0.00975 ( 21) metal coordination : angle 1.65544 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 421 time to evaluate : 1.057 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 25 LYS cc_start: 0.8163 (mmtt) cc_final: 0.7886 (mmmt) REVERT: B 34 GLU cc_start: 0.8180 (tp30) cc_final: 0.7906 (tp30) REVERT: B 43 LYS cc_start: 0.9104 (ttmt) cc_final: 0.8687 (tptt) REVERT: C 319 ILE cc_start: 0.8848 (mm) cc_final: 0.8328 (mm) REVERT: C 390 LEU cc_start: 0.8586 (mt) cc_final: 0.8202 (mp) REVERT: C 566 MET cc_start: 0.2626 (mpp) cc_final: 0.2258 (mpp) REVERT: C 576 MET cc_start: 0.5988 (mmp) cc_final: 0.5452 (mmt) REVERT: C 665 MET cc_start: 0.1846 (tpp) cc_final: -0.0401 (ptt) REVERT: C 708 ARG cc_start: 0.7794 (ppt170) cc_final: 0.7503 (tpp-160) REVERT: E 146 MET cc_start: 0.8529 (ttp) cc_final: 0.7505 (tmm) REVERT: E 355 ASN cc_start: 0.8265 (t0) cc_final: 0.7581 (t0) REVERT: E 443 LEU cc_start: 0.8481 (mt) cc_final: 0.8243 (mt) REVERT: E 477 TYR cc_start: 0.8022 (t80) cc_final: 0.6487 (t80) REVERT: E 622 MET cc_start: 0.6481 (mmp) cc_final: 0.6152 (tpt) REVERT: H 28 GLU cc_start: 0.7408 (pm20) cc_final: 0.7093 (pm20) REVERT: H 30 ILE cc_start: 0.8812 (mm) cc_final: 0.8595 (mm) REVERT: H 75 MET cc_start: 0.8034 (mtm) cc_final: 0.7641 (mtt) REVERT: H 102 GLU cc_start: 0.8364 (tp30) cc_final: 0.7535 (mm-30) REVERT: G 358 MET cc_start: 0.4424 (mmp) cc_final: 0.3619 (mtp) REVERT: G 430 ASP cc_start: 0.6526 (t0) cc_final: 0.5882 (p0) outliers start: 3 outliers final: 0 residues processed: 423 average time/residue: 0.1592 time to fit residues: 107.0106 Evaluate side-chains 302 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 202 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 240 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 241 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 48 HIS ** B 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 ASN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 581 GLN E 36 ASN E 73 HIS ** E 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 487 ASN E 600 GLN ** E 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN A 116 HIS A 181 ASN A 420 GLN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 241 HIS ** G 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 476 HIS G 511 ASN G 530 ASN G 611 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.151357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.125361 restraints weight = 87592.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.120638 restraints weight = 120760.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.118577 restraints weight = 101306.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.118928 restraints weight = 88681.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.118340 restraints weight = 69697.358| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 27352 Z= 0.177 Angle : 0.624 11.957 36972 Z= 0.324 Chirality : 0.042 0.174 4179 Planarity : 0.004 0.101 4762 Dihedral : 4.773 79.144 3674 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.03 % Allowed : 3.68 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.14), residues: 3357 helix: 0.30 (0.12), residues: 1915 sheet: -2.35 (0.59), residues: 58 loop : -1.30 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 43 TYR 0.026 0.002 TYR C 510 PHE 0.031 0.002 PHE B 77 TRP 0.030 0.002 TRP A 93 HIS 0.020 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00398 (27331) covalent geometry : angle 0.62313 (36963) hydrogen bonds : bond 0.04391 ( 1314) hydrogen bonds : angle 4.87831 ( 3882) metal coordination : bond 0.00907 ( 21) metal coordination : angle 1.62924 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 389 time to evaluate : 1.149 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 25 LYS cc_start: 0.8069 (mmtt) cc_final: 0.7787 (mmmt) REVERT: B 43 LYS cc_start: 0.9129 (ttmt) cc_final: 0.8733 (tptt) REVERT: B 77 PHE cc_start: 0.8340 (m-80) cc_final: 0.8074 (m-80) REVERT: C 304 VAL cc_start: 0.8750 (t) cc_final: 0.8543 (t) REVERT: C 319 ILE cc_start: 0.8865 (mm) cc_final: 0.8300 (mm) REVERT: C 438 MET cc_start: 0.8674 (ptp) cc_final: 0.8430 (ptp) REVERT: C 566 MET cc_start: 0.2450 (mpp) cc_final: 0.2105 (mpp) REVERT: C 642 MET cc_start: 0.6640 (mmm) cc_final: 0.6253 (mmm) REVERT: C 665 MET cc_start: 0.1823 (tpp) cc_final: -0.0255 (ptt) REVERT: C 708 ARG cc_start: 0.7797 (ppt170) cc_final: 0.7511 (tpp-160) REVERT: J 36 ASP cc_start: 0.8313 (p0) cc_final: 0.7672 (t0) REVERT: E 74 LYS cc_start: 0.8693 (tmmt) cc_final: 0.8264 (ttmt) REVERT: E 146 MET cc_start: 0.8518 (ttp) cc_final: 0.7637 (tmm) REVERT: E 355 ASN cc_start: 0.8404 (t0) cc_final: 0.7615 (t0) REVERT: E 477 TYR cc_start: 0.8087 (t80) cc_final: 0.6864 (t80) REVERT: E 622 MET cc_start: 0.6658 (mmp) cc_final: 0.6287 (tpt) REVERT: H 28 GLU cc_start: 0.7488 (pm20) cc_final: 0.7157 (pm20) REVERT: H 75 MET cc_start: 0.8017 (mtm) cc_final: 0.7756 (mtt) REVERT: H 90 ILE cc_start: 0.9269 (pt) cc_final: 0.9027 (pt) REVERT: G 358 MET cc_start: 0.4471 (mmp) cc_final: 0.3527 (mtp) REVERT: G 430 ASP cc_start: 0.6439 (t0) cc_final: 0.5866 (p0) REVERT: G 437 MET cc_start: 0.8102 (tpp) cc_final: 0.7762 (tpp) outliers start: 1 outliers final: 1 residues processed: 390 average time/residue: 0.1797 time to fit residues: 111.8860 Evaluate side-chains 294 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 293 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 149 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 296 optimal weight: 20.0000 chunk 146 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 306 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 134 optimal weight: 0.8980 chunk 298 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 48 HIS ** B 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 581 GLN ** C 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN ** E 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN A 116 HIS G 75 GLN ** G 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 611 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.152169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.123194 restraints weight = 87957.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.122874 restraints weight = 108493.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.120338 restraints weight = 82745.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.119809 restraints weight = 81932.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.120254 restraints weight = 73367.453| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 27352 Z= 0.156 Angle : 0.623 12.008 36972 Z= 0.318 Chirality : 0.042 0.187 4179 Planarity : 0.004 0.074 4762 Dihedral : 4.768 79.246 3674 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.14), residues: 3357 helix: 0.34 (0.12), residues: 1912 sheet: -2.07 (0.63), residues: 60 loop : -1.32 (0.17), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 32 TYR 0.028 0.002 TYR E 477 PHE 0.032 0.002 PHE H 52 TRP 0.020 0.002 TRP A 93 HIS 0.015 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00351 (27331) covalent geometry : angle 0.62264 (36963) hydrogen bonds : bond 0.04155 ( 1314) hydrogen bonds : angle 4.72861 ( 3882) metal coordination : bond 0.00808 ( 21) metal coordination : angle 1.64081 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 1.221 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 25 LYS cc_start: 0.7975 (mmtt) cc_final: 0.7689 (mmmt) REVERT: B 43 LYS cc_start: 0.9119 (ttmt) cc_final: 0.8710 (tptt) REVERT: B 77 PHE cc_start: 0.8312 (m-80) cc_final: 0.8096 (m-80) REVERT: C 304 VAL cc_start: 0.8773 (t) cc_final: 0.8541 (t) REVERT: C 319 ILE cc_start: 0.8855 (mm) cc_final: 0.8311 (mm) REVERT: C 463 GLN cc_start: 0.8345 (tm-30) cc_final: 0.8122 (tm-30) REVERT: C 556 LEU cc_start: 0.8564 (mt) cc_final: 0.8317 (mt) REVERT: C 642 MET cc_start: 0.6555 (mmm) cc_final: 0.6157 (mmm) REVERT: C 651 PHE cc_start: 0.5731 (p90) cc_final: 0.5297 (p90) REVERT: C 665 MET cc_start: 0.1479 (tpp) cc_final: -0.0364 (ptt) REVERT: C 708 ARG cc_start: 0.7745 (ppt170) cc_final: 0.7492 (tpp-160) REVERT: J 33 TRP cc_start: 0.8508 (p-90) cc_final: 0.7783 (p-90) REVERT: J 36 ASP cc_start: 0.8227 (p0) cc_final: 0.7618 (t0) REVERT: E 74 LYS cc_start: 0.8691 (tmmt) cc_final: 0.8240 (ttmt) REVERT: E 146 MET cc_start: 0.8447 (ttp) cc_final: 0.7620 (tmm) REVERT: E 206 ILE cc_start: 0.8248 (mt) cc_final: 0.8011 (mt) REVERT: E 297 MET cc_start: 0.8181 (tpt) cc_final: 0.7895 (tpp) REVERT: E 355 ASN cc_start: 0.8454 (t0) cc_final: 0.7638 (t0) REVERT: E 622 MET cc_start: 0.6486 (mmp) cc_final: 0.6116 (tpt) REVERT: H 28 GLU cc_start: 0.7370 (pm20) cc_final: 0.6955 (pm20) REVERT: A 396 ILE cc_start: 0.8197 (tp) cc_final: 0.7937 (tp) REVERT: G 358 MET cc_start: 0.4330 (mmp) cc_final: 0.3316 (mtp) REVERT: G 430 ASP cc_start: 0.6281 (t0) cc_final: 0.5859 (p0) REVERT: G 437 MET cc_start: 0.8202 (tpp) cc_final: 0.7881 (tpp) outliers start: 0 outliers final: 0 residues processed: 393 average time/residue: 0.1809 time to fit residues: 114.5634 Evaluate side-chains 293 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 287 optimal weight: 6.9990 chunk 139 optimal weight: 0.3980 chunk 204 optimal weight: 50.0000 chunk 6 optimal weight: 20.0000 chunk 306 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 199 optimal weight: 0.6980 chunk 254 optimal weight: 8.9990 chunk 128 optimal weight: 0.8980 chunk 192 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 48 HIS ** B 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 497 GLN C 581 GLN C 600 GLN ** C 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN ** E 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 625 HIS ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN A 181 ASN A 199 HIS ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 470 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.151793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.123142 restraints weight = 87751.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.122226 restraints weight = 127049.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.122628 restraints weight = 103142.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.121918 restraints weight = 71140.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.122215 restraints weight = 69247.294| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 27352 Z= 0.162 Angle : 0.619 12.455 36972 Z= 0.316 Chirality : 0.042 0.191 4179 Planarity : 0.004 0.125 4762 Dihedral : 4.741 79.173 3674 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.14), residues: 3357 helix: 0.42 (0.12), residues: 1909 sheet: -1.89 (0.67), residues: 58 loop : -1.33 (0.17), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 32 TYR 0.023 0.002 TYR C 544 PHE 0.032 0.002 PHE H 52 TRP 0.016 0.002 TRP F 33 HIS 0.012 0.001 HIS E 73 Details of bonding type rmsd covalent geometry : bond 0.00369 (27331) covalent geometry : angle 0.61877 (36963) hydrogen bonds : bond 0.04035 ( 1314) hydrogen bonds : angle 4.67865 ( 3882) metal coordination : bond 0.00778 ( 21) metal coordination : angle 1.56480 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 1.154 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 25 LYS cc_start: 0.7852 (mmtt) cc_final: 0.7649 (mmmt) REVERT: B 43 LYS cc_start: 0.9071 (ttmt) cc_final: 0.8725 (tptt) REVERT: C 304 VAL cc_start: 0.8765 (t) cc_final: 0.8522 (t) REVERT: C 319 ILE cc_start: 0.8842 (mm) cc_final: 0.8288 (mm) REVERT: C 463 GLN cc_start: 0.8502 (tm-30) cc_final: 0.8264 (tm-30) REVERT: C 556 LEU cc_start: 0.8519 (mt) cc_final: 0.8223 (mt) REVERT: C 642 MET cc_start: 0.6511 (mmm) cc_final: 0.6096 (mmm) REVERT: C 651 PHE cc_start: 0.5570 (p90) cc_final: 0.5272 (p90) REVERT: C 665 MET cc_start: 0.1610 (tpp) cc_final: -0.0286 (ptt) REVERT: J 33 TRP cc_start: 0.8578 (p-90) cc_final: 0.7970 (p-90) REVERT: J 36 ASP cc_start: 0.8142 (p0) cc_final: 0.7408 (t0) REVERT: E 146 MET cc_start: 0.8396 (ttp) cc_final: 0.7539 (tmm) REVERT: E 355 ASN cc_start: 0.8418 (t0) cc_final: 0.7599 (t0) REVERT: E 476 MET cc_start: 0.8902 (mtt) cc_final: 0.8534 (mtt) REVERT: E 622 MET cc_start: 0.6197 (mmp) cc_final: 0.5938 (tpt) REVERT: H 28 GLU cc_start: 0.7388 (pm20) cc_final: 0.7097 (pm20) REVERT: H 30 ILE cc_start: 0.8801 (mm) cc_final: 0.8409 (mm) REVERT: G 358 MET cc_start: 0.4255 (mmp) cc_final: 0.3212 (mtp) REVERT: G 430 ASP cc_start: 0.5937 (t0) cc_final: 0.5718 (p0) REVERT: G 437 MET cc_start: 0.8101 (tpp) cc_final: 0.7874 (tpp) outliers start: 0 outliers final: 0 residues processed: 384 average time/residue: 0.1812 time to fit residues: 112.0583 Evaluate side-chains 293 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 109 optimal weight: 0.5980 chunk 273 optimal weight: 0.9980 chunk 298 optimal weight: 10.0000 chunk 147 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 90 optimal weight: 0.0070 chunk 246 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 157 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 48 HIS ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 581 GLN ** C 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN ** E 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 HIS ** E 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 611 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.153099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.125172 restraints weight = 87397.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.122910 restraints weight = 118685.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.121101 restraints weight = 87784.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.119202 restraints weight = 91497.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.119551 restraints weight = 88557.952| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27352 Z= 0.128 Angle : 0.609 13.271 36972 Z= 0.308 Chirality : 0.042 0.243 4179 Planarity : 0.004 0.071 4762 Dihedral : 4.656 79.176 3674 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.14), residues: 3357 helix: 0.48 (0.12), residues: 1906 sheet: -2.01 (0.63), residues: 60 loop : -1.34 (0.17), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 32 TYR 0.027 0.001 TYR C 90 PHE 0.036 0.001 PHE B 77 TRP 0.013 0.001 TRP A 93 HIS 0.006 0.001 HIS N 68 Details of bonding type rmsd covalent geometry : bond 0.00283 (27331) covalent geometry : angle 0.60844 (36963) hydrogen bonds : bond 0.03870 ( 1314) hydrogen bonds : angle 4.57862 ( 3882) metal coordination : bond 0.01228 ( 21) metal coordination : angle 1.79905 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 390 time to evaluate : 1.225 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LEU cc_start: 0.8579 (mt) cc_final: 0.8358 (mt) REVERT: F 25 LYS cc_start: 0.7955 (mmtt) cc_final: 0.7748 (mmmt) REVERT: B 43 LYS cc_start: 0.9162 (ttmt) cc_final: 0.8719 (tptt) REVERT: B 45 MET cc_start: 0.8280 (mtm) cc_final: 0.7947 (mtt) REVERT: C 236 MET cc_start: 0.8090 (mmp) cc_final: 0.7843 (mmm) REVERT: C 556 LEU cc_start: 0.8475 (mt) cc_final: 0.8153 (mt) REVERT: C 605 MET cc_start: 0.7053 (ppp) cc_final: 0.6548 (ppp) REVERT: C 642 MET cc_start: 0.6687 (mmm) cc_final: 0.6195 (mmm) REVERT: C 651 PHE cc_start: 0.6018 (p90) cc_final: 0.5652 (p90) REVERT: C 665 MET cc_start: 0.1064 (tpp) cc_final: -0.0558 (ptt) REVERT: J 33 TRP cc_start: 0.8575 (p-90) cc_final: 0.7982 (p-90) REVERT: J 36 ASP cc_start: 0.8086 (p0) cc_final: 0.7357 (t0) REVERT: E 74 LYS cc_start: 0.8597 (tmmt) cc_final: 0.8124 (ttmm) REVERT: E 78 GLU cc_start: 0.7454 (pt0) cc_final: 0.7185 (mt-10) REVERT: E 151 MET cc_start: 0.8399 (tpp) cc_final: 0.8157 (tpp) REVERT: E 476 MET cc_start: 0.8925 (mtt) cc_final: 0.8664 (mtt) REVERT: E 622 MET cc_start: 0.6845 (mmp) cc_final: 0.6434 (tpt) REVERT: N 67 LEU cc_start: 0.7915 (mp) cc_final: 0.7667 (tt) REVERT: H 28 GLU cc_start: 0.7317 (pm20) cc_final: 0.7050 (pm20) REVERT: H 30 ILE cc_start: 0.8660 (mm) cc_final: 0.8287 (mm) REVERT: A 210 ARG cc_start: 0.5382 (tpm170) cc_final: 0.4099 (tmm160) REVERT: A 396 ILE cc_start: 0.8180 (tp) cc_final: 0.7928 (tp) REVERT: G 358 MET cc_start: 0.4764 (mmp) cc_final: 0.3452 (mtm) REVERT: G 430 ASP cc_start: 0.6705 (t0) cc_final: 0.6268 (p0) REVERT: G 437 MET cc_start: 0.8447 (tpp) cc_final: 0.8105 (tpp) outliers start: 0 outliers final: 0 residues processed: 390 average time/residue: 0.1875 time to fit residues: 116.7799 Evaluate side-chains 302 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 9 optimal weight: 2.9990 chunk 301 optimal weight: 7.9990 chunk 233 optimal weight: 3.9990 chunk 310 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 294 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 260 optimal weight: 7.9990 chunk 276 optimal weight: 30.0000 chunk 174 optimal weight: 10.0000 chunk 322 optimal weight: 8.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 47 ASN F 48 HIS ** B 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 HIS C 581 GLN E 36 ASN ** E 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN A 181 ASN ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 541 GLN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 464 GLN G 495 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.145913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.116877 restraints weight = 86781.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.110297 restraints weight = 119759.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.107194 restraints weight = 114419.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.107401 restraints weight = 95053.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.107874 restraints weight = 72715.955| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.099 27352 Z= 0.379 Angle : 0.851 13.608 36972 Z= 0.441 Chirality : 0.051 0.352 4179 Planarity : 0.005 0.096 4762 Dihedral : 5.299 77.845 3674 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.42 % Favored : 92.55 % Rotamer: Outliers : 0.03 % Allowed : 2.01 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.14), residues: 3357 helix: 0.03 (0.11), residues: 1906 sheet: -1.91 (0.77), residues: 48 loop : -1.51 (0.16), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 482 TYR 0.041 0.003 TYR C 510 PHE 0.063 0.003 PHE H 52 TRP 0.069 0.004 TRP F 33 HIS 0.011 0.002 HIS E 255 Details of bonding type rmsd covalent geometry : bond 0.00855 (27331) covalent geometry : angle 0.84984 (36963) hydrogen bonds : bond 0.04846 ( 1314) hydrogen bonds : angle 5.24919 ( 3882) metal coordination : bond 0.01927 ( 21) metal coordination : angle 2.61027 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 345 time to evaluate : 1.148 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 6 MET cc_start: 0.5574 (pmm) cc_final: 0.5312 (pmm) REVERT: F 25 LYS cc_start: 0.8283 (mmtt) cc_final: 0.7882 (mmmt) REVERT: B 42 ILE cc_start: 0.8321 (mt) cc_final: 0.8069 (mt) REVERT: B 43 LYS cc_start: 0.9252 (ttmt) cc_final: 0.8813 (tptt) REVERT: B 45 MET cc_start: 0.8252 (mtm) cc_final: 0.7794 (mtt) REVERT: B 77 PHE cc_start: 0.8504 (m-80) cc_final: 0.8272 (m-80) REVERT: B 79 TYR cc_start: 0.8461 (t80) cc_final: 0.8222 (t80) REVERT: B 110 LEU cc_start: 0.8529 (mm) cc_final: 0.8324 (mm) REVERT: C 236 MET cc_start: 0.8056 (mmp) cc_final: 0.7830 (mmm) REVERT: C 319 ILE cc_start: 0.8971 (mm) cc_final: 0.8461 (mm) REVERT: C 438 MET cc_start: 0.8717 (ptp) cc_final: 0.8380 (ptp) REVERT: C 476 MET cc_start: 0.9210 (mtm) cc_final: 0.8822 (mtm) REVERT: C 651 PHE cc_start: 0.6495 (p90) cc_final: 0.6016 (p90) REVERT: C 665 MET cc_start: 0.1482 (tpp) cc_final: -0.0232 (ptt) REVERT: E 311 MET cc_start: 0.8950 (ttt) cc_final: 0.8704 (ttt) REVERT: E 355 ASN cc_start: 0.8238 (t0) cc_final: 0.8001 (t0) REVERT: E 607 GLU cc_start: 0.8165 (mp0) cc_final: 0.7848 (mp0) REVERT: E 622 MET cc_start: 0.6780 (mmp) cc_final: 0.6367 (ttt) REVERT: H 28 GLU cc_start: 0.7823 (pm20) cc_final: 0.7298 (pm20) REVERT: A 210 ARG cc_start: 0.5277 (tpm170) cc_final: 0.3966 (tmm160) REVERT: G 430 ASP cc_start: 0.6609 (t0) cc_final: 0.6124 (p0) REVERT: G 437 MET cc_start: 0.8550 (tpp) cc_final: 0.8130 (tpp) outliers start: 1 outliers final: 0 residues processed: 346 average time/residue: 0.1795 time to fit residues: 100.2591 Evaluate side-chains 275 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 287 optimal weight: 20.0000 chunk 255 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 288 optimal weight: 6.9990 chunk 224 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 293 optimal weight: 9.9990 chunk 232 optimal weight: 30.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 581 GLN E 36 ASN E 355 ASN ** I 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 464 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.150007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 118)---------------| | r_work = 0.3868 r_free = 0.3868 target = 0.113799 restraints weight = 88005.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.107762 restraints weight = 79313.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.108335 restraints weight = 76562.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.108531 restraints weight = 70214.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.108646 restraints weight = 68500.261| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 27352 Z= 0.159 Angle : 0.667 12.937 36972 Z= 0.341 Chirality : 0.044 0.225 4179 Planarity : 0.004 0.073 4762 Dihedral : 4.970 77.841 3674 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.29 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.14), residues: 3357 helix: 0.27 (0.12), residues: 1910 sheet: -1.70 (0.77), residues: 48 loop : -1.45 (0.17), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 75 TYR 0.037 0.002 TYR E 90 PHE 0.041 0.002 PHE H 52 TRP 0.030 0.002 TRP G 209 HIS 0.008 0.001 HIS G 325 Details of bonding type rmsd covalent geometry : bond 0.00359 (27331) covalent geometry : angle 0.66597 (36963) hydrogen bonds : bond 0.04104 ( 1314) hydrogen bonds : angle 4.78032 ( 3882) metal coordination : bond 0.01175 ( 21) metal coordination : angle 2.06675 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 1.178 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 6 MET cc_start: 0.5911 (pmm) cc_final: 0.5598 (pmm) REVERT: D 14 ILE cc_start: 0.9431 (mp) cc_final: 0.9223 (mm) REVERT: D 47 ASP cc_start: 0.8374 (t70) cc_final: 0.8168 (t70) REVERT: F 25 LYS cc_start: 0.8238 (mmtt) cc_final: 0.7869 (mmmt) REVERT: F 66 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7371 (pm20) REVERT: B 30 ILE cc_start: 0.8500 (mm) cc_final: 0.7513 (mm) REVERT: B 42 ILE cc_start: 0.8446 (mt) cc_final: 0.8177 (mt) REVERT: B 43 LYS cc_start: 0.9235 (ttmt) cc_final: 0.8772 (tptt) REVERT: B 45 MET cc_start: 0.8508 (mtm) cc_final: 0.8046 (mtt) REVERT: B 77 PHE cc_start: 0.8851 (m-80) cc_final: 0.8608 (m-80) REVERT: B 79 TYR cc_start: 0.8782 (t80) cc_final: 0.8225 (t80) REVERT: B 82 ARG cc_start: 0.8855 (tmt170) cc_final: 0.8643 (tpt90) REVERT: B 105 MET cc_start: 0.8610 (mtp) cc_final: 0.8290 (ttm) REVERT: C 26 MET cc_start: 0.8866 (mpp) cc_final: 0.8659 (mpp) REVERT: C 236 MET cc_start: 0.8328 (mmp) cc_final: 0.7945 (mmm) REVERT: C 438 MET cc_start: 0.8563 (ptp) cc_final: 0.8349 (ptp) REVERT: C 457 MET cc_start: 0.8887 (tpt) cc_final: 0.8676 (tpt) REVERT: C 556 LEU cc_start: 0.8575 (mt) cc_final: 0.8189 (mm) REVERT: C 651 PHE cc_start: 0.6408 (p90) cc_final: 0.5880 (p90) REVERT: C 665 MET cc_start: 0.1036 (tpp) cc_final: -0.0337 (ptt) REVERT: J 33 TRP cc_start: 0.8476 (p-90) cc_final: 0.7903 (p-90) REVERT: E 137 MET cc_start: 0.6877 (ppp) cc_final: 0.6658 (ppp) REVERT: E 355 ASN cc_start: 0.8081 (t160) cc_final: 0.7879 (t0) REVERT: E 607 GLU cc_start: 0.8424 (mp0) cc_final: 0.8091 (mp0) REVERT: E 622 MET cc_start: 0.7496 (mmp) cc_final: 0.6889 (mmm) REVERT: N 67 LEU cc_start: 0.7895 (mp) cc_final: 0.7568 (tt) REVERT: H 28 GLU cc_start: 0.7534 (pm20) cc_final: 0.7286 (pm20) REVERT: H 30 ILE cc_start: 0.8770 (mm) cc_final: 0.8376 (mm) REVERT: H 37 LEU cc_start: 0.8855 (tp) cc_final: 0.8544 (tt) REVERT: A 210 ARG cc_start: 0.5864 (tpm170) cc_final: 0.4506 (tmm160) REVERT: G 1 MET cc_start: 0.3025 (tpt) cc_final: 0.2702 (mmm) REVERT: G 358 MET cc_start: 0.5754 (mmp) cc_final: 0.4718 (mtm) REVERT: G 430 ASP cc_start: 0.7166 (t0) cc_final: 0.6605 (p0) REVERT: G 437 MET cc_start: 0.8772 (tpp) cc_final: 0.8302 (tpp) outliers start: 0 outliers final: 0 residues processed: 368 average time/residue: 0.1762 time to fit residues: 105.3072 Evaluate side-chains 281 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 261 optimal weight: 7.9990 chunk 293 optimal weight: 20.0000 chunk 5 optimal weight: 0.0770 chunk 314 optimal weight: 6.9990 chunk 233 optimal weight: 0.0270 chunk 77 optimal weight: 0.8980 chunk 221 optimal weight: 50.0000 chunk 236 optimal weight: 9.9990 chunk 271 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 152 optimal weight: 0.8980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 48 HIS C 581 GLN E 36 ASN E 355 ASN ** E 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN A 181 ASN A 362 GLN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 611 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.151155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.119094 restraints weight = 88580.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.117715 restraints weight = 104336.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.115860 restraints weight = 78517.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.114772 restraints weight = 78611.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.115020 restraints weight = 74101.230| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27352 Z= 0.135 Angle : 0.650 13.457 36972 Z= 0.328 Chirality : 0.043 0.217 4179 Planarity : 0.004 0.068 4762 Dihedral : 4.789 77.881 3674 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.34 % Favored : 93.63 % Rotamer: Outliers : 0.03 % Allowed : 0.59 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.14), residues: 3357 helix: 0.38 (0.12), residues: 1905 sheet: -1.64 (0.73), residues: 54 loop : -1.38 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 148 TYR 0.026 0.002 TYR E 596 PHE 0.032 0.002 PHE B 77 TRP 0.026 0.002 TRP A 93 HIS 0.008 0.001 HIS G 325 Details of bonding type rmsd covalent geometry : bond 0.00299 (27331) covalent geometry : angle 0.64903 (36963) hydrogen bonds : bond 0.03901 ( 1314) hydrogen bonds : angle 4.63344 ( 3882) metal coordination : bond 0.01364 ( 21) metal coordination : angle 2.65466 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 368 time to evaluate : 1.188 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 6 MET cc_start: 0.5564 (pmm) cc_final: 0.5311 (pmm) REVERT: F 25 LYS cc_start: 0.8053 (mmtt) cc_final: 0.7773 (mmmt) REVERT: B 43 LYS cc_start: 0.9200 (ttmt) cc_final: 0.8768 (tptt) REVERT: C 294 MET cc_start: 0.8011 (ppp) cc_final: 0.7273 (ppp) REVERT: C 556 LEU cc_start: 0.8497 (mt) cc_final: 0.8142 (mm) REVERT: C 651 PHE cc_start: 0.6002 (p90) cc_final: 0.5797 (p90) REVERT: C 665 MET cc_start: 0.1025 (tpp) cc_final: -0.0285 (ptt) REVERT: J 33 TRP cc_start: 0.8488 (p-90) cc_final: 0.7916 (p-90) REVERT: J 36 ASP cc_start: 0.8025 (p0) cc_final: 0.7058 (t0) REVERT: E 74 LYS cc_start: 0.8573 (tmmt) cc_final: 0.8216 (ttmm) REVERT: E 137 MET cc_start: 0.6833 (ppp) cc_final: 0.6566 (ppp) REVERT: E 294 MET cc_start: 0.8769 (tpp) cc_final: 0.8514 (ttm) REVERT: E 596 TYR cc_start: 0.6839 (t80) cc_final: 0.6072 (t80) REVERT: E 622 MET cc_start: 0.6818 (mmp) cc_final: 0.6266 (ttt) REVERT: N 67 LEU cc_start: 0.7922 (mp) cc_final: 0.7670 (tt) REVERT: H 28 GLU cc_start: 0.7430 (pm20) cc_final: 0.7042 (pm20) REVERT: A 210 ARG cc_start: 0.5373 (tpm170) cc_final: 0.4090 (tmm160) REVERT: G 358 MET cc_start: 0.5118 (mmp) cc_final: 0.4105 (mtm) REVERT: G 430 ASP cc_start: 0.6612 (t0) cc_final: 0.6313 (p0) REVERT: G 437 MET cc_start: 0.8406 (tpp) cc_final: 0.8043 (tpp) outliers start: 1 outliers final: 0 residues processed: 368 average time/residue: 0.1740 time to fit residues: 104.1995 Evaluate side-chains 287 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 100 optimal weight: 10.0000 chunk 203 optimal weight: 50.0000 chunk 219 optimal weight: 40.0000 chunk 138 optimal weight: 1.9990 chunk 299 optimal weight: 10.0000 chunk 183 optimal weight: 40.0000 chunk 1 optimal weight: 6.9990 chunk 65 optimal weight: 0.3980 chunk 266 optimal weight: 9.9990 chunk 230 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN ** E 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 378 ASN ** G 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.145564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.117655 restraints weight = 86236.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.114353 restraints weight = 128817.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.112386 restraints weight = 98439.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.112317 restraints weight = 102336.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.111794 restraints weight = 83288.849| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.105 27352 Z= 0.414 Angle : 0.880 15.242 36972 Z= 0.456 Chirality : 0.052 0.365 4179 Planarity : 0.005 0.079 4762 Dihedral : 5.320 77.879 3674 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.60 % Favored : 92.34 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.14), residues: 3357 helix: 0.01 (0.11), residues: 1906 sheet: -1.75 (0.78), residues: 48 loop : -1.54 (0.16), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 551 TYR 0.044 0.003 TYR H 79 PHE 0.054 0.003 PHE C 469 TRP 0.083 0.004 TRP F 33 HIS 0.011 0.002 HIS E 445 Details of bonding type rmsd covalent geometry : bond 0.00933 (27331) covalent geometry : angle 0.87771 (36963) hydrogen bonds : bond 0.04740 ( 1314) hydrogen bonds : angle 5.29017 ( 3882) metal coordination : bond 0.02108 ( 21) metal coordination : angle 4.27886 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5192.02 seconds wall clock time: 91 minutes 0.12 seconds (5460.12 seconds total)