Starting phenix.real_space_refine on Thu May 29 22:19:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wqg_37744/05_2025/8wqg_37744_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wqg_37744/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wqg_37744/05_2025/8wqg_37744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wqg_37744/05_2025/8wqg_37744.map" model { file = "/net/cci-nas-00/data/ceres_data/8wqg_37744/05_2025/8wqg_37744_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wqg_37744/05_2025/8wqg_37744_neut.cif" } resolution = 4.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 26832 Number of models: 1 Model: "" Number of chains: 14 Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 735 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 7, 'TRANS': 85} Chain breaks: 1 Chain: "F" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 693 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 83} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "C" Number of atoms: 5902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5902 Classifications: {'peptide': 720} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 701} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 679 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 5902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5902 Classifications: {'peptide': 720} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 701} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 402 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 96 Chain: "H" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "I" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 735 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 7, 'TRANS': 85} Chain breaks: 1 Chain: "K" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 400 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 203 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 96 Chain: "A" Number of atoms: 4929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4929 Classifications: {'peptide': 627} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 4929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4929 Classifications: {'peptide': 627} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1009 SG CYS F 53 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: 14.65, per 1000 atoms: 0.55 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: 6.09 Conformation dependent library (CDL) restraints added in 3.3 seconds 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: 2.57 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: 8.64 Time building geometry restraints manager: 7.14 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 105 or resid 200 through 202)) selection = chain 'J' } ncs_group { reference = chain 'K' selection = (chain 'N' and (resid 1 through 37 or (resid 38 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 76)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 17.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.580 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 61.780 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.780 ------------------------------------------------------------------------------- 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 : 10.99 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (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 TRP 0.018 0.002 TRP F 27 HIS 0.010 0.001 HIS G 537 PHE 0.021 0.001 PHE E 202 TYR 0.019 0.001 TYR C 510 ARG 0.005 0.000 ARG I 68 Details of bonding type rmsd hydrogen bonds : bond 0.22986 ( 1314) hydrogen bonds : angle 7.40413 ( 3882) metal coordination : bond 0.00773 ( 21) metal coordination : angle 2.25703 ( 9) covalent geometry : bond 0.00305 (27331) covalent geometry : angle 0.60180 (36963) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 558 time to evaluate : 2.897 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: D 43 ARG cc_start: 0.7997 (mpt90) cc_final: 0.7733 (mtm-85) REVERT: F 25 LYS cc_start: 0.7983 (mmtt) cc_final: 0.7682 (mmmt) REVERT: B 33 ARG cc_start: 0.8539 (ttm-80) cc_final: 0.8279 (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: 0.9066 (p) REVERT: B 77 PHE cc_start: 0.8779 (m-10) cc_final: 0.8554 (m-80) REVERT: B 79 TYR cc_start: 0.8717 (t80) cc_final: 0.8115 (t80) REVERT: B 105 MET cc_start: 0.9123 (mtt) cc_final: 0.8838 (mtt) REVERT: C 99 ASP cc_start: 0.8393 (m-30) cc_final: 0.8090 (p0) REVERT: C 102 ASP cc_start: 0.7536 (t0) cc_final: 0.6506 (t70) REVERT: C 390 LEU cc_start: 0.8765 (mt) cc_final: 0.8474 (mt) REVERT: C 465 CYS cc_start: 0.8450 (m) cc_final: 0.8229 (m) REVERT: C 642 MET cc_start: 0.6394 (tpt) cc_final: 0.6030 (mmm) REVERT: C 665 MET cc_start: 0.1000 (tpp) cc_final: -0.1063 (ptt) REVERT: C 708 ARG cc_start: 0.8035 (ppt170) cc_final: 0.7408 (tpp-160) REVERT: E 355 ASN cc_start: 0.8035 (t0) cc_final: 0.7480 (t0) REVERT: E 622 MET cc_start: 0.6863 (mmp) cc_final: 0.6633 (tpt) REVERT: H 28 GLU cc_start: 0.7568 (pm20) cc_final: 0.7078 (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: 0.8169 (tp40) REVERT: A 310 ASN cc_start: 0.7744 (m110) cc_final: 0.7259 (m-40) REVERT: A 321 ARG cc_start: 0.5630 (ttt90) cc_final: 0.5347 (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: 0.2927 (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: 0.8174 (p) outliers start: 1 outliers final: 0 residues processed: 559 average time/residue: 0.4030 time to fit residues: 345.1975 Evaluate side-chains 322 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 3.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 282 optimal weight: 4.9990 chunk 253 optimal weight: 5.9990 chunk 140 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 170 optimal weight: 9.9990 chunk 135 optimal weight: 1.9990 chunk 261 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 303 optimal weight: 9.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 581 GLN C 667 GLN E 36 ASN E 73 HIS ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 624 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.150530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.123629 restraints weight = 87377.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.119033 restraints weight = 125965.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.116164 restraints weight = 115206.065| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 27352 Z= 0.212 Angle : 0.662 14.273 36972 Z= 0.351 Chirality : 0.043 0.244 4179 Planarity : 0.005 0.146 4762 Dihedral : 4.944 80.389 3674 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.17 % Allowed : 6.53 % Favored : 93.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.14), residues: 3357 helix: 0.14 (0.12), residues: 1885 sheet: -2.13 (0.56), residues: 63 loop : -1.28 (0.17), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 93 HIS 0.017 0.001 HIS N 68 PHE 0.037 0.002 PHE A 485 TYR 0.029 0.002 TYR H 79 ARG 0.012 0.001 ARG D 9 Details of bonding type rmsd hydrogen bonds : bond 0.05417 ( 1314) hydrogen bonds : angle 5.36275 ( 3882) metal coordination : bond 0.01061 ( 21) metal coordination : angle 1.85401 ( 9) covalent geometry : bond 0.00467 (27331) covalent geometry : angle 0.66097 (36963) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 426 time to evaluate : 2.968 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: F 25 LYS cc_start: 0.8348 (mmtt) cc_final: 0.8026 (mmmt) REVERT: B 43 LYS cc_start: 0.9111 (ttmt) cc_final: 0.8715 (tptt) REVERT: B 73 VAL cc_start: 0.9072 (p) cc_final: 0.8705 (p) REVERT: C 103 CYS cc_start: 0.8651 (m) cc_final: 0.8367 (m) REVERT: C 390 LEU cc_start: 0.8710 (mt) cc_final: 0.8333 (mp) REVERT: C 651 PHE cc_start: 0.5861 (p90) cc_final: 0.5580 (p90) REVERT: C 665 MET cc_start: 0.1818 (tpp) cc_final: -0.0611 (ptt) REVERT: C 667 GLN cc_start: 0.5147 (OUTLIER) cc_final: 0.4726 (pm20) REVERT: C 708 ARG cc_start: 0.7838 (ppt170) cc_final: 0.7519 (tpp-160) REVERT: E 78 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7655 (pt0) REVERT: E 355 ASN cc_start: 0.8433 (t0) cc_final: 0.7713 (t0) REVERT: E 487 ASN cc_start: 0.7967 (m-40) cc_final: 0.6127 (m110) REVERT: E 539 MET cc_start: 0.7443 (tmm) cc_final: 0.7225 (tmm) REVERT: E 596 TYR cc_start: 0.6559 (t80) cc_final: 0.4736 (t80) REVERT: E 622 MET cc_start: 0.6643 (mmp) cc_final: 0.6402 (tpt) REVERT: H 28 GLU cc_start: 0.7732 (pm20) cc_final: 0.7441 (pm20) REVERT: H 37 LEU cc_start: 0.8998 (tp) cc_final: 0.8404 (tt) REVERT: H 39 SER cc_start: 0.9101 (t) cc_final: 0.8416 (p) REVERT: H 75 MET cc_start: 0.8050 (mtm) cc_final: 0.7801 (mtt) REVERT: H 90 ILE cc_start: 0.9279 (pt) cc_final: 0.9042 (pt) REVERT: H 102 GLU cc_start: 0.8509 (tp30) cc_final: 0.7704 (mm-30) REVERT: A 437 MET cc_start: 0.7692 (mmm) cc_final: 0.7363 (mmm) outliers start: 5 outliers final: 0 residues processed: 431 average time/residue: 0.3934 time to fit residues: 265.7311 Evaluate side-chains 313 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 312 time to evaluate : 3.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 33 optimal weight: 6.9990 chunk 229 optimal weight: 40.0000 chunk 278 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 208 optimal weight: 0.0870 chunk 125 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 153 optimal weight: 0.8980 chunk 250 optimal weight: 10.0000 chunk 223 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 497 GLN C 581 GLN E 36 ASN E 111 GLN ** E 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 ASN A 375 GLN ** 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 G 611 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.152896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.126024 restraints weight = 88081.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.122100 restraints weight = 118677.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.119778 restraints weight = 95110.178| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.2553 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= 0.148 Angle : 0.615 13.137 36972 Z= 0.321 Chirality : 0.042 0.203 4179 Planarity : 0.004 0.078 4762 Dihedral : 4.815 79.279 3674 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.14 % Allowed : 4.24 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.14), residues: 3357 helix: 0.28 (0.12), residues: 1886 sheet: -2.11 (0.57), residues: 63 loop : -1.29 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 91 HIS 0.012 0.001 HIS N 68 PHE 0.056 0.002 PHE B 77 TYR 0.017 0.002 TYR H 79 ARG 0.007 0.000 ARG J 91 Details of bonding type rmsd hydrogen bonds : bond 0.04779 ( 1314) hydrogen bonds : angle 4.96167 ( 3882) metal coordination : bond 0.00949 ( 21) metal coordination : angle 1.67211 ( 9) covalent geometry : bond 0.00315 (27331) covalent geometry : angle 0.61440 (36963) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 428 time to evaluate : 2.976 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: 0.8217 (mmtt) cc_final: 0.7924 (mmmt) REVERT: B 43 LYS cc_start: 0.9135 (ttmt) cc_final: 0.8709 (tptt) REVERT: C 304 VAL cc_start: 0.8770 (t) cc_final: 0.8562 (t) REVERT: C 319 ILE cc_start: 0.8907 (mm) cc_final: 0.8396 (mm) REVERT: C 390 LEU cc_start: 0.8608 (mt) cc_final: 0.8250 (mp) REVERT: C 512 LEU cc_start: 0.7216 (mt) cc_final: 0.6973 (mt) REVERT: C 566 MET cc_start: 0.2529 (mpp) cc_final: 0.2165 (mpp) REVERT: C 576 MET cc_start: 0.6141 (mmp) cc_final: 0.5554 (mmt) REVERT: C 651 PHE cc_start: 0.5989 (p90) cc_final: 0.5784 (p90) REVERT: C 665 MET cc_start: 0.1863 (tpp) cc_final: -0.0359 (ptt) REVERT: C 708 ARG cc_start: 0.7803 (ppt170) cc_final: 0.7461 (tpp-160) REVERT: E 146 MET cc_start: 0.8198 (ttp) cc_final: 0.7185 (tmm) REVERT: E 355 ASN cc_start: 0.8300 (t0) cc_final: 0.7526 (t0) REVERT: E 443 LEU cc_start: 0.8264 (mt) cc_final: 0.8035 (mt) REVERT: E 477 TYR cc_start: 0.7936 (t80) cc_final: 0.6559 (t80) REVERT: E 539 MET cc_start: 0.7389 (tmm) cc_final: 0.7183 (tmm) REVERT: E 622 MET cc_start: 0.6702 (mmp) cc_final: 0.6361 (tpt) REVERT: H 28 GLU cc_start: 0.7470 (pm20) cc_final: 0.7176 (pm20) REVERT: H 30 ILE cc_start: 0.8809 (mm) cc_final: 0.8588 (mm) REVERT: H 75 MET cc_start: 0.8016 (mtm) cc_final: 0.7682 (mtt) REVERT: H 102 GLU cc_start: 0.8310 (tp30) cc_final: 0.7564 (mm-30) REVERT: G 358 MET cc_start: 0.4608 (mmp) cc_final: 0.3733 (mtp) REVERT: G 430 ASP cc_start: 0.6720 (t0) cc_final: 0.6007 (p0) outliers start: 4 outliers final: 0 residues processed: 430 average time/residue: 0.3795 time to fit residues: 257.0032 Evaluate side-chains 296 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 2.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 162 optimal weight: 0.5980 chunk 151 optimal weight: 0.9990 chunk 289 optimal weight: 10.0000 chunk 142 optimal weight: 0.8980 chunk 258 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 200 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 48 HIS C 296 ASN C 581 GLN E 36 ASN ** E 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 432 GLN E 487 ASN E 600 GLN E 625 HIS ** 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 611 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.151796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.124702 restraints weight = 88298.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.120771 restraints weight = 125110.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.117760 restraints weight = 103149.348| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 27352 Z= 0.174 Angle : 0.627 12.074 36972 Z= 0.325 Chirality : 0.042 0.164 4179 Planarity : 0.005 0.151 4762 Dihedral : 4.799 79.101 3674 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.14), residues: 3357 helix: 0.28 (0.12), residues: 1910 sheet: -2.28 (0.59), residues: 60 loop : -1.32 (0.17), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 93 HIS 0.010 0.001 HIS N 68 PHE 0.034 0.002 PHE H 52 TYR 0.033 0.002 TYR E 90 ARG 0.008 0.000 ARG D 43 Details of bonding type rmsd hydrogen bonds : bond 0.04356 ( 1314) hydrogen bonds : angle 4.85914 ( 3882) metal coordination : bond 0.00911 ( 21) metal coordination : angle 1.65710 ( 9) covalent geometry : bond 0.00390 (27331) covalent geometry : angle 0.62610 (36963) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 385 time to evaluate : 3.114 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: 0.8138 (mmtt) cc_final: 0.7824 (mmmt) REVERT: B 43 LYS cc_start: 0.9125 (ttmt) cc_final: 0.8703 (tptt) REVERT: B 73 VAL cc_start: 0.9172 (p) cc_final: 0.8966 (p) REVERT: B 82 ARG cc_start: 0.8475 (tpt90) cc_final: 0.8259 (tpt90) REVERT: C 304 VAL cc_start: 0.8789 (t) cc_final: 0.8541 (t) REVERT: C 319 ILE cc_start: 0.8847 (mm) cc_final: 0.8272 (mm) REVERT: C 390 LEU cc_start: 0.8606 (mt) cc_final: 0.8221 (tp) REVERT: C 438 MET cc_start: 0.8684 (ptp) cc_final: 0.8453 (ptp) REVERT: C 480 MET cc_start: 0.8348 (mmt) cc_final: 0.7794 (mmt) REVERT: C 651 PHE cc_start: 0.6149 (p90) cc_final: 0.5944 (p90) REVERT: C 665 MET cc_start: 0.1634 (tpp) cc_final: -0.0363 (ptt) REVERT: C 708 ARG cc_start: 0.7819 (ppt170) cc_final: 0.7479 (tpp-160) REVERT: J 33 TRP cc_start: 0.8559 (p-90) cc_final: 0.7898 (p-90) REVERT: E 74 LYS cc_start: 0.8661 (tmmt) cc_final: 0.8249 (ttmt) REVERT: E 146 MET cc_start: 0.8216 (ttp) cc_final: 0.7250 (tmm) REVERT: E 477 TYR cc_start: 0.7848 (t80) cc_final: 0.6602 (t80) REVERT: E 480 MET cc_start: 0.8305 (tpp) cc_final: 0.7925 (tpp) REVERT: E 539 MET cc_start: 0.7378 (tmm) cc_final: 0.7138 (tmm) REVERT: E 622 MET cc_start: 0.6766 (mmp) cc_final: 0.6433 (tpt) REVERT: H 75 MET cc_start: 0.8037 (mtm) cc_final: 0.7825 (mtt) REVERT: H 90 ILE cc_start: 0.9260 (pt) cc_final: 0.9027 (pt) REVERT: G 358 MET cc_start: 0.4739 (mmp) cc_final: 0.3712 (mtp) REVERT: G 430 ASP cc_start: 0.6633 (t0) cc_final: 0.6007 (p0) REVERT: G 437 MET cc_start: 0.8186 (tpp) cc_final: 0.7830 (tpp) outliers start: 0 outliers final: 0 residues processed: 385 average time/residue: 0.3677 time to fit residues: 226.3659 Evaluate side-chains 290 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 2.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 92 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 262 optimal weight: 0.4980 chunk 116 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 chunk 8 optimal weight: 10.0000 chunk 195 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 310 optimal weight: 9.9990 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 ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN C 581 GLN ** C 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN E 355 ASN ** E 508 GLN ** 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 199 HIS ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.151476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.121432 restraints weight = 87759.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.120600 restraints weight = 107258.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.117283 restraints weight = 81780.431| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27352 Z= 0.177 Angle : 0.632 11.745 36972 Z= 0.326 Chirality : 0.042 0.175 4179 Planarity : 0.004 0.091 4762 Dihedral : 4.814 79.137 3674 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.14), residues: 3357 helix: 0.36 (0.12), residues: 1903 sheet: -2.13 (0.58), residues: 62 loop : -1.39 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 93 HIS 0.013 0.001 HIS G 325 PHE 0.039 0.002 PHE H 52 TYR 0.033 0.002 TYR E 477 ARG 0.011 0.000 ARG E 32 Details of bonding type rmsd hydrogen bonds : bond 0.04212 ( 1314) hydrogen bonds : angle 4.79150 ( 3882) metal coordination : bond 0.00881 ( 21) metal coordination : angle 1.70232 ( 9) covalent geometry : bond 0.00398 (27331) covalent geometry : angle 0.63122 (36963) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 390 time to evaluate : 3.010 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: F 25 LYS cc_start: 0.8081 (mmtt) cc_final: 0.7763 (mmmt) REVERT: B 43 LYS cc_start: 0.9137 (ttmt) cc_final: 0.8735 (tptt) REVERT: B 77 PHE cc_start: 0.8541 (m-80) cc_final: 0.8290 (m-80) REVERT: C 304 VAL cc_start: 0.8817 (t) cc_final: 0.8523 (t) REVERT: C 319 ILE cc_start: 0.8863 (mm) cc_final: 0.8329 (mm) REVERT: C 390 LEU cc_start: 0.8624 (mt) cc_final: 0.8269 (tp) REVERT: C 438 MET cc_start: 0.8575 (ptp) cc_final: 0.8276 (ptp) REVERT: C 463 GLN cc_start: 0.8597 (tm-30) cc_final: 0.8275 (tm-30) REVERT: C 480 MET cc_start: 0.8532 (mmt) cc_final: 0.8011 (mmt) REVERT: C 556 LEU cc_start: 0.8518 (mt) cc_final: 0.8228 (mt) REVERT: C 642 MET cc_start: 0.6662 (mmm) cc_final: 0.6303 (mmm) REVERT: C 651 PHE cc_start: 0.6212 (p90) cc_final: 0.5967 (p90) REVERT: C 665 MET cc_start: 0.1379 (tpp) cc_final: -0.0400 (ptt) REVERT: C 708 ARG cc_start: 0.7807 (ppt170) cc_final: 0.7512 (tpp-160) REVERT: J 33 TRP cc_start: 0.8498 (p-90) cc_final: 0.7830 (p-90) REVERT: J 36 ASP cc_start: 0.8237 (p0) cc_final: 0.7611 (t0) REVERT: E 74 LYS cc_start: 0.8610 (tmmt) cc_final: 0.8399 (ttmt) REVERT: E 355 ASN cc_start: 0.8157 (t160) cc_final: 0.7772 (t0) REVERT: E 480 MET cc_start: 0.8377 (tpp) cc_final: 0.7722 (tpp) REVERT: E 487 ASN cc_start: 0.7491 (m-40) cc_final: 0.7222 (m-40) REVERT: E 580 TYR cc_start: 0.6584 (m-10) cc_final: 0.6357 (m-10) REVERT: E 622 MET cc_start: 0.6773 (mmp) cc_final: 0.6412 (tpt) REVERT: G 358 MET cc_start: 0.4707 (mmp) cc_final: 0.3544 (mtp) REVERT: G 430 ASP cc_start: 0.6438 (t0) cc_final: 0.5941 (p0) REVERT: G 437 MET cc_start: 0.8319 (tpp) cc_final: 0.7969 (tpp) outliers start: 0 outliers final: 0 residues processed: 390 average time/residue: 0.3640 time to fit residues: 228.1368 Evaluate side-chains 294 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 3.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 333 optimal weight: 2.9990 chunk 246 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 313 optimal weight: 9.9990 chunk 173 optimal weight: 0.0980 chunk 24 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 122 optimal weight: 0.8980 chunk 285 optimal weight: 4.9990 chunk 316 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 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 432 GLN A 75 GLN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4471 r_free = 0.4471 target = 0.152474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.123661 restraints weight = 87423.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.122747 restraints weight = 114598.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.120412 restraints weight = 88956.218| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.3273 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= 0.140 Angle : 0.614 12.478 36972 Z= 0.312 Chirality : 0.041 0.190 4179 Planarity : 0.005 0.128 4762 Dihedral : 4.752 79.341 3674 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.14), residues: 3357 helix: 0.46 (0.12), residues: 1909 sheet: -1.76 (0.62), residues: 62 loop : -1.39 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 33 HIS 0.008 0.001 HIS G 325 PHE 0.037 0.001 PHE H 52 TYR 0.025 0.002 TYR C 510 ARG 0.010 0.000 ARG E 32 Details of bonding type rmsd hydrogen bonds : bond 0.04014 ( 1314) hydrogen bonds : angle 4.66232 ( 3882) metal coordination : bond 0.01384 ( 21) metal coordination : angle 2.11808 ( 9) covalent geometry : bond 0.00314 (27331) covalent geometry : angle 0.61296 (36963) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 394 time to evaluate : 2.887 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: F 25 LYS cc_start: 0.8034 (mmtt) cc_final: 0.7751 (mmmt) REVERT: B 30 ILE cc_start: 0.8185 (mm) cc_final: 0.7948 (mm) REVERT: B 43 LYS cc_start: 0.9155 (ttmt) cc_final: 0.8776 (tptt) REVERT: B 77 PHE cc_start: 0.8440 (m-80) cc_final: 0.8122 (m-80) REVERT: B 105 MET cc_start: 0.7437 (tpp) cc_final: 0.7159 (tpp) REVERT: C 304 VAL cc_start: 0.8789 (t) cc_final: 0.8499 (t) REVERT: C 319 ILE cc_start: 0.8836 (mm) cc_final: 0.8288 (mm) REVERT: C 390 LEU cc_start: 0.8572 (mt) cc_final: 0.8320 (mp) REVERT: C 438 MET cc_start: 0.8502 (ptp) cc_final: 0.8234 (ptp) REVERT: C 480 MET cc_start: 0.8494 (mmt) cc_final: 0.8010 (mmt) REVERT: C 556 LEU cc_start: 0.8443 (mt) cc_final: 0.7885 (mt) REVERT: C 642 MET cc_start: 0.6616 (mmm) cc_final: 0.6148 (mmm) REVERT: C 665 MET cc_start: 0.1443 (tpp) cc_final: -0.0348 (ptt) REVERT: C 708 ARG cc_start: 0.7790 (ppt170) cc_final: 0.7505 (tpp-160) REVERT: J 33 TRP cc_start: 0.8457 (p-90) cc_final: 0.7887 (p-90) REVERT: J 36 ASP cc_start: 0.8103 (p0) cc_final: 0.7400 (t0) REVERT: E 146 MET cc_start: 0.8465 (ttp) cc_final: 0.7547 (tmm) REVERT: E 382 LYS cc_start: 0.8594 (mmmt) cc_final: 0.8389 (pptt) REVERT: E 480 MET cc_start: 0.8535 (tpp) cc_final: 0.8228 (tpp) REVERT: E 622 MET cc_start: 0.6599 (mmp) cc_final: 0.6295 (tpt) REVERT: I 32 GLU cc_start: 0.7017 (mm-30) cc_final: 0.6374 (tp30) REVERT: I 52 ASP cc_start: 0.7035 (p0) cc_final: 0.6540 (t0) REVERT: G 358 MET cc_start: 0.4467 (mmp) cc_final: 0.3165 (mtm) REVERT: G 430 ASP cc_start: 0.6291 (t0) cc_final: 0.5907 (p0) REVERT: G 437 MET cc_start: 0.8290 (tpp) cc_final: 0.7986 (tpp) outliers start: 0 outliers final: 0 residues processed: 394 average time/residue: 0.3639 time to fit residues: 230.6992 Evaluate side-chains 288 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 2.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 0 optimal weight: 20.0000 chunk 99 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 226 optimal weight: 5.9990 chunk 309 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 329 optimal weight: 0.8980 chunk 330 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 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 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 590 ASN ** 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 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 530 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.152129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.122826 restraints weight = 87586.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.119266 restraints weight = 116190.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.115975 restraints weight = 87123.530| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 27352 Z= 0.148 Angle : 0.626 13.463 36972 Z= 0.318 Chirality : 0.042 0.239 4179 Planarity : 0.004 0.092 4762 Dihedral : 4.750 79.391 3674 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.03 % Allowed : 1.77 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.14), residues: 3357 helix: 0.47 (0.12), residues: 1910 sheet: -1.87 (0.61), residues: 62 loop : -1.44 (0.17), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 93 HIS 0.021 0.001 HIS B 35 PHE 0.037 0.001 PHE H 52 TYR 0.030 0.002 TYR C 90 ARG 0.008 0.000 ARG E 32 Details of bonding type rmsd hydrogen bonds : bond 0.03938 ( 1314) hydrogen bonds : angle 4.63405 ( 3882) metal coordination : bond 0.01133 ( 21) metal coordination : angle 1.56835 ( 9) covalent geometry : bond 0.00335 (27331) covalent geometry : angle 0.62570 (36963) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 376 time to evaluate : 2.883 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: D 6 MET cc_start: 0.6131 (pmm) cc_final: 0.5829 (pmm) REVERT: F 25 LYS cc_start: 0.8179 (mmtt) cc_final: 0.7859 (mmmt) REVERT: B 30 ILE cc_start: 0.8116 (mm) cc_final: 0.7902 (mm) REVERT: B 43 LYS cc_start: 0.9251 (ttmt) cc_final: 0.8828 (tptt) REVERT: B 77 PHE cc_start: 0.8642 (m-80) cc_final: 0.8387 (m-80) REVERT: B 82 ARG cc_start: 0.8567 (tpt90) cc_final: 0.8144 (tpt90) REVERT: B 105 MET cc_start: 0.7701 (tpp) cc_final: 0.7478 (tpp) REVERT: C 304 VAL cc_start: 0.8791 (t) cc_final: 0.8518 (t) REVERT: C 390 LEU cc_start: 0.8613 (mt) cc_final: 0.8290 (tp) REVERT: C 480 MET cc_start: 0.8445 (mmt) cc_final: 0.8111 (mmt) REVERT: C 556 LEU cc_start: 0.8496 (mt) cc_final: 0.8115 (mt) REVERT: C 642 MET cc_start: 0.6716 (mmm) cc_final: 0.6205 (mmm) REVERT: C 665 MET cc_start: 0.0970 (tpp) cc_final: -0.0605 (ptt) REVERT: C 708 ARG cc_start: 0.7830 (ppt170) cc_final: 0.7419 (tpp-160) REVERT: J 33 TRP cc_start: 0.8483 (p-90) cc_final: 0.7972 (p-90) REVERT: J 36 ASP cc_start: 0.8149 (p0) cc_final: 0.7402 (t0) REVERT: E 146 MET cc_start: 0.8447 (ttp) cc_final: 0.7765 (tmm) REVERT: E 382 LYS cc_start: 0.8636 (mmmt) cc_final: 0.8406 (pptt) REVERT: E 480 MET cc_start: 0.8313 (tpp) cc_final: 0.8049 (tpt) REVERT: E 622 MET cc_start: 0.6943 (mmp) cc_final: 0.6457 (ttt) REVERT: I 32 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6565 (tp30) REVERT: G 358 MET cc_start: 0.5143 (mmp) cc_final: 0.3819 (mtp) REVERT: G 430 ASP cc_start: 0.6806 (t0) cc_final: 0.6327 (p0) REVERT: G 437 MET cc_start: 0.8591 (tpp) cc_final: 0.8205 (tpp) outliers start: 1 outliers final: 0 residues processed: 377 average time/residue: 0.3464 time to fit residues: 211.1684 Evaluate side-chains 292 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 2.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 33 optimal weight: 0.8980 chunk 322 optimal weight: 9.9990 chunk 295 optimal weight: 8.9990 chunk 130 optimal weight: 0.9980 chunk 250 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 57 optimal weight: 0.0670 chunk 234 optimal weight: 30.0000 chunk 158 optimal weight: 0.8980 chunk 251 optimal weight: 8.9990 chunk 244 optimal weight: 20.0000 overall best weight: 0.9720 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 581 GLN E 36 ASN E 73 HIS E 432 GLN E 487 ASN E 590 ASN ** E 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 495 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.152227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.123783 restraints weight = 88057.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.122641 restraints weight = 126283.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.121387 restraints weight = 100030.274| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27352 Z= 0.146 Angle : 0.628 13.771 36972 Z= 0.317 Chirality : 0.043 0.332 4179 Planarity : 0.004 0.096 4762 Dihedral : 4.728 79.200 3674 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.03 % Allowed : 1.35 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.14), residues: 3357 helix: 0.47 (0.12), residues: 1916 sheet: -1.92 (0.60), residues: 62 loop : -1.43 (0.17), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 93 HIS 0.014 0.001 HIS B 35 PHE 0.025 0.002 PHE C 651 TYR 0.026 0.002 TYR C 510 ARG 0.011 0.000 ARG E 32 Details of bonding type rmsd hydrogen bonds : bond 0.03914 ( 1314) hydrogen bonds : angle 4.59162 ( 3882) metal coordination : bond 0.00949 ( 21) metal coordination : angle 1.43766 ( 9) covalent geometry : bond 0.00328 (27331) covalent geometry : angle 0.62778 (36963) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 373 time to evaluate : 2.888 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: B 30 ILE cc_start: 0.7928 (mm) cc_final: 0.6985 (mm) REVERT: B 43 LYS cc_start: 0.9175 (ttmt) cc_final: 0.8800 (tptt) REVERT: B 105 MET cc_start: 0.7270 (tpp) cc_final: 0.7050 (tpp) REVERT: C 304 VAL cc_start: 0.8784 (t) cc_final: 0.8500 (t) REVERT: C 390 LEU cc_start: 0.8645 (mt) cc_final: 0.8367 (mp) REVERT: C 463 GLN cc_start: 0.8523 (tm-30) cc_final: 0.8182 (tm-30) REVERT: C 480 MET cc_start: 0.8337 (mmt) cc_final: 0.8045 (mmt) REVERT: C 605 MET cc_start: 0.7054 (ppp) cc_final: 0.6752 (ppp) REVERT: C 642 MET cc_start: 0.6513 (mmm) cc_final: 0.6029 (mmm) REVERT: C 665 MET cc_start: 0.0895 (tpp) cc_final: -0.0677 (ptt) REVERT: C 708 ARG cc_start: 0.7754 (ppt170) cc_final: 0.7496 (tpp-160) REVERT: J 33 TRP cc_start: 0.8466 (p-90) cc_final: 0.8031 (p-90) REVERT: J 36 ASP cc_start: 0.8012 (p0) cc_final: 0.7274 (t0) REVERT: E 146 MET cc_start: 0.8433 (ttp) cc_final: 0.7686 (tmm) REVERT: E 622 MET cc_start: 0.6561 (mmp) cc_final: 0.6217 (tpt) REVERT: I 32 GLU cc_start: 0.7076 (mm-30) cc_final: 0.6593 (tp30) REVERT: A 210 ARG cc_start: 0.5108 (tpm170) cc_final: 0.3884 (tmm160) REVERT: G 358 MET cc_start: 0.4471 (mmp) cc_final: 0.3156 (mtm) REVERT: G 430 ASP cc_start: 0.6197 (t0) cc_final: 0.5984 (p0) REVERT: G 437 MET cc_start: 0.8199 (tpp) cc_final: 0.7950 (tpp) outliers start: 1 outliers final: 1 residues processed: 374 average time/residue: 0.3633 time to fit residues: 219.7265 Evaluate side-chains 296 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 295 time to evaluate : 3.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 294 optimal weight: 6.9990 chunk 290 optimal weight: 0.5980 chunk 3 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 208 optimal weight: 50.0000 chunk 139 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 177 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 133 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 581 GLN E 36 ASN ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.152927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.123512 restraints weight = 88557.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.123142 restraints weight = 119960.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.122463 restraints weight = 99439.777| |-----------------------------------------------------------------------------| r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27352 Z= 0.137 Angle : 0.637 13.790 36972 Z= 0.322 Chirality : 0.043 0.349 4179 Planarity : 0.004 0.096 4762 Dihedral : 4.718 78.981 3674 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.14), residues: 3357 helix: 0.49 (0.12), residues: 1917 sheet: -1.80 (0.60), residues: 62 loop : -1.42 (0.16), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 93 HIS 0.013 0.001 HIS B 35 PHE 0.039 0.002 PHE B 77 TYR 0.025 0.002 TYR C 510 ARG 0.008 0.000 ARG E 32 Details of bonding type rmsd hydrogen bonds : bond 0.03870 ( 1314) hydrogen bonds : angle 4.60849 ( 3882) metal coordination : bond 0.01045 ( 21) metal coordination : angle 1.42911 ( 9) covalent geometry : bond 0.00309 (27331) covalent geometry : angle 0.63705 (36963) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 382 time to evaluate : 3.338 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: B 43 LYS cc_start: 0.9170 (ttmt) cc_final: 0.8783 (tptt) REVERT: B 77 PHE cc_start: 0.8218 (m-80) cc_final: 0.7992 (m-80) REVERT: B 105 MET cc_start: 0.7244 (tpp) cc_final: 0.6919 (tpp) REVERT: C 304 VAL cc_start: 0.8787 (t) cc_final: 0.8498 (t) REVERT: C 438 MET cc_start: 0.8601 (ptp) cc_final: 0.8371 (ptp) REVERT: C 480 MET cc_start: 0.8405 (mmt) cc_final: 0.8132 (mmt) REVERT: C 605 MET cc_start: 0.7122 (ppp) cc_final: 0.6691 (ppp) REVERT: C 642 MET cc_start: 0.6527 (mmm) cc_final: 0.6047 (mmm) REVERT: C 651 PHE cc_start: 0.5810 (p90) cc_final: 0.5577 (p90) REVERT: C 665 MET cc_start: 0.0955 (tpp) cc_final: -0.0566 (ptt) REVERT: C 708 ARG cc_start: 0.7742 (ppt170) cc_final: 0.7480 (tpp-160) REVERT: J 33 TRP cc_start: 0.8487 (p-90) cc_final: 0.7976 (p-90) REVERT: J 36 ASP cc_start: 0.7987 (p0) cc_final: 0.7296 (t0) REVERT: E 137 MET cc_start: 0.6922 (ppp) cc_final: 0.6631 (ppp) REVERT: E 146 MET cc_start: 0.8246 (ttp) cc_final: 0.7495 (tmm) REVERT: E 480 MET cc_start: 0.8152 (mmm) cc_final: 0.7767 (tpp) REVERT: E 622 MET cc_start: 0.6404 (mmp) cc_final: 0.6109 (ttt) REVERT: I 32 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6543 (tp30) REVERT: A 210 ARG cc_start: 0.5113 (tpm170) cc_final: 0.3884 (tmm160) REVERT: A 309 ARG cc_start: 0.5773 (tmm-80) cc_final: 0.5563 (tmm-80) REVERT: G 358 MET cc_start: 0.4394 (mmp) cc_final: 0.3132 (mtm) REVERT: G 430 ASP cc_start: 0.6355 (t0) cc_final: 0.6130 (p0) REVERT: G 437 MET cc_start: 0.8163 (tpp) cc_final: 0.7921 (tpp) outliers start: 0 outliers final: 0 residues processed: 382 average time/residue: 0.3587 time to fit residues: 221.1173 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 : 3.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 306 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 142 optimal weight: 0.0470 chunk 323 optimal weight: 0.7980 chunk 277 optimal weight: 6.9990 chunk 207 optimal weight: 40.0000 chunk 211 optimal weight: 40.0000 chunk 215 optimal weight: 30.0000 chunk 309 optimal weight: 9.9990 chunk 278 optimal weight: 20.0000 chunk 173 optimal weight: 0.6980 overall best weight: 3.7082 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 HIS C 581 GLN E 36 ASN ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 496 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 ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 541 GLN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 378 ASN ** G 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.146428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.118603 restraints weight = 86596.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.114959 restraints weight = 128725.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.112563 restraints weight = 100379.818| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 27352 Z= 0.371 Angle : 0.872 14.866 36972 Z= 0.452 Chirality : 0.051 0.247 4179 Planarity : 0.005 0.096 4762 Dihedral : 5.349 77.911 3674 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.14), residues: 3357 helix: 0.06 (0.12), residues: 1910 sheet: -1.47 (0.62), residues: 63 loop : -1.57 (0.16), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.090 0.004 TRP F 33 HIS 0.017 0.002 HIS B 35 PHE 0.078 0.003 PHE E 202 TYR 0.037 0.003 TYR H 79 ARG 0.020 0.001 ARG E 32 Details of bonding type rmsd hydrogen bonds : bond 0.04771 ( 1314) hydrogen bonds : angle 5.23996 ( 3882) metal coordination : bond 0.01815 ( 21) metal coordination : angle 2.75036 ( 9) covalent geometry : bond 0.00837 (27331) covalent geometry : angle 0.87139 (36963) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 2.872 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: B 35 HIS cc_start: 0.7725 (m-70) cc_final: 0.7435 (m170) REVERT: B 43 LYS cc_start: 0.9198 (ttmt) cc_final: 0.8823 (tptt) REVERT: B 105 MET cc_start: 0.7351 (tpp) cc_final: 0.7077 (tpp) REVERT: C 304 VAL cc_start: 0.8830 (t) cc_final: 0.8514 (t) REVERT: C 390 LEU cc_start: 0.8896 (mt) cc_final: 0.8687 (mt) REVERT: C 438 MET cc_start: 0.8717 (ptp) cc_final: 0.8366 (ptp) REVERT: C 463 GLN cc_start: 0.8788 (tm-30) cc_final: 0.8500 (tm-30) REVERT: C 556 LEU cc_start: 0.8466 (mm) cc_final: 0.8221 (mm) REVERT: C 642 MET cc_start: 0.6814 (mmm) cc_final: 0.6387 (mmm) REVERT: C 651 PHE cc_start: 0.6122 (p90) cc_final: 0.5737 (p90) REVERT: C 665 MET cc_start: 0.1377 (tpp) cc_final: -0.0261 (ptt) REVERT: E 294 MET cc_start: 0.8749 (tpp) cc_final: 0.8477 (ttm) REVERT: E 297 MET cc_start: 0.8096 (tpt) cc_final: 0.7880 (tpp) REVERT: E 426 ASP cc_start: 0.7892 (t70) cc_final: 0.7636 (t0) REVERT: E 476 MET cc_start: 0.8759 (mtt) cc_final: 0.8383 (mtt) REVERT: E 539 MET cc_start: 0.7568 (tmm) cc_final: 0.7262 (tmm) REVERT: E 622 MET cc_start: 0.6339 (mmp) cc_final: 0.6029 (ttt) REVERT: H 67 SER cc_start: 0.7155 (m) cc_final: 0.6816 (p) REVERT: A 210 ARG cc_start: 0.4975 (tpm170) cc_final: 0.3779 (tmm160) REVERT: G 430 ASP cc_start: 0.6245 (t0) cc_final: 0.5975 (p0) REVERT: G 437 MET cc_start: 0.8332 (tpp) cc_final: 0.7992 (tpp) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.3436 time to fit residues: 190.6757 Evaluate side-chains 262 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 3.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 0 optimal weight: 10.0000 chunk 147 optimal weight: 0.5980 chunk 124 optimal weight: 0.0670 chunk 300 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 271 optimal weight: 10.0000 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 216 optimal weight: 9.9990 overall best weight: 1.5322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 581 GLN E 36 ASN E 73 HIS ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 355 ASN ** E 487 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** ** I 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN A 420 GLN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.149132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.117073 restraints weight = 88054.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.114129 restraints weight = 100303.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.109391 restraints weight = 76152.840| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 27352 Z= 0.196 Angle : 0.712 12.112 36972 Z= 0.363 Chirality : 0.045 0.334 4179 Planarity : 0.004 0.092 4762 Dihedral : 5.111 77.868 3674 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.64 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.14), residues: 3357 helix: 0.23 (0.12), residues: 1913 sheet: -1.40 (0.63), residues: 63 loop : -1.49 (0.17), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F 33 HIS 0.014 0.001 HIS B 35 PHE 0.055 0.002 PHE E 202 TYR 0.032 0.002 TYR E 477 ARG 0.015 0.000 ARG E 32 Details of bonding type rmsd hydrogen bonds : bond 0.04206 ( 1314) hydrogen bonds : angle 4.85078 ( 3882) metal coordination : bond 0.01139 ( 21) metal coordination : angle 2.21055 ( 9) covalent geometry : bond 0.00449 (27331) covalent geometry : angle 0.71127 (36963) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9080.70 seconds wall clock time: 160 minutes 49.18 seconds (9649.18 seconds total)