Starting phenix.real_space_refine on Sat Jun 28 05:55:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wqg_37744/06_2025/8wqg_37744_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wqg_37744/06_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_37744/06_2025/8wqg_37744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wqg_37744/06_2025/8wqg_37744.map" model { file = "/net/cci-nas-00/data/ceres_data/8wqg_37744/06_2025/8wqg_37744_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wqg_37744/06_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-5710/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: 15.04, per 1000 atoms: 0.56 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: 6.77 Conformation dependent library (CDL) restraints added in 3.6 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: 2.95 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: 9.43 Time building geometry restraints manager: 8.10 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: 7.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.020 Extract box with map and model: 1.010 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 65.770 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.160 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.080 ------------------------------------------------------------------------------- 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 : 3.368 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: 0.4064 time to fit residues: 349.1198 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 : 3.118 ------------------------------------------------------------------------------- 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 = 0.123639 restraints weight = 87380.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.119199 restraints weight = 125808.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.116851 restraints weight = 106895.361| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 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 80.388 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 5.36266 ( 3882) metal coordination : bond 0.01061 ( 21) metal coordination : angle 1.85396 ( 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 432 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 427 time to evaluate : 2.890 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: 0.8251 (mmtt) cc_final: 0.7967 (mmmt) REVERT: B 43 LYS cc_start: 0.9075 (ttmt) cc_final: 0.8698 (tptt) REVERT: B 73 VAL cc_start: 0.9002 (p) cc_final: 0.8629 (p) REVERT: C 103 CYS cc_start: 0.8570 (m) cc_final: 0.8279 (m) REVERT: C 390 LEU cc_start: 0.8662 (mt) cc_final: 0.8268 (mp) REVERT: C 651 PHE cc_start: 0.5794 (p90) cc_final: 0.5546 (p90) REVERT: C 665 MET cc_start: 0.1877 (tpp) cc_final: -0.0565 (ptt) REVERT: C 667 GLN cc_start: 0.5140 (OUTLIER) cc_final: 0.4718 (pm20) REVERT: C 708 ARG cc_start: 0.7812 (ppt170) cc_final: 0.7526 (tpp-160) REVERT: E 355 ASN cc_start: 0.8372 (t0) cc_final: 0.7695 (t0) REVERT: E 487 ASN cc_start: 0.7904 (m-40) cc_final: 0.6052 (m110) REVERT: E 596 TYR cc_start: 0.6469 (t80) cc_final: 0.4619 (t80) REVERT: E 622 MET cc_start: 0.6536 (mmp) cc_final: 0.6323 (tpt) REVERT: H 28 GLU cc_start: 0.7672 (pm20) cc_final: 0.7424 (pm20) REVERT: H 37 LEU cc_start: 0.8989 (tp) cc_final: 0.8398 (tt) REVERT: H 39 SER cc_start: 0.9097 (t) cc_final: 0.8428 (p) REVERT: H 75 MET cc_start: 0.7966 (mtm) cc_final: 0.7735 (mtt) REVERT: H 90 ILE cc_start: 0.9250 (pt) cc_final: 0.9033 (pt) REVERT: H 102 GLU cc_start: 0.8462 (tp30) cc_final: 0.7671 (mm-30) REVERT: A 437 MET cc_start: 0.7542 (mmm) cc_final: 0.7231 (mmm) outliers start: 5 outliers final: 0 residues processed: 432 average time/residue: 0.3899 time to fit residues: 263.7848 Evaluate side-chains 310 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 309 time to evaluate : 2.891 ------------------------------------------------------------------------------- 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: 10.0000 chunk 40 optimal weight: 0.8980 chunk 208 optimal weight: 0.0270 chunk 125 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 250 optimal weight: 9.9990 chunk 223 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 overall best weight: 1.1042 ------------------------------------------------------------------------------- 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 296 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** ** I 42 GLN ** 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 611 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.151965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.124628 restraints weight = 87994.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.120479 restraints weight = 121270.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.118295 restraints weight = 97344.828| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27352 Z= 0.168 Angle : 0.625 13.231 36972 Z= 0.327 Chirality : 0.042 0.210 4179 Planarity : 0.004 0.081 4762 Dihedral : 4.856 79.419 3674 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.10 % Allowed : 3.99 % Favored : 95.90 % 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: -0.69 (0.14), residues: 3357 helix: 0.25 (0.12), residues: 1881 sheet: -2.12 (0.57), residues: 63 loop : -1.29 (0.17), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 91 HIS 0.012 0.001 HIS N 68 PHE 0.056 0.002 PHE B 77 TYR 0.020 0.002 TYR H 79 ARG 0.008 0.000 ARG B 33 Details of bonding type rmsd hydrogen bonds : bond 0.04877 ( 1314) hydrogen bonds : angle 5.04203 ( 3882) metal coordination : bond 0.01022 ( 21) metal coordination : angle 1.71841 ( 9) covalent geometry : bond 0.00374 (27331) covalent geometry : angle 0.62491 (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 420 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 417 time to evaluate : 2.820 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: B 43 LYS cc_start: 0.9131 (ttmt) cc_final: 0.8703 (tptt) REVERT: B 82 ARG cc_start: 0.8480 (tpt90) cc_final: 0.8271 (tpt90) REVERT: C 304 VAL cc_start: 0.8802 (t) cc_final: 0.8572 (t) REVERT: C 319 ILE cc_start: 0.8918 (mm) cc_final: 0.8425 (mm) REVERT: C 390 LEU cc_start: 0.8600 (mt) cc_final: 0.8253 (mp) REVERT: C 463 GLN cc_start: 0.8589 (tm-30) cc_final: 0.8328 (tm-30) REVERT: C 576 MET cc_start: 0.6313 (mmp) cc_final: 0.5821 (mmt) REVERT: C 651 PHE cc_start: 0.6059 (p90) cc_final: 0.5830 (p90) REVERT: C 665 MET cc_start: 0.1827 (tpp) cc_final: -0.0412 (ptt) REVERT: C 708 ARG cc_start: 0.7801 (ppt170) cc_final: 0.7467 (tpp-160) REVERT: E 477 TYR cc_start: 0.8049 (t80) cc_final: 0.6568 (t80) REVERT: E 487 ASN cc_start: 0.7290 (m-40) cc_final: 0.6831 (m110) REVERT: E 622 MET cc_start: 0.6721 (mmp) cc_final: 0.6369 (tpt) REVERT: H 28 GLU cc_start: 0.7433 (pm20) cc_final: 0.7075 (pm20) REVERT: H 75 MET cc_start: 0.8160 (mtm) cc_final: 0.7815 (mtt) REVERT: G 358 MET cc_start: 0.4784 (mmp) cc_final: 0.3831 (mtp) outliers start: 3 outliers final: 0 residues processed: 419 average time/residue: 0.3838 time to fit residues: 253.4034 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 : 2.961 ------------------------------------------------------------------------------- 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: 0.8980 chunk 151 optimal weight: 0.5980 chunk 289 optimal weight: 9.9990 chunk 142 optimal weight: 0.9990 chunk 258 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 0.0070 chunk 33 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 200 optimal weight: 0.0270 chunk 141 optimal weight: 2.9990 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 48 HIS C 581 GLN E 36 ASN E 355 ASN E 432 GLN E 600 GLN E 625 HIS ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN 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 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 476 HIS G 611 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.153096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.124337 restraints weight = 88367.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.123197 restraints weight = 111463.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.120240 restraints weight = 83695.731| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 27352 Z= 0.133 Angle : 0.600 12.035 36972 Z= 0.311 Chirality : 0.041 0.165 4179 Planarity : 0.004 0.133 4762 Dihedral : 4.734 79.389 3674 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % 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: -0.62 (0.14), residues: 3357 helix: 0.34 (0.12), residues: 1900 sheet: -2.30 (0.58), residues: 60 loop : -1.32 (0.17), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 27 HIS 0.010 0.001 HIS N 68 PHE 0.031 0.002 PHE B 77 TYR 0.024 0.002 TYR C 510 ARG 0.009 0.000 ARG E 32 Details of bonding type rmsd hydrogen bonds : bond 0.04292 ( 1314) hydrogen bonds : angle 4.78045 ( 3882) metal coordination : bond 0.00957 ( 21) metal coordination : angle 1.62332 ( 9) covalent geometry : bond 0.00288 (27331) covalent geometry : angle 0.59924 (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 399 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 399 time to evaluate : 2.995 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: 0.8104 (mmtt) cc_final: 0.7776 (mmmt) REVERT: B 43 LYS cc_start: 0.9141 (ttmt) cc_final: 0.8703 (tptt) REVERT: B 73 VAL cc_start: 0.9176 (p) cc_final: 0.8901 (p) REVERT: B 82 ARG cc_start: 0.8438 (tpt90) cc_final: 0.8197 (tpt90) REVERT: C 304 VAL cc_start: 0.8767 (t) cc_final: 0.8512 (t) REVERT: C 319 ILE cc_start: 0.8840 (mm) cc_final: 0.8316 (mm) REVERT: C 390 LEU cc_start: 0.8558 (mt) cc_final: 0.8225 (mp) REVERT: C 605 MET cc_start: 0.5955 (ptt) cc_final: 0.5700 (ptt) REVERT: C 665 MET cc_start: 0.1648 (tpp) cc_final: -0.0347 (ptt) REVERT: C 708 ARG cc_start: 0.7817 (ppt170) cc_final: 0.7475 (tpp-160) REVERT: E 74 LYS cc_start: 0.8776 (tmmt) cc_final: 0.8242 (ttmt) REVERT: E 146 MET cc_start: 0.8420 (ttp) cc_final: 0.7708 (tmm) REVERT: E 236 MET cc_start: 0.7741 (mmt) cc_final: 0.7442 (mmt) REVERT: E 480 MET cc_start: 0.8107 (tpp) cc_final: 0.7795 (tpp) REVERT: E 622 MET cc_start: 0.6587 (mmp) cc_final: 0.6342 (tpt) REVERT: H 28 GLU cc_start: 0.6974 (pm20) cc_final: 0.6708 (pm20) REVERT: H 75 MET cc_start: 0.8001 (mtm) cc_final: 0.7788 (mtt) REVERT: H 90 ILE cc_start: 0.9239 (pt) cc_final: 0.8968 (pt) REVERT: H 102 GLU cc_start: 0.8358 (tp30) cc_final: 0.7557 (mm-30) REVERT: G 358 MET cc_start: 0.4663 (mmp) cc_final: 0.3693 (mtp) REVERT: G 430 ASP cc_start: 0.6611 (t0) cc_final: 0.6001 (p0) REVERT: G 437 MET cc_start: 0.8157 (tpp) cc_final: 0.7797 (tpp) outliers start: 0 outliers final: 0 residues processed: 399 average time/residue: 0.3740 time to fit residues: 238.9147 Evaluate side-chains 302 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 3.014 ------------------------------------------------------------------------------- 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: 0.8980 chunk 84 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 262 optimal weight: 20.0000 chunk 116 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 195 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 310 optimal weight: 9.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 111 GLN C 581 GLN C 681 GLN E 36 ASN E 73 HIS ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 G 75 GLN G 241 HIS ** G 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 470 GLN G 611 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.152819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.123833 restraints weight = 88065.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.122522 restraints weight = 114272.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.123528 restraints weight = 100524.250| |-----------------------------------------------------------------------------| r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 27352 Z= 0.147 Angle : 0.610 12.198 36972 Z= 0.313 Chirality : 0.042 0.346 4179 Planarity : 0.004 0.091 4762 Dihedral : 4.690 79.399 3674 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.14), residues: 3357 helix: 0.41 (0.12), residues: 1904 sheet: -2.09 (0.59), residues: 62 loop : -1.34 (0.17), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 93 HIS 0.013 0.001 HIS G 325 PHE 0.036 0.002 PHE H 52 TYR 0.028 0.002 TYR C 544 ARG 0.010 0.000 ARG E 32 Details of bonding type rmsd hydrogen bonds : bond 0.04127 ( 1314) hydrogen bonds : angle 4.70869 ( 3882) metal coordination : bond 0.00773 ( 21) metal coordination : angle 1.58398 ( 9) covalent geometry : bond 0.00325 (27331) covalent geometry : angle 0.60945 (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 391 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 391 time to evaluate : 3.168 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: F 25 LYS cc_start: 0.8006 (mmtt) cc_final: 0.7695 (mmmt) REVERT: B 43 LYS cc_start: 0.9065 (ttmt) cc_final: 0.8711 (tptt) REVERT: C 304 VAL cc_start: 0.8828 (t) cc_final: 0.8546 (t) REVERT: C 390 LEU cc_start: 0.8643 (mt) cc_final: 0.8279 (mp) REVERT: C 438 MET cc_start: 0.8661 (ptp) cc_final: 0.8430 (ptp) REVERT: C 480 MET cc_start: 0.8369 (mmt) cc_final: 0.7518 (mmt) REVERT: C 642 MET cc_start: 0.6424 (mmm) cc_final: 0.6052 (mmm) REVERT: C 665 MET cc_start: 0.1566 (tpp) cc_final: -0.0368 (ptt) REVERT: C 708 ARG cc_start: 0.7725 (ppt170) cc_final: 0.7496 (tpp-160) REVERT: J 33 TRP cc_start: 0.8599 (p-90) cc_final: 0.7831 (p-90) REVERT: J 36 ASP cc_start: 0.8300 (p0) cc_final: 0.7710 (t0) REVERT: E 74 LYS cc_start: 0.8661 (tmmt) cc_final: 0.8079 (ttmm) REVERT: E 146 MET cc_start: 0.8438 (ttp) cc_final: 0.7703 (tmm) REVERT: E 236 MET cc_start: 0.7842 (mmt) cc_final: 0.7598 (mmt) REVERT: E 382 LYS cc_start: 0.8614 (mmmt) cc_final: 0.8347 (pptt) REVERT: E 476 MET cc_start: 0.8764 (mtt) cc_final: 0.8401 (mtt) REVERT: E 480 MET cc_start: 0.8231 (tpp) cc_final: 0.7611 (tpp) REVERT: E 622 MET cc_start: 0.6444 (mmp) cc_final: 0.6192 (tpt) REVERT: H 28 GLU cc_start: 0.7220 (pm20) cc_final: 0.6970 (pm20) REVERT: H 30 ILE cc_start: 0.8602 (mm) cc_final: 0.8231 (mm) REVERT: H 52 PHE cc_start: 0.7316 (m-10) cc_final: 0.6969 (m-10) REVERT: H 75 MET cc_start: 0.8117 (mtm) cc_final: 0.7887 (mtt) REVERT: H 102 GLU cc_start: 0.8389 (tp30) cc_final: 0.7535 (mm-30) REVERT: A 396 ILE cc_start: 0.8175 (tp) cc_final: 0.7887 (tp) REVERT: G 358 MET cc_start: 0.4092 (mmp) cc_final: 0.3155 (mtp) REVERT: G 430 ASP cc_start: 0.6095 (t0) cc_final: 0.5763 (p0) REVERT: G 437 MET cc_start: 0.8125 (tpp) cc_final: 0.7860 (tpp) outliers start: 0 outliers final: 0 residues processed: 391 average time/residue: 0.3943 time to fit residues: 248.0666 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 : 3.114 ------------------------------------------------------------------------------- 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: 9.9990 chunk 35 optimal weight: 7.9990 chunk 313 optimal weight: 5.9990 chunk 173 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 285 optimal weight: 8.9990 chunk 316 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 E 36 ASN ** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 487 ASN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN A 116 HIS ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.150734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.124421 restraints weight = 87347.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.118590 restraints weight = 121355.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.117379 restraints weight = 106029.927| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27352 Z= 0.194 Angle : 0.633 12.315 36972 Z= 0.327 Chirality : 0.043 0.174 4179 Planarity : 0.004 0.083 4762 Dihedral : 4.766 79.138 3674 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % 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: 0.45 (0.12), residues: 1902 sheet: -1.88 (0.64), residues: 60 loop : -1.39 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 93 HIS 0.013 0.001 HIS B 35 PHE 0.033 0.002 PHE B 77 TYR 0.028 0.002 TYR C 510 ARG 0.008 0.000 ARG D 43 Details of bonding type rmsd hydrogen bonds : bond 0.04110 ( 1314) hydrogen bonds : angle 4.72020 ( 3882) metal coordination : bond 0.00904 ( 21) metal coordination : angle 1.71625 ( 9) covalent geometry : bond 0.00439 (27331) covalent geometry : angle 0.63257 (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 364 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 3.228 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: F 25 LYS cc_start: 0.8002 (mmtt) cc_final: 0.7771 (mmmt) REVERT: B 43 LYS cc_start: 0.9084 (ttmt) cc_final: 0.8740 (tptt) REVERT: B 77 PHE cc_start: 0.8356 (m-80) cc_final: 0.7951 (m-80) REVERT: B 105 MET cc_start: 0.7299 (tpp) cc_final: 0.7033 (tpp) REVERT: C 304 VAL cc_start: 0.8821 (t) cc_final: 0.8544 (t) REVERT: C 390 LEU cc_start: 0.8724 (mt) cc_final: 0.8419 (tp) REVERT: C 438 MET cc_start: 0.8662 (ptp) cc_final: 0.8447 (ptp) REVERT: C 480 MET cc_start: 0.8487 (mmt) cc_final: 0.7736 (mmt) REVERT: C 642 MET cc_start: 0.6477 (mmm) cc_final: 0.6100 (mmm) REVERT: C 651 PHE cc_start: 0.5799 (p90) cc_final: 0.5309 (p90) REVERT: C 665 MET cc_start: 0.1576 (tpp) cc_final: -0.0269 (ptt) REVERT: C 678 MET cc_start: 0.8650 (ppp) cc_final: 0.8433 (ppp) REVERT: C 708 ARG cc_start: 0.7774 (ppt170) cc_final: 0.7487 (tpp-160) REVERT: J 36 ASP cc_start: 0.8249 (p0) cc_final: 0.7565 (t0) REVERT: E 146 MET cc_start: 0.8467 (ttp) cc_final: 0.7515 (tmm) REVERT: E 236 MET cc_start: 0.8108 (mmt) cc_final: 0.7897 (mmt) REVERT: E 480 MET cc_start: 0.8211 (tpp) cc_final: 0.7767 (tpp) REVERT: E 622 MET cc_start: 0.6655 (mmp) cc_final: 0.6444 (tpt) REVERT: H 30 ILE cc_start: 0.8892 (mm) cc_final: 0.8534 (mm) REVERT: H 75 MET cc_start: 0.8121 (mtm) cc_final: 0.7806 (mtt) REVERT: G 358 MET cc_start: 0.4399 (mmp) cc_final: 0.3123 (mtm) REVERT: G 430 ASP cc_start: 0.6163 (t0) cc_final: 0.5826 (p0) REVERT: G 437 MET cc_start: 0.8270 (tpp) cc_final: 0.7991 (tpp) outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.4235 time to fit residues: 251.4051 Evaluate side-chains 285 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 3.064 ------------------------------------------------------------------------------- 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: 0.9980 chunk 124 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 226 optimal weight: 7.9990 chunk 309 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 329 optimal weight: 0.7980 chunk 330 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 E 36 ASN ** E 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 495 ASN G 530 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.152399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.123510 restraints weight = 87716.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.122712 restraints weight = 113572.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.122460 restraints weight = 91306.899| |-----------------------------------------------------------------------------| r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27352 Z= 0.140 Angle : 0.624 13.506 36972 Z= 0.316 Chirality : 0.042 0.252 4179 Planarity : 0.004 0.097 4762 Dihedral : 4.710 79.149 3674 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.03 % Allowed : 1.74 % Favored : 98.23 % 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: -0.50 (0.14), residues: 3357 helix: 0.48 (0.12), residues: 1907 sheet: -1.81 (0.61), residues: 62 loop : -1.38 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 93 HIS 0.013 0.001 HIS B 35 PHE 0.030 0.002 PHE B 77 TYR 0.023 0.002 TYR C 544 ARG 0.006 0.000 ARG B 82 Details of bonding type rmsd hydrogen bonds : bond 0.03919 ( 1314) hydrogen bonds : angle 4.60819 ( 3882) metal coordination : bond 0.01192 ( 21) metal coordination : angle 1.74008 ( 9) covalent geometry : bond 0.00311 (27331) covalent geometry : angle 0.62334 (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 388 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 387 time to evaluate : 2.759 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: F 25 LYS cc_start: 0.7994 (mmtt) cc_final: 0.7748 (mmmt) REVERT: F 66 GLU cc_start: 0.7028 (mm-30) cc_final: 0.6332 (mp0) REVERT: B 30 ILE cc_start: 0.8160 (mm) cc_final: 0.7163 (mm) REVERT: B 43 LYS cc_start: 0.9108 (ttmt) cc_final: 0.8706 (tptt) REVERT: B 45 MET cc_start: 0.8013 (mtm) cc_final: 0.7717 (mtt) REVERT: B 75 MET cc_start: 0.7759 (mtt) cc_final: 0.7265 (mtt) REVERT: C 304 VAL cc_start: 0.8783 (t) cc_final: 0.8519 (t) REVERT: C 390 LEU cc_start: 0.8649 (mt) cc_final: 0.8352 (mp) REVERT: C 556 LEU cc_start: 0.8234 (mm) cc_final: 0.7768 (tp) REVERT: C 642 MET cc_start: 0.6487 (mmm) cc_final: 0.6013 (mmm) REVERT: C 651 PHE cc_start: 0.5660 (p90) cc_final: 0.5219 (p90) REVERT: C 665 MET cc_start: 0.1077 (tpp) cc_final: -0.0635 (ptt) REVERT: C 678 MET cc_start: 0.8601 (ppp) cc_final: 0.8370 (ppp) REVERT: C 708 ARG cc_start: 0.7742 (ppt170) cc_final: 0.7503 (tpp-160) REVERT: J 33 TRP cc_start: 0.8572 (p-90) cc_final: 0.7890 (p-90) REVERT: J 36 ASP cc_start: 0.8163 (p0) cc_final: 0.7493 (t0) REVERT: E 74 LYS cc_start: 0.8758 (tmmt) cc_final: 0.8272 (ttmm) REVERT: E 146 MET cc_start: 0.8416 (ttp) cc_final: 0.7445 (tmm) REVERT: E 382 LYS cc_start: 0.8655 (mmmt) cc_final: 0.8395 (pptt) REVERT: E 622 MET cc_start: 0.6329 (mmp) cc_final: 0.6077 (tpt) REVERT: H 28 GLU cc_start: 0.6936 (pm20) cc_final: 0.6665 (pm20) REVERT: A 437 MET cc_start: 0.7543 (tpt) cc_final: 0.7281 (mmm) REVERT: G 358 MET cc_start: 0.4413 (mmp) cc_final: 0.3221 (mtm) REVERT: G 437 MET cc_start: 0.8132 (tpp) cc_final: 0.7876 (tpp) outliers start: 1 outliers final: 0 residues processed: 388 average time/residue: 0.3662 time to fit residues: 229.9713 Evaluate side-chains 300 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 2.863 ------------------------------------------------------------------------------- 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: 1.9990 chunk 322 optimal weight: 6.9990 chunk 295 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 250 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 234 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 chunk 251 optimal weight: 0.8980 chunk 244 optimal weight: 20.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 C 600 GLN ** C 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 541 GLN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.150937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.123701 restraints weight = 87922.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.118909 restraints weight = 123764.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.116028 restraints weight = 110516.936| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 27352 Z= 0.189 Angle : 0.655 12.659 36972 Z= 0.334 Chirality : 0.044 0.225 4179 Planarity : 0.004 0.096 4762 Dihedral : 4.769 78.587 3674 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.14), residues: 3357 helix: 0.41 (0.12), residues: 1914 sheet: -1.88 (0.62), residues: 60 loop : -1.43 (0.17), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 93 HIS 0.016 0.001 HIS B 35 PHE 0.039 0.002 PHE E 202 TYR 0.024 0.002 TYR C 544 ARG 0.009 0.000 ARG E 32 Details of bonding type rmsd hydrogen bonds : bond 0.04066 ( 1314) hydrogen bonds : angle 4.68552 ( 3882) metal coordination : bond 0.01058 ( 21) metal coordination : angle 1.63702 ( 9) covalent geometry : bond 0.00430 (27331) covalent geometry : angle 0.65442 (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 367 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 2.950 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: F 25 LYS cc_start: 0.8063 (mmtt) cc_final: 0.7805 (mmmt) REVERT: F 66 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6422 (mp0) REVERT: B 42 ILE cc_start: 0.8156 (mt) cc_final: 0.7950 (mt) REVERT: B 43 LYS cc_start: 0.9135 (ttmt) cc_final: 0.8728 (tptt) REVERT: B 45 MET cc_start: 0.8097 (mtm) cc_final: 0.7745 (mtt) REVERT: C 304 VAL cc_start: 0.8836 (t) cc_final: 0.8543 (t) REVERT: C 390 LEU cc_start: 0.8834 (mt) cc_final: 0.8535 (tp) REVERT: C 438 MET cc_start: 0.8745 (ptp) cc_final: 0.8469 (ptp) REVERT: C 556 LEU cc_start: 0.8401 (mm) cc_final: 0.8005 (tp) REVERT: C 642 MET cc_start: 0.6562 (mmm) cc_final: 0.6079 (mmm) REVERT: C 651 PHE cc_start: 0.5867 (p90) cc_final: 0.5503 (p90) REVERT: C 665 MET cc_start: 0.1014 (tpp) cc_final: -0.0621 (ptt) REVERT: C 708 ARG cc_start: 0.7835 (ppt170) cc_final: 0.7551 (tpp-160) REVERT: J 36 ASP cc_start: 0.8191 (p0) cc_final: 0.7402 (t0) REVERT: E 74 LYS cc_start: 0.8627 (tmmt) cc_final: 0.8410 (ttmt) REVERT: E 146 MET cc_start: 0.8466 (ttp) cc_final: 0.7512 (tmm) REVERT: E 236 MET cc_start: 0.7757 (mmt) cc_final: 0.7470 (tpp) REVERT: E 477 TYR cc_start: 0.8145 (t80) cc_final: 0.7468 (t80) REVERT: E 622 MET cc_start: 0.6536 (mmp) cc_final: 0.6216 (tpt) REVERT: H 30 ILE cc_start: 0.8839 (mm) cc_final: 0.8465 (mm) REVERT: H 37 LEU cc_start: 0.8956 (tp) cc_final: 0.8618 (tt) REVERT: A 210 ARG cc_start: 0.5059 (tpm170) cc_final: 0.3868 (tmm160) REVERT: A 437 MET cc_start: 0.7741 (tpt) cc_final: 0.7448 (mmm) REVERT: G 358 MET cc_start: 0.4550 (mmp) cc_final: 0.3203 (mtm) REVERT: G 437 MET cc_start: 0.8327 (tpp) cc_final: 0.7999 (tpp) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.3891 time to fit residues: 230.7839 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 : 3.087 ------------------------------------------------------------------------------- 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: 8.9990 chunk 290 optimal weight: 6.9990 chunk 3 optimal weight: 0.4980 chunk 63 optimal weight: 0.7980 chunk 208 optimal weight: 8.9990 chunk 139 optimal weight: 1.9990 chunk 76 optimal weight: 0.3980 chunk 177 optimal weight: 8.9990 chunk 130 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 581 GLN E 36 ASN E 355 ASN ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 590 ASN ** I 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.152618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.125169 restraints weight = 88410.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.121109 restraints weight = 119033.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.118140 restraints weight = 93499.081| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27352 Z= 0.133 Angle : 0.640 12.493 36972 Z= 0.323 Chirality : 0.042 0.231 4179 Planarity : 0.004 0.094 4762 Dihedral : 4.724 78.441 3674 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % 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: -0.50 (0.14), residues: 3357 helix: 0.48 (0.12), residues: 1914 sheet: -1.78 (0.62), residues: 62 loop : -1.37 (0.17), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 93 HIS 0.012 0.001 HIS B 35 PHE 0.034 0.002 PHE B 77 TYR 0.047 0.002 TYR E 477 ARG 0.006 0.000 ARG E 32 Details of bonding type rmsd hydrogen bonds : bond 0.03913 ( 1314) hydrogen bonds : angle 4.59092 ( 3882) metal coordination : bond 0.01022 ( 21) metal coordination : angle 1.53083 ( 9) covalent geometry : bond 0.00299 (27331) covalent geometry : angle 0.63936 (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 372 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 4.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 25 LYS cc_start: 0.8093 (mmtt) cc_final: 0.7807 (mmmt) REVERT: F 66 GLU cc_start: 0.7220 (mm-30) cc_final: 0.6434 (mp0) REVERT: B 42 ILE cc_start: 0.8187 (mt) cc_final: 0.7975 (mt) REVERT: B 43 LYS cc_start: 0.9185 (ttmt) cc_final: 0.8753 (tptt) REVERT: B 45 MET cc_start: 0.8285 (mtm) cc_final: 0.7868 (mtt) REVERT: B 82 ARG cc_start: 0.8464 (tpt90) cc_final: 0.8099 (tpt90) REVERT: C 304 VAL cc_start: 0.8843 (t) cc_final: 0.8561 (t) REVERT: C 438 MET cc_start: 0.8670 (ptp) cc_final: 0.8409 (ptp) REVERT: C 480 MET cc_start: 0.8338 (mmt) cc_final: 0.7687 (mmt) REVERT: C 556 LEU cc_start: 0.8175 (mm) cc_final: 0.7937 (mm) REVERT: C 642 MET cc_start: 0.6673 (mmm) cc_final: 0.6175 (mmm) REVERT: C 651 PHE cc_start: 0.5989 (p90) cc_final: 0.5594 (p90) REVERT: C 665 MET cc_start: 0.0773 (tpp) cc_final: -0.0747 (ptt) REVERT: C 708 ARG cc_start: 0.7842 (ppt170) cc_final: 0.7503 (tpp-160) REVERT: J 36 ASP cc_start: 0.8150 (p0) cc_final: 0.7368 (t0) REVERT: E 74 LYS cc_start: 0.8584 (tmmt) cc_final: 0.8383 (ttmt) REVERT: E 137 MET cc_start: 0.7009 (ppp) cc_final: 0.6721 (ppp) REVERT: E 146 MET cc_start: 0.8386 (ttp) cc_final: 0.7941 (tmm) REVERT: E 294 MET cc_start: 0.8716 (tpp) cc_final: 0.8301 (ttm) REVERT: E 538 GLN cc_start: 0.8453 (tm-30) cc_final: 0.8189 (tm-30) REVERT: E 622 MET cc_start: 0.6720 (mmp) cc_final: 0.6249 (ttt) REVERT: H 30 ILE cc_start: 0.8643 (mm) cc_final: 0.8262 (mm) REVERT: A 210 ARG cc_start: 0.5378 (tpm170) cc_final: 0.4036 (tmm160) REVERT: A 437 MET cc_start: 0.8043 (tpt) cc_final: 0.7811 (mmm) REVERT: G 358 MET cc_start: 0.4667 (mmp) cc_final: 0.3284 (mtm) REVERT: G 437 MET cc_start: 0.8430 (tpp) cc_final: 0.8069 (tpp) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.4090 time to fit residues: 248.5195 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 : 4.949 ------------------------------------------------------------------------------- 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: 6.9990 chunk 92 optimal weight: 5.9990 chunk 142 optimal weight: 0.0670 chunk 323 optimal weight: 2.9990 chunk 277 optimal weight: 6.9990 chunk 207 optimal weight: 0.9990 chunk 211 optimal weight: 30.0000 chunk 215 optimal weight: 4.9990 chunk 309 optimal weight: 10.0000 chunk 278 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- 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 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 HIS C 581 GLN C 681 GLN E 36 ASN E 355 ASN ** 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 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 382 HIS ** 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 = 0.4400 r_free = 0.4400 target = 0.148026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.116792 restraints weight = 87836.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.114021 restraints weight = 126843.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.112349 restraints weight = 94590.303| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 27352 Z= 0.273 Angle : 0.758 13.883 36972 Z= 0.388 Chirality : 0.046 0.261 4179 Planarity : 0.004 0.091 4762 Dihedral : 5.008 77.844 3674 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.14), residues: 3357 helix: 0.29 (0.12), residues: 1913 sheet: -1.86 (0.65), residues: 60 loop : -1.44 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP F 33 HIS 0.011 0.001 HIS B 35 PHE 0.040 0.002 PHE E 202 TYR 0.032 0.002 TYR C 510 ARG 0.017 0.001 ARG E 475 Details of bonding type rmsd hydrogen bonds : bond 0.04307 ( 1314) hydrogen bonds : angle 4.92331 ( 3882) metal coordination : bond 0.01323 ( 21) metal coordination : angle 2.07029 ( 9) covalent geometry : bond 0.00619 (27331) covalent geometry : angle 0.75777 (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 343 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 2.874 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: F 25 LYS cc_start: 0.8283 (mmtt) cc_final: 0.7905 (mmmt) REVERT: B 42 ILE cc_start: 0.8280 (mt) cc_final: 0.8007 (mt) REVERT: B 43 LYS cc_start: 0.9236 (ttmt) cc_final: 0.8770 (tptt) REVERT: B 45 MET cc_start: 0.8293 (mtm) cc_final: 0.7862 (mtt) REVERT: B 77 PHE cc_start: 0.8642 (m-80) cc_final: 0.8399 (m-80) REVERT: B 79 TYR cc_start: 0.8559 (t80) cc_final: 0.8248 (t80) REVERT: B 82 ARG cc_start: 0.8587 (tpt90) cc_final: 0.8356 (tpt90) REVERT: C 294 MET cc_start: 0.8272 (ppp) cc_final: 0.7567 (ppp) REVERT: C 304 VAL cc_start: 0.8838 (t) cc_final: 0.8556 (t) REVERT: C 358 LEU cc_start: 0.7811 (mp) cc_final: 0.7509 (mp) REVERT: C 556 LEU cc_start: 0.8194 (mm) cc_final: 0.7910 (tp) REVERT: C 642 MET cc_start: 0.6874 (mmm) cc_final: 0.6367 (mmm) REVERT: C 651 PHE cc_start: 0.6239 (p90) cc_final: 0.5756 (p90) REVERT: C 665 MET cc_start: 0.0767 (tpp) cc_final: -0.0632 (ptt) REVERT: C 708 ARG cc_start: 0.7896 (ppt170) cc_final: 0.7543 (tpp-160) REVERT: E 74 LYS cc_start: 0.8718 (tmmt) cc_final: 0.8467 (ttmm) REVERT: E 476 MET cc_start: 0.8924 (mtt) cc_final: 0.8543 (mtt) REVERT: E 622 MET cc_start: 0.6845 (mmp) cc_final: 0.6428 (ttt) REVERT: E 688 MET cc_start: 0.5798 (ppp) cc_final: 0.5545 (ppp) REVERT: A 210 ARG cc_start: 0.5452 (tpm170) cc_final: 0.4128 (tmm160) REVERT: A 437 MET cc_start: 0.8235 (tpt) cc_final: 0.7958 (mmp) REVERT: G 280 MET cc_start: 0.1802 (ptt) cc_final: 0.1477 (ptt) REVERT: G 358 MET cc_start: 0.5050 (mmp) cc_final: 0.3574 (mtm) REVERT: G 437 MET cc_start: 0.8595 (tpp) cc_final: 0.8174 (tpp) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.4313 time to fit residues: 238.9206 Evaluate side-chains 269 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 3.132 ------------------------------------------------------------------------------- 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: 20.0000 chunk 147 optimal weight: 0.5980 chunk 124 optimal weight: 0.3980 chunk 300 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 271 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 50 optimal weight: 0.0980 chunk 216 optimal weight: 10.0000 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN ** E 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.151433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.120169 restraints weight = 88744.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.119809 restraints weight = 103514.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.119569 restraints weight = 80634.627| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27352 Z= 0.135 Angle : 0.666 13.453 36972 Z= 0.334 Chirality : 0.043 0.233 4179 Planarity : 0.004 0.086 4762 Dihedral : 4.845 77.823 3674 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.99 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % 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: -0.52 (0.14), residues: 3357 helix: 0.45 (0.12), residues: 1912 sheet: -1.72 (0.64), residues: 60 loop : -1.37 (0.17), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 93 HIS 0.012 0.001 HIS B 35 PHE 0.033 0.002 PHE B 77 TYR 0.023 0.002 TYR E 477 ARG 0.008 0.000 ARG B 63 Details of bonding type rmsd hydrogen bonds : bond 0.03926 ( 1314) hydrogen bonds : angle 4.63695 ( 3882) metal coordination : bond 0.01069 ( 21) metal coordination : angle 1.84464 ( 9) covalent geometry : bond 0.00300 (27331) covalent geometry : angle 0.66566 (36963) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9899.56 seconds wall clock time: 178 minutes 29.68 seconds (10709.68 seconds total)