Starting phenix.real_space_refine on Thu May 16 15:25:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqg_37744/05_2024/8wqg_37744_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqg_37744/05_2024/8wqg_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqg_37744/05_2024/8wqg_37744.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqg_37744/05_2024/8wqg_37744.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqg_37744/05_2024/8wqg_37744_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqg_37744/05_2024/8wqg_37744_neut.pdb" } 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 Residue "D ASP 47": "OD1" <-> "OD2" Residue "C ASP 170": "OD1" <-> "OD2" Residue "C PHE 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 145": "OD1" <-> "OD2" Residue "E GLU 412": "OE1" <-> "OE2" Residue "E TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 87": "OD1" <-> "OD2" Residue "G PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 26832 Number of models: 1 Model: "" Number of chains: 14 Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 735 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 7, 'TRANS': 85} Chain breaks: 1 Chain: "F" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 693 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 83} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "C" Number of atoms: 5902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5902 Classifications: {'peptide': 720} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 701} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 679 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 5902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5902 Classifications: {'peptide': 720} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 701} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 402 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 96 Chain: "H" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "I" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 735 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 7, 'TRANS': 85} Chain breaks: 1 Chain: "K" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 400 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 203 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 96 Chain: "A" Number of atoms: 4929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4929 Classifications: {'peptide': 627} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 4929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4929 Classifications: {'peptide': 627} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1009 SG CYS F 53 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: 13.09, per 1000 atoms: 0.49 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.23 Conformation dependent library (CDL) restraints added in 5.5 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: 2.72 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: 9.12 Time building geometry restraints manager: 11.81 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: 99.21 - 106.89: 625 106.89 - 114.58: 16421 114.58 - 122.26: 15812 122.26 - 129.94: 3911 129.94 - 137.62: 194 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 2.440 nonbonded pdb=" OH TYR B 79 " pdb=" O PRO B 91 " model vdw 2.151 2.440 nonbonded pdb=" OD2 ASP A 263 " pdb=" ND2 ASN A 266 " model vdw 2.155 2.520 nonbonded pdb=" OD1 ASP G 384 " pdb=" NH2 ARG G 387 " model vdw 2.177 2.520 ... (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 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: 12.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 35.630 Check model and map are aligned: 0.310 Set scattering table: 0.240 Process input model: 74.660 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.210 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.720 ------------------------------------------------------------------------------- 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 27331 Z= 0.200 Angle : 0.602 17.323 36963 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 558 time to evaluate : 3.200 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: 0.4442 time to fit residues: 382.8326 Evaluate side-chains 322 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 3.219 ------------------------------------------------------------------------------- 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: 2.9990 chunk 253 optimal weight: 20.0000 chunk 140 optimal weight: 0.4980 chunk 86 optimal weight: 5.9990 chunk 170 optimal weight: 8.9990 chunk 135 optimal weight: 0.7980 chunk 261 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 303 optimal weight: 10.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 497 GLN 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 116 HIS A 181 ASN A 310 ASN ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 340 ASN ** G 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 423 ASN G 435 ASN ** G 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 27331 Z= 0.291 Angle : 0.639 14.605 36963 Z= 0.339 Chirality : 0.042 0.232 4179 Planarity : 0.004 0.098 4762 Dihedral : 4.876 78.752 3674 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.34 % Favored : 93.63 % Rotamer: Outliers : 0.21 % Allowed : 6.36 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.14), residues: 3357 helix: 0.19 (0.12), residues: 1879 sheet: -1.97 (0.58), residues: 63 loop : -1.25 (0.17), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 93 HIS 0.017 0.001 HIS N 68 PHE 0.023 0.002 PHE H 52 TYR 0.030 0.002 TYR H 79 ARG 0.007 0.000 ARG D 9 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6714 Ramachandran restraints generated. 3357 Oldfield, 0 Emsley, 3357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 424 time to evaluate : 3.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 25 LYS cc_start: 0.8290 (mmtt) cc_final: 0.7919 (mttp) REVERT: B 33 ARG cc_start: 0.8769 (ttm-80) cc_final: 0.8240 (ttm110) REVERT: B 43 LYS cc_start: 0.9167 (ttmt) cc_final: 0.8735 (tptt) REVERT: B 73 VAL cc_start: 0.9461 (p) cc_final: 0.9127 (p) REVERT: B 79 TYR cc_start: 0.8660 (t80) cc_final: 0.8133 (t80) REVERT: B 105 MET cc_start: 0.8959 (mtt) cc_final: 0.8745 (mtt) REVERT: C 96 LYS cc_start: 0.9109 (tppp) cc_final: 0.8611 (tptm) REVERT: C 99 ASP cc_start: 0.8519 (m-30) cc_final: 0.8119 (p0) REVERT: C 390 LEU cc_start: 0.8729 (mt) cc_final: 0.8411 (mp) REVERT: C 465 CYS cc_start: 0.8273 (m) cc_final: 0.8015 (m) REVERT: C 566 MET cc_start: 0.2264 (mpp) cc_final: 0.1964 (mpp) REVERT: C 605 MET cc_start: 0.7372 (ptp) cc_final: 0.7058 (ptp) REVERT: C 651 PHE cc_start: 0.5991 (p90) cc_final: 0.5638 (p90) REVERT: C 665 MET cc_start: 0.1436 (tpp) cc_final: -0.0857 (ptt) REVERT: C 667 GLN cc_start: 0.5007 (OUTLIER) cc_final: 0.4606 (pm20) REVERT: C 708 ARG cc_start: 0.7950 (ppt170) cc_final: 0.7436 (tpp-160) REVERT: E 78 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7631 (pt0) REVERT: E 355 ASN cc_start: 0.8296 (t0) cc_final: 0.7703 (t0) REVERT: E 539 MET cc_start: 0.7413 (tmm) cc_final: 0.7117 (tmm) REVERT: E 607 GLU cc_start: 0.8207 (mp0) cc_final: 0.7872 (mp0) REVERT: E 622 MET cc_start: 0.7138 (mmp) cc_final: 0.6725 (tpt) REVERT: H 28 GLU cc_start: 0.7634 (pm20) cc_final: 0.7113 (pm20) REVERT: H 37 LEU cc_start: 0.9077 (tp) cc_final: 0.8482 (tt) REVERT: H 39 SER cc_start: 0.9086 (t) cc_final: 0.8449 (p) REVERT: H 75 MET cc_start: 0.8489 (mtm) cc_final: 0.7960 (mtt) REVERT: H 90 ILE cc_start: 0.9384 (pt) cc_final: 0.9091 (pt) REVERT: H 102 GLU cc_start: 0.8667 (tp30) cc_final: 0.7814 (mm-30) REVERT: A 321 ARG cc_start: 0.5852 (ttt90) cc_final: 0.5537 (mtp85) outliers start: 6 outliers final: 1 residues processed: 430 average time/residue: 0.4085 time to fit residues: 275.8781 Evaluate side-chains 320 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 318 time to evaluate : 3.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 168 optimal weight: 7.9990 chunk 94 optimal weight: 20.0000 chunk 252 optimal weight: 8.9990 chunk 206 optimal weight: 20.0000 chunk 83 optimal weight: 6.9990 chunk 303 optimal weight: 0.0970 chunk 328 optimal weight: 0.9980 chunk 270 optimal weight: 6.9990 chunk 301 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 243 optimal weight: 5.9990 overall best weight: 3.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 48 HIS ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 ASN ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 HIS C 347 HIS C 497 GLN ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 581 GLN E 36 ASN ** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 HIS A 181 ASN A 541 GLN ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 495 ASN ** G 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.095 27331 Z= 0.530 Angle : 0.794 12.817 36963 Z= 0.418 Chirality : 0.048 0.272 4179 Planarity : 0.005 0.116 4762 Dihedral : 5.321 79.835 3674 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 23.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.21 % Favored : 92.76 % Rotamer: Outliers : 0.21 % Allowed : 6.43 % Favored : 93.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.14), residues: 3357 helix: -0.02 (0.12), residues: 1876 sheet: -2.25 (0.53), residues: 71 loop : -1.41 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP E 147 HIS 0.012 0.002 HIS N 68 PHE 0.061 0.003 PHE B 77 TYR 0.045 0.002 TYR H 79 ARG 0.010 0.001 ARG J 91 *********************** 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 378 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 372 time to evaluate : 3.556 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: 0.8315 (mmtt) cc_final: 0.7721 (mttp) REVERT: B 43 LYS cc_start: 0.9210 (ttmt) cc_final: 0.8746 (tptt) REVERT: B 79 TYR cc_start: 0.8742 (t80) cc_final: 0.8218 (t80) REVERT: C 304 VAL cc_start: 0.8802 (t) cc_final: 0.8548 (t) REVERT: C 438 MET cc_start: 0.8564 (ptp) cc_final: 0.8364 (ptp) REVERT: C 476 MET cc_start: 0.9116 (mtm) cc_final: 0.8786 (mtm) REVERT: C 493 PHE cc_start: 0.7622 (t80) cc_final: 0.7294 (t80) REVERT: C 605 MET cc_start: 0.7550 (ptp) cc_final: 0.7282 (ptp) REVERT: C 651 PHE cc_start: 0.6564 (p90) cc_final: 0.6043 (p90) REVERT: C 665 MET cc_start: 0.1629 (tpp) cc_final: -0.0518 (ptt) REVERT: C 708 ARG cc_start: 0.7985 (ppt170) cc_final: 0.7539 (tpp-160) REVERT: E 78 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7858 (mt-10) REVERT: E 622 MET cc_start: 0.7176 (mmp) cc_final: 0.6673 (tpt) REVERT: H 28 GLU cc_start: 0.7874 (pm20) cc_final: 0.7227 (pm20) REVERT: H 37 LEU cc_start: 0.9213 (tp) cc_final: 0.8612 (tt) REVERT: H 39 SER cc_start: 0.9296 (t) cc_final: 0.8718 (p) REVERT: A 321 ARG cc_start: 0.5992 (ttt90) cc_final: 0.5628 (mtp85) REVERT: G 31 ASP cc_start: 0.3993 (m-30) cc_final: 0.3746 (p0) REVERT: G 326 MET cc_start: 0.7502 (tpp) cc_final: 0.6947 (tpp) outliers start: 6 outliers final: 3 residues processed: 377 average time/residue: 0.3918 time to fit residues: 234.4568 Evaluate side-chains 277 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 274 time to evaluate : 3.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 300 optimal weight: 20.0000 chunk 228 optimal weight: 50.0000 chunk 157 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 145 optimal weight: 0.8980 chunk 204 optimal weight: 40.0000 chunk 304 optimal weight: 20.0000 chunk 322 optimal weight: 7.9990 chunk 159 optimal weight: 0.7980 chunk 289 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- 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 108 ASN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 HIS ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS E 313 GLN ** E 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 625 HIS ** E 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 ASN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 241 HIS ** G 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 378 ASN ** G 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 476 HIS ** G 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.092 27331 Z= 0.559 Angle : 0.810 12.544 36963 Z= 0.428 Chirality : 0.048 0.254 4179 Planarity : 0.005 0.061 4762 Dihedral : 5.557 82.027 3674 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 25.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.34 % Favored : 91.60 % Rotamer: Outliers : 0.07 % Allowed : 6.15 % Favored : 93.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.14), residues: 3357 helix: -0.23 (0.11), residues: 1876 sheet: -2.04 (0.61), residues: 61 loop : -1.57 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP E 147 HIS 0.011 0.002 HIS N 68 PHE 0.039 0.003 PHE C 469 TYR 0.042 0.003 TYR H 79 ARG 0.009 0.001 ARG E 32 *********************** 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 346 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 344 time to evaluate : 3.247 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: F 25 LYS cc_start: 0.8261 (mmtt) cc_final: 0.7837 (mmmt) REVERT: B 33 ARG cc_start: 0.8785 (ttm-80) cc_final: 0.8422 (ttm170) REVERT: B 34 GLU cc_start: 0.8177 (tp30) cc_final: 0.7952 (tp30) REVERT: B 43 LYS cc_start: 0.9283 (ttmt) cc_final: 0.8760 (tptt) REVERT: B 77 PHE cc_start: 0.8836 (m-80) cc_final: 0.8593 (m-80) REVERT: B 79 TYR cc_start: 0.8659 (t80) cc_final: 0.8131 (t80) REVERT: C 188 PHE cc_start: 0.8201 (m-80) cc_final: 0.7934 (m-80) REVERT: C 304 VAL cc_start: 0.8807 (t) cc_final: 0.8520 (t) REVERT: C 319 ILE cc_start: 0.8962 (mm) cc_final: 0.8453 (mm) REVERT: C 493 PHE cc_start: 0.7703 (t80) cc_final: 0.7364 (t80) REVERT: C 510 TYR cc_start: 0.7727 (t80) cc_final: 0.7513 (t80) REVERT: C 556 LEU cc_start: 0.9009 (mt) cc_final: 0.8701 (mt) REVERT: C 651 PHE cc_start: 0.6639 (p90) cc_final: 0.6092 (p90) REVERT: C 665 MET cc_start: 0.1503 (tpp) cc_final: -0.0456 (ptt) REVERT: C 708 ARG cc_start: 0.7965 (ppt170) cc_final: 0.7574 (tpp-160) REVERT: E 622 MET cc_start: 0.7047 (mmp) cc_final: 0.6629 (tpt) REVERT: H 28 GLU cc_start: 0.7960 (pm20) cc_final: 0.7364 (pm20) REVERT: A 321 ARG cc_start: 0.5914 (ttt90) cc_final: 0.5545 (mtp85) REVERT: G 326 MET cc_start: 0.7564 (tpp) cc_final: 0.7081 (tpp) outliers start: 2 outliers final: 0 residues processed: 346 average time/residue: 0.3825 time to fit residues: 212.8569 Evaluate side-chains 261 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 3.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 268 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 240 optimal weight: 30.0000 chunk 133 optimal weight: 0.9990 chunk 275 optimal weight: 10.0000 chunk 223 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 164 optimal weight: 8.9990 chunk 289 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 ASN ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 581 GLN C 600 GLN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 HIS ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 355 ASN E 590 ASN E 663 GLN H 55 ASN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN A 181 ASN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 241 HIS ** G 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.092 27331 Z= 0.524 Angle : 0.787 12.919 36963 Z= 0.414 Chirality : 0.047 0.246 4179 Planarity : 0.005 0.096 4762 Dihedral : 5.620 82.748 3674 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 26.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.58 % Favored : 91.36 % Rotamer: Outliers : 0.07 % Allowed : 4.55 % Favored : 95.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.14), residues: 3357 helix: -0.23 (0.12), residues: 1883 sheet: -1.97 (0.63), residues: 61 loop : -1.60 (0.17), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP F 33 HIS 0.012 0.002 HIS E 73 PHE 0.053 0.003 PHE E 202 TYR 0.038 0.002 TYR C 510 ARG 0.011 0.001 ARG E 32 *********************** 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 346 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 344 time to evaluate : 3.236 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: F 25 LYS cc_start: 0.8195 (mmtt) cc_final: 0.7836 (mmmt) REVERT: B 33 ARG cc_start: 0.8817 (ttm-80) cc_final: 0.8220 (ttm170) REVERT: B 34 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7699 (tm-30) REVERT: B 43 LYS cc_start: 0.9256 (ttmt) cc_final: 0.8752 (tptt) REVERT: B 79 TYR cc_start: 0.8692 (t80) cc_final: 0.8078 (t80) REVERT: C 188 PHE cc_start: 0.8153 (m-80) cc_final: 0.7875 (m-80) REVERT: C 304 VAL cc_start: 0.8742 (t) cc_final: 0.8442 (t) REVERT: C 319 ILE cc_start: 0.8956 (mm) cc_final: 0.8446 (mm) REVERT: C 438 MET cc_start: 0.8592 (ptp) cc_final: 0.8354 (ptp) REVERT: C 605 MET cc_start: 0.6077 (ptt) cc_final: 0.5629 (ptt) REVERT: C 651 PHE cc_start: 0.6653 (p90) cc_final: 0.6098 (p90) REVERT: C 665 MET cc_start: 0.1270 (tpp) cc_final: -0.0516 (ptt) REVERT: C 708 ARG cc_start: 0.7973 (ppt170) cc_final: 0.7593 (tpp-160) REVERT: E 78 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7756 (pt0) REVERT: E 480 MET cc_start: 0.8724 (tpp) cc_final: 0.8486 (tpp) REVERT: E 539 MET cc_start: 0.7617 (tmm) cc_final: 0.7283 (tmm) REVERT: E 622 MET cc_start: 0.7023 (mmp) cc_final: 0.6654 (tpt) REVERT: H 28 GLU cc_start: 0.7838 (pm20) cc_final: 0.7287 (pm20) REVERT: H 75 MET cc_start: 0.8606 (mtm) cc_final: 0.8067 (mtt) REVERT: H 82 ARG cc_start: 0.8128 (tmt170) cc_final: 0.7912 (ttp80) REVERT: A 321 ARG cc_start: 0.5887 (ttt90) cc_final: 0.5567 (mmm160) outliers start: 2 outliers final: 1 residues processed: 346 average time/residue: 0.3810 time to fit residues: 212.4110 Evaluate side-chains 261 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 260 time to evaluate : 3.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 108 optimal weight: 0.4980 chunk 290 optimal weight: 30.0000 chunk 63 optimal weight: 0.9990 chunk 189 optimal weight: 0.1980 chunk 79 optimal weight: 0.8980 chunk 323 optimal weight: 2.9990 chunk 268 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 169 optimal weight: 0.6980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 48 HIS ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 HIS ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN ** C 513 GLN ** 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 590 ASN H 55 ASN A 75 GLN A 181 ASN A 199 HIS ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 241 HIS ** G 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 611 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27331 Z= 0.198 Angle : 0.629 13.210 36963 Z= 0.325 Chirality : 0.042 0.178 4179 Planarity : 0.004 0.059 4762 Dihedral : 5.135 80.865 3674 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.82 % Favored : 93.15 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.82 (0.14), residues: 3357 helix: 0.20 (0.12), residues: 1887 sheet: -1.89 (0.60), residues: 67 loop : -1.45 (0.17), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 91 HIS 0.010 0.001 HIS N 68 PHE 0.037 0.002 PHE H 52 TYR 0.023 0.002 TYR G 472 ARG 0.010 0.000 ARG E 32 *********************** 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 390 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 390 time to evaluate : 3.362 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: F 25 LYS cc_start: 0.7981 (mmtt) cc_final: 0.7604 (mmmt) REVERT: F 90 THR cc_start: 0.8385 (t) cc_final: 0.8068 (p) REVERT: F 99 ARG cc_start: 0.5395 (ptm160) cc_final: 0.5170 (ptm160) REVERT: B 18 TYR cc_start: 0.8601 (m-80) cc_final: 0.8305 (m-10) REVERT: B 33 ARG cc_start: 0.8666 (ttm-80) cc_final: 0.8178 (ttm170) REVERT: B 34 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7664 (tm-30) REVERT: B 42 ILE cc_start: 0.8704 (mt) cc_final: 0.8504 (mt) REVERT: B 43 LYS cc_start: 0.9247 (ttmt) cc_final: 0.8720 (tptt) REVERT: B 79 TYR cc_start: 0.8689 (t80) cc_final: 0.8128 (t80) REVERT: B 80 LYS cc_start: 0.8996 (tttt) cc_final: 0.8737 (ptmt) REVERT: C 304 VAL cc_start: 0.8760 (t) cc_final: 0.8456 (t) REVERT: C 556 LEU cc_start: 0.8538 (mt) cc_final: 0.8213 (mt) REVERT: C 642 MET cc_start: 0.7045 (mmm) cc_final: 0.6754 (mmm) REVERT: C 651 PHE cc_start: 0.6433 (p90) cc_final: 0.6056 (p90) REVERT: C 665 MET cc_start: 0.0945 (tpp) cc_final: -0.0651 (ptt) REVERT: C 708 ARG cc_start: 0.7876 (ppt170) cc_final: 0.7494 (tpp-160) REVERT: J 33 TRP cc_start: 0.8202 (p-90) cc_final: 0.7735 (p-90) REVERT: E 26 MET cc_start: 0.7466 (mtp) cc_final: 0.6819 (mmm) REVERT: E 78 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7704 (pt0) REVERT: E 480 MET cc_start: 0.8576 (tpp) cc_final: 0.8131 (tpp) REVERT: E 538 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8398 (tm-30) REVERT: E 622 MET cc_start: 0.6861 (mmp) cc_final: 0.6548 (tpt) REVERT: H 28 GLU cc_start: 0.7507 (pm20) cc_final: 0.6977 (pm20) REVERT: A 321 ARG cc_start: 0.5843 (ttt90) cc_final: 0.5489 (mtp85) REVERT: G 358 MET cc_start: 0.5794 (mmp) cc_final: 0.4821 (mtm) REVERT: G 430 ASP cc_start: 0.7388 (t0) cc_final: 0.6632 (p0) outliers start: 0 outliers final: 0 residues processed: 390 average time/residue: 0.3992 time to fit residues: 248.9969 Evaluate side-chains 280 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 3.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 311 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 184 optimal weight: 30.0000 chunk 235 optimal weight: 20.0000 chunk 182 optimal weight: 40.0000 chunk 272 optimal weight: 30.0000 chunk 180 optimal weight: 20.0000 chunk 321 optimal weight: 0.8980 chunk 201 optimal weight: 0.7980 chunk 196 optimal weight: 4.9990 chunk 148 optimal weight: 0.6980 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 48 HIS ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 581 GLN ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 474 HIS ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 590 ASN H 55 ASN H 58 ASN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN A 181 ASN ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 27331 Z= 0.422 Angle : 0.734 12.802 36963 Z= 0.380 Chirality : 0.046 0.315 4179 Planarity : 0.005 0.070 4762 Dihedral : 5.315 80.150 3674 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 23.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.45 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.97 (0.14), residues: 3357 helix: 0.05 (0.12), residues: 1887 sheet: -1.42 (0.72), residues: 55 loop : -1.51 (0.17), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A 93 HIS 0.009 0.001 HIS N 68 PHE 0.042 0.002 PHE H 52 TYR 0.027 0.002 TYR H 79 ARG 0.016 0.001 ARG E 32 *********************** 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 351 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 351 time to evaluate : 3.019 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: 0.8171 (mmtt) cc_final: 0.7811 (mmmt) REVERT: B 33 ARG cc_start: 0.8731 (ttm-80) cc_final: 0.8204 (ttm170) REVERT: B 34 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7604 (tm-30) REVERT: B 43 LYS cc_start: 0.9281 (ttmt) cc_final: 0.8774 (tptt) REVERT: B 79 TYR cc_start: 0.8691 (t80) cc_final: 0.8153 (t80) REVERT: B 105 MET cc_start: 0.7798 (tpp) cc_final: 0.7588 (tpp) REVERT: C 304 VAL cc_start: 0.8779 (t) cc_final: 0.8493 (t) REVERT: C 319 ILE cc_start: 0.8932 (mm) cc_final: 0.8396 (mm) REVERT: C 438 MET cc_start: 0.8635 (ptp) cc_final: 0.8376 (ptp) REVERT: C 476 MET cc_start: 0.8906 (mtm) cc_final: 0.8454 (mtm) REVERT: C 493 PHE cc_start: 0.7732 (t80) cc_final: 0.7472 (t80) REVERT: C 642 MET cc_start: 0.7095 (mmm) cc_final: 0.6803 (mmm) REVERT: C 651 PHE cc_start: 0.6582 (p90) cc_final: 0.6145 (p90) REVERT: C 665 MET cc_start: 0.1045 (tpp) cc_final: -0.0520 (ptt) REVERT: C 708 ARG cc_start: 0.7895 (ppt170) cc_final: 0.7540 (tpp-160) REVERT: J 33 TRP cc_start: 0.8376 (p-90) cc_final: 0.7835 (p-90) REVERT: E 480 MET cc_start: 0.8643 (tpp) cc_final: 0.8175 (tpp) REVERT: E 539 MET cc_start: 0.7831 (tmm) cc_final: 0.7325 (tmm) REVERT: E 622 MET cc_start: 0.6882 (mmp) cc_final: 0.6589 (tpt) REVERT: H 37 LEU cc_start: 0.9151 (tp) cc_final: 0.8598 (tt) REVERT: H 39 SER cc_start: 0.9237 (t) cc_final: 0.8729 (p) REVERT: A 321 ARG cc_start: 0.5808 (ttt90) cc_final: 0.5592 (mmm160) REVERT: G 159 MET cc_start: 0.1355 (mtp) cc_final: 0.0879 (mmm) REVERT: G 326 MET cc_start: 0.7284 (tpp) cc_final: 0.6655 (tpp) REVERT: G 358 MET cc_start: 0.5886 (mmp) cc_final: 0.4707 (mtm) REVERT: G 430 ASP cc_start: 0.7208 (t0) cc_final: 0.6535 (p0) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.4003 time to fit residues: 228.0567 Evaluate side-chains 266 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 3.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 199 optimal weight: 0.0570 chunk 128 optimal weight: 1.9990 chunk 192 optimal weight: 0.0870 chunk 96 optimal weight: 0.2980 chunk 63 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 204 optimal weight: 40.0000 chunk 219 optimal weight: 7.9990 chunk 159 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 253 optimal weight: 10.0000 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 ASN ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 581 GLN J 98 ASN E 36 ASN E 73 HIS E 320 HIS ** E 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 590 ASN E 600 GLN H 55 ASN ** I 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN A 181 ASN ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 325 HIS ** G 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 611 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27331 Z= 0.196 Angle : 0.643 13.124 36963 Z= 0.326 Chirality : 0.042 0.246 4179 Planarity : 0.004 0.080 4762 Dihedral : 5.074 79.431 3674 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.23 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % 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: 0.29 (0.12), residues: 1897 sheet: -1.36 (0.80), residues: 40 loop : -1.42 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 93 HIS 0.009 0.001 HIS G 241 PHE 0.033 0.002 PHE B 77 TYR 0.021 0.001 TYR G 472 ARG 0.009 0.000 ARG E 32 *********************** 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 370 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 370 time to evaluate : 3.596 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: 0.7908 (mmtt) cc_final: 0.7588 (mmmt) REVERT: B 18 TYR cc_start: 0.8817 (m-10) cc_final: 0.8403 (m-10) REVERT: B 33 ARG cc_start: 0.8587 (ttm-80) cc_final: 0.8127 (ttm170) REVERT: B 34 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7601 (tm-30) REVERT: B 43 LYS cc_start: 0.9343 (ttmt) cc_final: 0.8784 (tptt) REVERT: B 79 TYR cc_start: 0.8623 (t80) cc_final: 0.8182 (t80) REVERT: B 80 LYS cc_start: 0.8999 (tttt) cc_final: 0.8718 (ptmt) REVERT: B 110 LEU cc_start: 0.8882 (mm) cc_final: 0.8680 (mm) REVERT: C 304 VAL cc_start: 0.8761 (t) cc_final: 0.8452 (t) REVERT: C 556 LEU cc_start: 0.8544 (mt) cc_final: 0.8007 (mt) REVERT: C 642 MET cc_start: 0.6915 (mmm) cc_final: 0.6638 (mmm) REVERT: C 651 PHE cc_start: 0.6330 (p90) cc_final: 0.6020 (p90) REVERT: C 665 MET cc_start: 0.0804 (tpp) cc_final: -0.0501 (ptt) REVERT: C 708 ARG cc_start: 0.7871 (ppt170) cc_final: 0.7487 (tpp-160) REVERT: J 33 TRP cc_start: 0.8163 (p-90) cc_final: 0.7844 (p-90) REVERT: E 78 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7585 (pt0) REVERT: E 137 MET cc_start: 0.6748 (ppp) cc_final: 0.6451 (ppp) REVERT: E 146 MET cc_start: 0.8353 (ttp) cc_final: 0.7756 (tmm) REVERT: E 538 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8405 (tm-30) REVERT: E 622 MET cc_start: 0.6814 (mmp) cc_final: 0.6513 (tpt) REVERT: A 321 ARG cc_start: 0.5964 (ttt90) cc_final: 0.5448 (mtp85) REVERT: G 159 MET cc_start: 0.1028 (mtp) cc_final: 0.0654 (mmm) REVERT: G 326 MET cc_start: 0.7253 (tpp) cc_final: 0.6630 (tpp) REVERT: G 358 MET cc_start: 0.5822 (mmp) cc_final: 0.4762 (mtm) REVERT: G 430 ASP cc_start: 0.7123 (t0) cc_final: 0.6588 (p0) REVERT: G 437 MET cc_start: 0.8260 (tpp) cc_final: 0.7834 (tpp) outliers start: 0 outliers final: 0 residues processed: 370 average time/residue: 0.3897 time to fit residues: 231.6433 Evaluate side-chains 277 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 3.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 292 optimal weight: 5.9990 chunk 308 optimal weight: 10.0000 chunk 281 optimal weight: 20.0000 chunk 299 optimal weight: 8.9990 chunk 180 optimal weight: 30.0000 chunk 130 optimal weight: 1.9990 chunk 235 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 271 optimal weight: 0.0770 chunk 283 optimal weight: 30.0000 chunk 298 optimal weight: 2.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 HIS ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 581 GLN E 36 ASN E 313 GLN ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 590 ASN H 55 ASN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN A 181 ASN ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 HIS ** G 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 27331 Z= 0.503 Angle : 0.808 12.532 36963 Z= 0.420 Chirality : 0.048 0.335 4179 Planarity : 0.005 0.081 4762 Dihedral : 5.446 79.651 3674 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 25.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.63 % Favored : 92.25 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.14), residues: 3357 helix: 0.04 (0.12), residues: 1890 sheet: -1.34 (0.72), residues: 55 loop : -1.54 (0.17), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP E 147 HIS 0.010 0.002 HIS G 241 PHE 0.059 0.003 PHE E 202 TYR 0.028 0.002 TYR E 219 ARG 0.012 0.001 ARG E 32 *********************** 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 344 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 344 time to evaluate : 3.238 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: D 6 MET cc_start: 0.5759 (pmm) cc_final: 0.5499 (pmm) REVERT: F 25 LYS cc_start: 0.8222 (mmtt) cc_final: 0.7830 (mmmt) REVERT: B 18 TYR cc_start: 0.8933 (m-10) cc_final: 0.8554 (m-10) REVERT: B 30 ILE cc_start: 0.7969 (mm) cc_final: 0.7725 (mm) REVERT: B 33 ARG cc_start: 0.8747 (ttm-80) cc_final: 0.8208 (ttm170) REVERT: B 34 GLU cc_start: 0.8430 (tm-30) cc_final: 0.7869 (tm-30) REVERT: B 43 LYS cc_start: 0.9346 (ttmt) cc_final: 0.8857 (tptt) REVERT: B 79 TYR cc_start: 0.8699 (t80) cc_final: 0.8222 (t80) REVERT: B 105 MET cc_start: 0.8063 (ttm) cc_final: 0.7722 (tpp) REVERT: C 304 VAL cc_start: 0.8752 (t) cc_final: 0.8457 (t) REVERT: C 319 ILE cc_start: 0.8955 (mm) cc_final: 0.8433 (mm) REVERT: C 438 MET cc_start: 0.8646 (ptp) cc_final: 0.8339 (ptp) REVERT: C 476 MET cc_start: 0.8896 (mtm) cc_final: 0.8490 (mtm) REVERT: C 642 MET cc_start: 0.7135 (mmm) cc_final: 0.6848 (mmm) REVERT: C 651 PHE cc_start: 0.6671 (p90) cc_final: 0.6262 (p90) REVERT: C 665 MET cc_start: 0.0931 (tpp) cc_final: -0.0519 (ptt) REVERT: C 708 ARG cc_start: 0.7869 (ppt170) cc_final: 0.7526 (tpp-160) REVERT: C 717 MET cc_start: 0.5838 (ppp) cc_final: 0.5307 (ptt) REVERT: E 78 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7855 (mt-10) REVERT: E 480 MET cc_start: 0.8499 (mmm) cc_final: 0.8234 (mmm) REVERT: E 538 GLN cc_start: 0.8835 (tm-30) cc_final: 0.8401 (tm-30) REVERT: E 539 MET cc_start: 0.7643 (tmm) cc_final: 0.7240 (tmm) REVERT: E 622 MET cc_start: 0.6867 (mmp) cc_final: 0.6422 (ttt) REVERT: H 37 LEU cc_start: 0.9197 (tp) cc_final: 0.8655 (tt) REVERT: H 39 SER cc_start: 0.9278 (t) cc_final: 0.8815 (p) REVERT: I 11 LYS cc_start: 0.8374 (mmmt) cc_final: 0.8161 (mmmt) REVERT: A 321 ARG cc_start: 0.5898 (ttt90) cc_final: 0.5547 (mmm160) REVERT: G 326 MET cc_start: 0.7333 (tpp) cc_final: 0.6742 (tpp) REVERT: G 358 MET cc_start: 0.5759 (mmp) cc_final: 0.4528 (mtm) REVERT: G 430 ASP cc_start: 0.7100 (t0) cc_final: 0.6545 (p0) REVERT: G 437 MET cc_start: 0.8394 (tpp) cc_final: 0.7933 (tpp) outliers start: 0 outliers final: 0 residues processed: 344 average time/residue: 0.3928 time to fit residues: 218.7354 Evaluate side-chains 260 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 3.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 196 optimal weight: 6.9990 chunk 317 optimal weight: 1.9990 chunk 193 optimal weight: 0.9980 chunk 150 optimal weight: 0.9990 chunk 220 optimal weight: 9.9990 chunk 332 optimal weight: 2.9990 chunk 306 optimal weight: 0.9980 chunk 264 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 204 optimal weight: 50.0000 chunk 162 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 ASN ** 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 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 581 GLN E 36 ASN ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 590 ASN H 55 ASN ** I 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 ASN ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 HIS ** G 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 611 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 27331 Z= 0.241 Angle : 0.679 12.846 36963 Z= 0.346 Chirality : 0.044 0.350 4179 Planarity : 0.004 0.081 4762 Dihedral : 5.181 79.531 3674 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.58 % Favored : 93.36 % 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: -0.77 (0.14), residues: 3357 helix: 0.22 (0.12), residues: 1893 sheet: -1.40 (0.77), residues: 40 loop : -1.43 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 93 HIS 0.009 0.001 HIS C 71 PHE 0.036 0.002 PHE C 507 TYR 0.022 0.002 TYR G 472 ARG 0.009 0.000 ARG G 387 ********************** 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 357 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 357 time to evaluate : 3.104 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: D 6 MET cc_start: 0.5713 (pmm) cc_final: 0.5480 (pmm) REVERT: F 25 LYS cc_start: 0.7981 (mmtt) cc_final: 0.7608 (mmmt) REVERT: B 18 TYR cc_start: 0.8871 (m-10) cc_final: 0.8564 (m-10) REVERT: B 30 ILE cc_start: 0.7822 (mm) cc_final: 0.7552 (mm) REVERT: B 33 ARG cc_start: 0.8636 (ttm-80) cc_final: 0.8125 (ttm170) REVERT: B 34 GLU cc_start: 0.8402 (tm-30) cc_final: 0.7901 (tm-30) REVERT: B 43 LYS cc_start: 0.9310 (ttmt) cc_final: 0.8777 (tptt) REVERT: B 79 TYR cc_start: 0.8676 (t80) cc_final: 0.8186 (t80) REVERT: B 105 MET cc_start: 0.7863 (ttm) cc_final: 0.7464 (tpp) REVERT: C 304 VAL cc_start: 0.8758 (t) cc_final: 0.8458 (t) REVERT: C 319 ILE cc_start: 0.8901 (mm) cc_final: 0.8354 (mm) REVERT: C 438 MET cc_start: 0.8635 (ptp) cc_final: 0.8381 (ptp) REVERT: C 642 MET cc_start: 0.7014 (mmm) cc_final: 0.6708 (mmm) REVERT: C 651 PHE cc_start: 0.6461 (p90) cc_final: 0.6100 (p90) REVERT: C 665 MET cc_start: 0.0853 (tpp) cc_final: -0.0375 (ptt) REVERT: C 708 ARG cc_start: 0.7862 (ppt170) cc_final: 0.7488 (tpp-160) REVERT: C 717 MET cc_start: 0.5755 (ppp) cc_final: 0.5223 (ptt) REVERT: J 33 TRP cc_start: 0.8192 (p-90) cc_final: 0.7911 (p-90) REVERT: E 78 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7646 (pt0) REVERT: E 382 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8442 (pptt) REVERT: E 538 GLN cc_start: 0.8768 (tm-30) cc_final: 0.8411 (tm-30) REVERT: E 539 MET cc_start: 0.7632 (tmm) cc_final: 0.7235 (tmm) REVERT: E 622 MET cc_start: 0.6748 (mmp) cc_final: 0.6333 (ttt) REVERT: H 30 ILE cc_start: 0.9142 (mm) cc_final: 0.8788 (mm) REVERT: A 321 ARG cc_start: 0.5799 (ttt90) cc_final: 0.5426 (mmm160) REVERT: G 159 MET cc_start: 0.0524 (tpt) cc_final: 0.0276 (tpp) REVERT: G 280 MET cc_start: 0.1548 (ptt) cc_final: 0.1306 (ptt) REVERT: G 326 MET cc_start: 0.7269 (tpp) cc_final: 0.6707 (tpp) REVERT: G 358 MET cc_start: 0.5809 (mmp) cc_final: 0.4688 (mtm) REVERT: G 430 ASP cc_start: 0.7167 (t0) cc_final: 0.6630 (p0) REVERT: G 437 MET cc_start: 0.8359 (tpp) cc_final: 0.7936 (tpp) outliers start: 0 outliers final: 0 residues processed: 357 average time/residue: 0.3745 time to fit residues: 215.8416 Evaluate side-chains 276 residues out of total 3005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 3.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 210 optimal weight: 10.0000 chunk 282 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 244 optimal weight: 30.0000 chunk 39 optimal weight: 6.9990 chunk 73 optimal weight: 0.4980 chunk 265 optimal weight: 9.9990 chunk 111 optimal weight: 0.9980 chunk 272 optimal weight: 20.0000 chunk 33 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 overall best weight: 2.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 HIS ** F 98 ASN ** 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 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 581 GLN E 36 ASN ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 590 ASN H 55 ASN ** I 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 ASN ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 HIS ** G 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 611 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.146371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.114009 restraints weight = 86613.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.112151 restraints weight = 116586.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.109478 restraints weight = 88351.999| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 27331 Z= 0.437 Angle : 0.769 12.524 36963 Z= 0.397 Chirality : 0.047 0.323 4179 Planarity : 0.005 0.072 4762 Dihedral : 5.384 79.806 3674 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 24.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.83 % Favored : 92.05 % 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: -0.96 (0.14), residues: 3357 helix: 0.06 (0.12), residues: 1898 sheet: -1.53 (0.79), residues: 40 loop : -1.52 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP F 33 HIS 0.008 0.001 HIS N 68 PHE 0.042 0.003 PHE E 202 TYR 0.025 0.002 TYR H 79 ARG 0.013 0.001 ARG D 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5985.06 seconds wall clock time: 112 minutes 24.03 seconds (6744.03 seconds total)