Starting phenix.real_space_refine on Sun Aug 11 00:23:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqh_37745/08_2024/8wqh_37745_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqh_37745/08_2024/8wqh_37745.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqh_37745/08_2024/8wqh_37745.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqh_37745/08_2024/8wqh_37745.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqh_37745/08_2024/8wqh_37745_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqh_37745/08_2024/8wqh_37745_neut.cif" } resolution = 3.44 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= 0.017 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 7310 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 170 5.16 5 C 15710 2.51 5 N 4286 2.21 5 O 4639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 292": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 24811 Number of models: 1 Model: "" Number of chains: 14 Chain: "C" Number of atoms: 5228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 5228 Classifications: {'peptide': 637} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 619} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 677 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 5228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 5228 Classifications: {'peptide': 637} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 619} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 674 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 81} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" 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: "F" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 759 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 8, 'TRANS': 87} Chain breaks: 1 Chain: "D" 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: "I" 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: "K" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 744 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 7, 'TRANS': 86} Chain breaks: 1 Chain: "G" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "H" 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: "L" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 60 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 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} Chain: "B" 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 5491 SG CYS J 53 69.612 47.587 58.135 1.00 40.04 S ATOM 5514 SG CYS J 56 71.778 50.108 56.205 1.00 46.84 S ATOM 5598 SG CYS J 68 69.555 47.679 54.261 1.00 44.33 S ATOM 5405 SG CYS J 42 67.857 40.500 60.325 1.00 27.76 S ATOM 5424 SG CYS J 45 65.773 43.558 61.056 1.00 27.35 S ATOM 5719 SG CYS J 83 69.507 43.962 60.989 1.00 32.13 S ATOM 5648 SG CYS J 75 73.129 29.471 61.249 1.00 37.99 S ATOM 5815 SG CYS J 94 72.528 32.002 63.980 1.00 37.20 S ATOM 11396 SG CYS B 53 64.636 86.310 156.869 1.00 56.17 S ATOM 11419 SG CYS B 56 65.810 83.699 159.420 1.00 63.30 S ATOM 11503 SG CYS B 68 63.798 86.699 160.524 1.00 60.44 S ATOM 11310 SG CYS B 42 62.700 93.184 154.318 1.00 40.53 S ATOM 11329 SG CYS B 45 62.476 89.619 152.573 1.00 40.68 S ATOM 11621 SG CYS B 83 65.053 90.170 154.647 1.00 42.80 S ATOM 11553 SG CYS B 75 68.375 104.708 153.829 1.00 57.67 S ATOM 11717 SG CYS B 94 68.011 102.193 151.360 1.00 50.39 S Time building chain proxies: 14.66, per 1000 atoms: 0.59 Number of scatterers: 24811 At special positions: 0 Unit cell: (117.26, 135.3, 213.2, 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 170 16.00 O 4639 8.00 N 4286 7.00 C 15710 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: 9.87 Conformation dependent library (CDL) restraints added in 4.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 200 " pdb="ZN ZN B 200 " - pdb=" ND1 HIS B 82 " pdb="ZN ZN B 200 " - pdb=" SG CYS B 68 " pdb="ZN ZN B 200 " - pdb=" SG CYS B 53 " pdb="ZN ZN B 200 " - pdb=" SG CYS B 56 " pdb=" ZN B 201 " pdb="ZN ZN B 201 " - pdb=" ND1 HIS B 80 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 83 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 45 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 42 " pdb=" ZN B 202 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 75 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 94 " pdb="ZN ZN B 202 " - pdb=" ND1 HIS B 77 " pdb=" ZN J 200 " pdb="ZN ZN J 200 " - pdb=" ND1 HIS J 82 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 68 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 56 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 53 " pdb=" ZN J 201 " pdb="ZN ZN J 201 " - pdb=" ND1 HIS J 80 " pdb="ZN ZN J 201 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 201 " - pdb=" SG CYS J 42 " pdb="ZN ZN J 201 " - pdb=" SG CYS J 83 " pdb=" ZN J 202 " pdb="ZN ZN J 202 " - pdb=" SG CYS J 75 " pdb="ZN ZN J 202 " - pdb=" SG CYS J 94 " pdb="ZN ZN J 202 " - pdb=" ND1 HIS J 77 " Number of angles added : 12 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5934 Finding SS restraints... Secondary structure from input PDB file: 149 helices and 15 sheets defined 61.8% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.85 Creating SS restraints... Processing helix chain 'C' and resid 9 through 26 removed outlier: 4.012A pdb=" N ASN C 15 " --> pdb=" O ASP C 11 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR C 19 " --> pdb=" O ASN C 15 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR C 20 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA C 23 " --> pdb=" O THR C 19 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET C 26 " --> pdb=" O LYS C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 47 removed outlier: 3.688A pdb=" N PHE C 39 " --> pdb=" O TRP C 35 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER C 40 " --> pdb=" O ASN C 36 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP C 41 " --> pdb=" O ASP C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 67 Processing helix chain 'C' and resid 68 through 79 Processing helix chain 'C' and resid 82 through 105 removed outlier: 3.688A pdb=" N GLU C 93 " --> pdb=" O ARG C 89 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR C 94 " --> pdb=" O TYR C 90 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 112 Processing helix chain 'C' and resid 138 through 146 removed outlier: 3.716A pdb=" N LEU C 144 " --> pdb=" O GLY C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 151 removed outlier: 3.610A pdb=" N LEU C 150 " --> pdb=" O MET C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 172 removed outlier: 4.217A pdb=" N LEU C 164 " --> pdb=" O ILE C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 191 removed outlier: 3.615A pdb=" N PHE C 188 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL C 189 " --> pdb=" O ILE C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 207 Processing helix chain 'C' and resid 207 through 228 Processing helix chain 'C' and resid 231 through 250 removed outlier: 3.649A pdb=" N MET C 236 " --> pdb=" O CYS C 232 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N GLU C 237 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE C 248 " --> pdb=" O LYS C 244 " (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: 3.504A pdb=" N MET C 270 " --> pdb=" O CYS C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 287 removed outlier: 4.082A pdb=" N HIS C 283 " --> pdb=" O HIS C 279 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASN C 284 " --> pdb=" O ALA C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 304 removed outlier: 3.522A pdb=" N ASN C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA C 303 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 328 removed outlier: 3.721A pdb=" N MET C 311 " --> pdb=" O GLY C 307 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN C 313 " --> pdb=" O PRO C 309 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG C 325 " --> pdb=" O ASP C 321 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA C 326 " --> pdb=" O GLU C 322 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER C 328 " --> pdb=" O LEU C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 357 removed outlier: 3.721A pdb=" N ILE C 354 " --> pdb=" O PHE C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 377 Processing helix chain 'C' and resid 386 through 400 removed outlier: 3.569A pdb=" N LEU C 398 " --> pdb=" O TYR C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 423 removed outlier: 3.611A pdb=" N THR C 416 " --> pdb=" O GLU C 412 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER C 417 " --> pdb=" O ASP C 413 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR C 420 " --> pdb=" O THR C 416 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL C 421 " --> pdb=" O SER C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 445 removed outlier: 3.875A pdb=" N PHE C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS C 445 " --> pdb=" O LYS C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 470 removed outlier: 7.992A pdb=" N TYR C 467 " --> pdb=" O GLN C 463 " (cutoff:3.500A) removed outlier: 9.684A pdb=" N GLU C 468 " --> pdb=" O ALA C 464 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE C 469 " --> pdb=" O CYS C 465 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR C 470 " --> pdb=" O GLY C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 497 removed outlier: 4.670A pdb=" N ALA C 484 " --> pdb=" O MET C 480 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASP C 485 " --> pdb=" O SER C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 530 through 548 removed outlier: 4.195A pdb=" N SER C 536 " --> pdb=" O GLU C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 591 removed outlier: 4.842A pdb=" N VAL C 584 " --> pdb=" O TYR C 580 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER C 591 " --> pdb=" O ALA C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 604 removed outlier: 4.307A pdb=" N ASP C 601 " --> pdb=" O LYS C 597 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER C 602 " --> pdb=" O GLU C 598 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 619 removed outlier: 4.045A pdb=" N LYS C 612 " --> pdb=" O LYS C 608 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 58 removed outlier: 3.818A pdb=" N ALA J 58 " --> pdb=" O ILE J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 89 Processing helix chain 'A' and resid 13 through 25 removed outlier: 3.575A pdb=" N THR A 19 " --> pdb=" O ASN A 15 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 47 removed outlier: 3.896A pdb=" N PHE A 39 " --> pdb=" O TRP A 35 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER A 40 " --> pdb=" O ASN A 36 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP A 41 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 44 " --> pdb=" O SER A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 79 removed outlier: 3.897A pdb=" N ARG A 70 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS A 71 " --> pdb=" O ASN A 67 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 105 removed outlier: 3.692A pdb=" N GLU A 93 " --> pdb=" O ARG A 89 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR A 94 " --> pdb=" O TYR A 90 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 112 Processing helix chain 'A' and resid 138 through 146 removed outlier: 3.887A pdb=" N LEU A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 155 through 173 removed outlier: 3.522A pdb=" N ARG A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 191 removed outlier: 3.560A pdb=" N PHE A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 200 No H-bonds generated for 'chain 'A' and resid 198 through 200' Processing helix chain 'A' and resid 201 through 207 Processing helix chain 'A' and resid 207 through 229 removed outlier: 3.535A pdb=" N THR A 213 " --> pdb=" O SER A 209 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU A 214 " --> pdb=" O PRO A 210 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN A 228 " --> pdb=" O SER A 224 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 250 removed outlier: 3.788A pdb=" N MET A 236 " --> pdb=" O CYS A 232 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 258 through 271 removed outlier: 3.575A pdb=" N VAL A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 281 Processing helix chain 'A' and resid 281 through 288 removed outlier: 3.581A pdb=" N GLN A 288 " --> pdb=" O ASN A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 302 Processing helix chain 'A' and resid 307 through 325 removed outlier: 4.190A pdb=" N MET A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN A 317 " --> pdb=" O GLN A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 357 removed outlier: 3.896A pdb=" N VAL A 340 " --> pdb=" O PRO A 336 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU A 341 " --> pdb=" O THR A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 377 removed outlier: 3.725A pdb=" N ASN A 377 " --> pdb=" O THR A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 400 Processing helix chain 'A' and resid 407 through 417 Processing helix chain 'A' and resid 417 through 423 removed outlier: 4.112A pdb=" N VAL A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 445 removed outlier: 3.587A pdb=" N PHE A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A 441 " --> pdb=" O ARG A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 465 Processing helix chain 'A' and resid 471 through 482 Processing helix chain 'A' and resid 483 through 496 Processing helix chain 'A' and resid 530 through 547 removed outlier: 4.046A pdb=" N LYS A 535 " --> pdb=" O GLN A 531 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N SER A 536 " --> pdb=" O GLU A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 591 removed outlier: 3.823A pdb=" N VAL A 584 " --> pdb=" O TYR A 580 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 585 " --> pdb=" O GLN A 581 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 586 " --> pdb=" O MET A 582 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE A 588 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 604 removed outlier: 4.812A pdb=" N SER A 602 " --> pdb=" O GLU A 598 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 621 Processing helix chain 'B' and resid 53 through 58 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'E' and resid 33 through 37 Processing helix chain 'E' and resid 39 through 46 Processing helix chain 'E' and resid 66 through 83 removed outlier: 3.888A pdb=" N LYS E 72 " --> pdb=" O HIS E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 110 Processing helix chain 'F' and resid 23 through 36 removed outlier: 3.945A pdb=" N LEU F 27 " --> pdb=" O THR F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 40 No H-bonds generated for 'chain 'F' and resid 38 through 40' Processing helix chain 'D' and resid 2 through 15 Processing helix chain 'D' and resid 16 through 25 Processing helix chain 'D' and resid 28 through 36 Processing helix chain 'D' and resid 48 through 56 Processing helix chain 'D' and resid 58 through 68 removed outlier: 3.914A pdb=" N HIS D 68 " --> pdb=" O LEU D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 98 Processing helix chain 'D' and resid 100 through 111 Processing helix chain 'D' and resid 123 through 132 Processing helix chain 'D' and resid 133 through 143 removed outlier: 3.653A pdb=" N VAL D 137 " --> pdb=" O ARG D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 163 Processing helix chain 'D' and resid 166 through 176 removed outlier: 3.907A pdb=" N VAL D 170 " --> pdb=" O HIS D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 198 removed outlier: 3.634A pdb=" N PHE D 193 " --> pdb=" O THR D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 209 Processing helix chain 'D' and resid 221 through 229 Processing helix chain 'D' and resid 231 through 236 Processing helix chain 'D' and resid 237 through 242 removed outlier: 3.820A pdb=" N SER D 240 " --> pdb=" O LEU D 237 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA D 242 " --> pdb=" O LEU D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 262 removed outlier: 3.622A pdb=" N ASN D 262 " --> pdb=" O ALA D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 285 Processing helix chain 'D' and resid 310 through 317 Processing helix chain 'D' and resid 320 through 337 removed outlier: 3.699A pdb=" N LEU D 324 " --> pdb=" O ASP D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 356 removed outlier: 3.900A pdb=" N ILE D 347 " --> pdb=" O VAL D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 377 Processing helix chain 'D' and resid 381 through 398 Processing helix chain 'D' and resid 403 through 428 removed outlier: 3.618A pdb=" N ILE D 407 " --> pdb=" O LYS D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 456 Processing helix chain 'D' and resid 460 through 478 Processing helix chain 'D' and resid 486 through 493 removed outlier: 3.543A pdb=" N LEU D 490 " --> pdb=" O THR D 486 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA D 491 " --> pdb=" O LEU D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 507 removed outlier: 3.700A pdb=" N VAL D 506 " --> pdb=" O HIS D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 521 Processing helix chain 'D' and resid 534 through 541 removed outlier: 3.654A pdb=" N ILE D 538 " --> pdb=" O SER D 534 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE D 539 " --> pdb=" O ALA D 535 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN D 541 " --> pdb=" O HIS D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 563 removed outlier: 4.041A pdb=" N ILE D 555 " --> pdb=" O THR D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 591 Processing helix chain 'D' and resid 596 through 609 removed outlier: 3.619A pdb=" N ASN D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 627 Processing helix chain 'I' and resid 33 through 37 Processing helix chain 'I' and resid 39 through 47 Processing helix chain 'I' and resid 66 through 83 removed outlier: 4.287A pdb=" N LYS I 72 " --> pdb=" O HIS I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 110 removed outlier: 4.669A pdb=" N LEU I 101 " --> pdb=" O PRO I 97 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N GLU I 102 " --> pdb=" O GLU I 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 36 removed outlier: 3.979A pdb=" N LEU K 27 " --> pdb=" O THR K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 42 removed outlier: 3.781A pdb=" N GLU K 41 " --> pdb=" O PRO K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 61 removed outlier: 4.023A pdb=" N GLY K 61 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 15 Processing helix chain 'H' and resid 16 through 25 Processing helix chain 'H' and resid 28 through 36 Processing helix chain 'H' and resid 48 through 56 removed outlier: 3.514A pdb=" N ASN H 56 " --> pdb=" O ILE H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 69 Processing helix chain 'H' and resid 90 through 99 removed outlier: 3.532A pdb=" N CYS H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 110 Processing helix chain 'H' and resid 123 through 132 removed outlier: 3.508A pdb=" N ASP H 131 " --> pdb=" O ALA H 127 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY H 132 " --> pdb=" O ALA H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 143 Processing helix chain 'H' and resid 156 through 163 removed outlier: 3.550A pdb=" N TYR H 163 " --> pdb=" O MET H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 176 removed outlier: 3.731A pdb=" N VAL H 170 " --> pdb=" O HIS H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 189 through 197 removed outlier: 3.642A pdb=" N PHE H 193 " --> pdb=" O THR H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 209 Processing helix chain 'H' and resid 221 through 229 Processing helix chain 'H' and resid 231 through 236 Processing helix chain 'H' and resid 237 through 242 removed outlier: 4.020A pdb=" N SER H 240 " --> pdb=" O LEU H 237 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA H 242 " --> pdb=" O LEU H 239 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 261 removed outlier: 3.762A pdb=" N ALA H 261 " --> pdb=" O GLY H 257 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 284 Processing helix chain 'H' and resid 310 through 317 removed outlier: 3.650A pdb=" N LEU H 314 " --> pdb=" O ASN H 310 " (cutoff:3.500A) Processing helix chain 'H' and resid 320 through 337 removed outlier: 3.530A pdb=" N GLY H 328 " --> pdb=" O LEU H 324 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL H 331 " --> pdb=" O GLU H 327 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU H 336 " --> pdb=" O ARG H 332 " (cutoff:3.500A) Processing helix chain 'H' and resid 343 through 355 removed outlier: 3.993A pdb=" N ILE H 347 " --> pdb=" O VAL H 343 " (cutoff:3.500A) Processing helix chain 'H' and resid 356 through 358 No H-bonds generated for 'chain 'H' and resid 356 through 358' Processing helix chain 'H' and resid 360 through 377 removed outlier: 3.812A pdb=" N LYS H 365 " --> pdb=" O GLU H 361 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU H 366 " --> pdb=" O GLN H 362 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP H 367 " --> pdb=" O CYS H 363 " (cutoff:3.500A) Processing helix chain 'H' and resid 381 through 398 Processing helix chain 'H' and resid 403 through 428 removed outlier: 3.772A pdb=" N ILE H 407 " --> pdb=" O LYS H 403 " (cutoff:3.500A) Processing helix chain 'H' and resid 432 through 456 Processing helix chain 'H' and resid 460 through 478 Processing helix chain 'H' and resid 486 through 493 Processing helix chain 'H' and resid 502 through 507 removed outlier: 3.671A pdb=" N VAL H 506 " --> pdb=" O HIS H 502 " (cutoff:3.500A) Processing helix chain 'H' and resid 511 through 521 Processing helix chain 'H' and resid 534 through 540 removed outlier: 3.732A pdb=" N ILE H 538 " --> pdb=" O SER H 534 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE H 539 " --> pdb=" O ALA H 535 " (cutoff:3.500A) Processing helix chain 'H' and resid 548 through 562 removed outlier: 3.999A pdb=" N ILE H 555 " --> pdb=" O THR H 551 " (cutoff:3.500A) Processing helix chain 'H' and resid 577 through 581 removed outlier: 3.652A pdb=" N SER H 580 " --> pdb=" O LEU H 577 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N THR H 581 " --> pdb=" O ASP H 578 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 577 through 581' Processing helix chain 'H' and resid 582 through 591 Processing helix chain 'H' and resid 596 through 608 removed outlier: 3.853A pdb=" N ASN H 608 " --> pdb=" O ALA H 604 " (cutoff:3.500A) Processing helix chain 'H' and resid 617 through 627 removed outlier: 3.908A pdb=" N GLU H 622 " --> pdb=" O ARG H 618 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE H 623 " --> pdb=" O THR H 619 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N HIS H 627 " --> pdb=" O PHE H 623 " (cutoff:3.500A) Processing helix chain 'L' and resid -22 through -18 Processing sheet with id=AA1, first strand: chain 'C' and resid 506 through 513 Processing sheet with id=AA2, first strand: chain 'C' and resid 506 through 513 removed outlier: 5.845A pdb=" N VAL J 24 " --> pdb=" O LYS C 565 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LYS C 565 " --> pdb=" O VAL J 24 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS J 26 " --> pdb=" O GLU C 563 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL C 574 " --> pdb=" O PHE C 651 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 593 through 594 Processing sheet with id=AA4, first strand: chain 'J' and resid 41 through 42 removed outlier: 3.682A pdb=" N ASN J 47 " --> pdb=" O CYS J 42 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 70 through 71 Processing sheet with id=AA6, first strand: chain 'A' and resid 506 through 513 removed outlier: 3.631A pdb=" N GLN A 508 " --> pdb=" O TRP B 27 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 31 " --> pdb=" O TYR A 510 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL B 24 " --> pdb=" O LYS A 565 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LYS A 565 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS B 26 " --> pdb=" O GLU A 563 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N VAL B 30 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU A 559 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 10.169A pdb=" N LEU B 32 " --> pdb=" O HIS A 557 " (cutoff:3.500A) removed outlier: 9.439A pdb=" N HIS A 557 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 11.030A pdb=" N ALA B 34 " --> pdb=" O TRP A 555 " (cutoff:3.500A) removed outlier: 10.789A pdb=" N TRP A 555 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 623 through 625 Processing sheet with id=AA8, first strand: chain 'B' and resid 70 through 72 Processing sheet with id=AA9, first strand: chain 'E' and resid 59 through 61 removed outlier: 4.681A pdb=" N LYS E 32 " --> pdb=" O PHE F 15 " (cutoff:3.500A) removed outlier: 10.348A pdb=" N ASP F 17 " --> pdb=" O LYS E 32 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA F 73 " --> pdb=" O PHE F 4 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 42 through 44 removed outlier: 3.790A pdb=" N ARG F 43 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA F 78 " --> pdb=" O ARG F 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 40 through 42 Processing sheet with id=AB3, first strand: chain 'D' and resid 78 through 79 removed outlier: 4.089A pdb=" N ILE D 86 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 31 through 32 Processing sheet with id=AB5, first strand: chain 'K' and resid 13 through 18 removed outlier: 6.392A pdb=" N PHE K 4 " --> pdb=" O ALA K 73 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL K 75 " --> pdb=" O PHE K 4 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N MET K 6 " --> pdb=" O VAL K 75 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LEU K 77 " --> pdb=" O MET K 6 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ARG K 8 " --> pdb=" O LEU K 77 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALA K 78 " --> pdb=" O ARG K 43 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG K 43 " --> pdb=" O ALA K 78 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 40 through 42 1256 hydrogen bonds defined for protein. 3708 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: 7.79 Time building geometry restraints manager: 10.58 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: 8200 1.34 - 1.46: 4245 1.46 - 1.58: 12589 1.58 - 1.69: 0 1.69 - 1.81: 262 Bond restraints: 25296 Sorted by residual: bond pdb=" C LEU A 308 " pdb=" N PRO A 309 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.58e+00 bond pdb=" N ASP F 47 " pdb=" CA ASP F 47 " ideal model delta sigma weight residual 1.457 1.478 -0.021 1.29e-02 6.01e+03 2.67e+00 bond pdb=" CB CYS B 45 " pdb=" SG CYS B 45 " ideal model delta sigma weight residual 1.808 1.765 0.043 3.30e-02 9.18e+02 1.70e+00 bond pdb=" CG1 ILE D 539 " pdb=" CD1 ILE D 539 " ideal model delta sigma weight residual 1.513 1.466 0.047 3.90e-02 6.57e+02 1.42e+00 bond pdb=" N ASN H 399 " pdb=" CA ASN H 399 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.19e+00 ... (remaining 25291 not shown) Histogram of bond angle deviations from ideal: 99.39 - 106.32: 582 106.32 - 113.25: 13894 113.25 - 120.18: 8968 120.18 - 127.11: 10500 127.11 - 134.03: 259 Bond angle restraints: 34203 Sorted by residual: angle pdb=" N VAL C 24 " pdb=" CA VAL C 24 " pdb=" C VAL C 24 " ideal model delta sigma weight residual 113.42 108.38 5.04 1.17e+00 7.31e-01 1.86e+01 angle pdb=" N GLU B 66 " pdb=" CA GLU B 66 " pdb=" C GLU B 66 " ideal model delta sigma weight residual 114.56 109.75 4.81 1.27e+00 6.20e-01 1.44e+01 angle pdb=" CB MET E 75 " pdb=" CG MET E 75 " pdb=" SD MET E 75 " ideal model delta sigma weight residual 112.70 122.96 -10.26 3.00e+00 1.11e-01 1.17e+01 angle pdb=" N MET C 270 " pdb=" CA MET C 270 " pdb=" C MET C 270 " ideal model delta sigma weight residual 114.56 110.84 3.72 1.27e+00 6.20e-01 8.60e+00 angle pdb=" C LEU D 398 " pdb=" N ASN D 399 " pdb=" CA ASN D 399 " ideal model delta sigma weight residual 122.46 126.43 -3.97 1.41e+00 5.03e-01 7.94e+00 ... (remaining 34198 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 13654 17.71 - 35.42: 1380 35.42 - 53.13: 236 53.13 - 70.84: 47 70.84 - 88.55: 18 Dihedral angle restraints: 15335 sinusoidal: 6208 harmonic: 9127 Sorted by residual: dihedral pdb=" CA LEU E 101 " pdb=" C LEU E 101 " pdb=" N GLU E 102 " pdb=" CA GLU E 102 " ideal model delta harmonic sigma weight residual 180.00 160.13 19.87 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA GLU D 359 " pdb=" C GLU D 359 " pdb=" N PHE D 360 " pdb=" CA PHE D 360 " ideal model delta harmonic sigma weight residual -180.00 -160.98 -19.02 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA CYS A 465 " pdb=" C CYS A 465 " pdb=" N GLY A 466 " pdb=" CA GLY A 466 " ideal model delta harmonic sigma weight residual -180.00 -162.10 -17.90 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 15332 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2893 0.043 - 0.086: 767 0.086 - 0.129: 168 0.129 - 0.172: 17 0.172 - 0.215: 4 Chirality restraints: 3849 Sorted by residual: chirality pdb=" CB VAL C 620 " pdb=" CA VAL C 620 " pdb=" CG1 VAL C 620 " pdb=" CG2 VAL C 620 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB ILE C 501 " pdb=" CA ILE C 501 " pdb=" CG1 ILE C 501 " pdb=" CG2 ILE C 501 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB ILE I 90 " pdb=" CA ILE I 90 " pdb=" CG1 ILE I 90 " pdb=" CG2 ILE I 90 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 3846 not shown) Planarity restraints: 4389 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 392 " -0.023 2.00e-02 2.50e+03 1.80e-02 5.67e+00 pdb=" CG PHE D 392 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE D 392 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE D 392 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 392 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 392 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE D 392 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 575 " 0.035 5.00e-02 4.00e+02 5.31e-02 4.52e+00 pdb=" N PRO D 576 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO D 576 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 576 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE H 616 " -0.032 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO H 617 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO H 617 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 617 " -0.027 5.00e-02 4.00e+02 ... (remaining 4386 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 250 2.62 - 3.19: 22249 3.19 - 3.76: 40248 3.76 - 4.33: 54057 4.33 - 4.90: 87807 Nonbonded interactions: 204611 Sorted by model distance: nonbonded pdb=" OD1 ASP B 97 " pdb="ZN ZN B 202 " model vdw 2.051 2.230 nonbonded pdb=" OH TYR C 235 " pdb=" O MET C 270 " model vdw 2.151 3.040 nonbonded pdb=" OG1 THR H 167 " pdb=" OD2 ASP H 201 " model vdw 2.154 3.040 nonbonded pdb=" OG1 THR D 167 " pdb=" OD2 ASP D 201 " model vdw 2.174 3.040 nonbonded pdb=" OH TYR C 219 " pdb=" OE1 GLU C 246 " model vdw 2.207 3.040 ... (remaining 204606 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = (chain 'J' 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 104 or resid 200 through 202)) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'I' } ncs_group { reference = (chain 'F' and resid 2 through 98) selection = chain 'K' } ncs_group { reference = (chain 'G' and (resid -22 through -17 or (resid -16 and (name N or name CA or na \ me C or name O or name CB )))) selection = (chain 'L' and resid -22 through -16) } 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 individual isotropic 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: 8.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.030 Extract box with map and model: 0.960 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 70.350 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.120 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 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 0.054 25296 Z= 0.195 Angle : 0.538 10.261 34203 Z= 0.293 Chirality : 0.040 0.215 3849 Planarity : 0.004 0.053 4389 Dihedral : 14.589 88.555 9401 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % 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: -0.88 (0.15), residues: 3059 helix: -0.12 (0.12), residues: 1777 sheet: -1.02 (0.70), residues: 54 loop : -1.12 (0.18), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 33 HIS 0.004 0.001 HIS D 476 PHE 0.040 0.001 PHE D 392 TYR 0.020 0.001 TYR I 76 ARG 0.003 0.000 ARG J 91 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 521 time to evaluate : 2.653 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: A 480 MET cc_start: 0.8275 (tpp) cc_final: 0.8067 (tpp) REVERT: A 542 LEU cc_start: 0.8634 (mm) cc_final: 0.8408 (mp) REVERT: B 86 ARG cc_start: 0.7920 (ttm-80) cc_final: 0.7679 (mtp85) REVERT: E 99 ILE cc_start: 0.8685 (tt) cc_final: 0.8459 (tt) REVERT: F 25 PHE cc_start: 0.5700 (t80) cc_final: 0.5380 (t80) REVERT: F 55 LYS cc_start: 0.5807 (pttm) cc_final: 0.5533 (ptpp) REVERT: D 329 LEU cc_start: 0.8683 (mt) cc_final: 0.8355 (mt) REVERT: D 330 ILE cc_start: 0.8620 (mt) cc_final: 0.8070 (pt) REVERT: D 350 ARG cc_start: 0.7657 (tpm170) cc_final: 0.7111 (mmt-90) REVERT: D 354 TYR cc_start: 0.6447 (t80) cc_final: 0.5946 (t80) REVERT: D 359 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6805 (mt-10) REVERT: D 373 LEU cc_start: 0.8877 (mt) cc_final: 0.8513 (tt) REVERT: D 392 PHE cc_start: 0.7774 (m-10) cc_final: 0.7404 (m-80) REVERT: K 51 LEU cc_start: 0.4906 (mp) cc_final: 0.4640 (mt) REVERT: H 102 GLU cc_start: 0.6116 (pm20) cc_final: 0.5708 (pm20) REVERT: H 304 ASN cc_start: 0.6971 (m-40) cc_final: 0.6403 (p0) REVERT: H 367 TRP cc_start: 0.8278 (m-10) cc_final: 0.7698 (m-10) REVERT: H 369 HIS cc_start: 0.7901 (t70) cc_final: 0.7594 (t-90) REVERT: L -18 ASP cc_start: 0.5050 (p0) cc_final: 0.4822 (p0) outliers start: 0 outliers final: 0 residues processed: 521 average time/residue: 0.3943 time to fit residues: 310.2958 Evaluate side-chains 316 residues out of total 2741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 316 time to evaluate : 2.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 255 optimal weight: 10.0000 chunk 228 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 154 optimal weight: 0.0970 chunk 122 optimal weight: 2.9990 chunk 236 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 176 optimal weight: 7.9990 chunk 274 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 36 ASN C 111 GLN C 221 GLN C 320 HIS C 521 GLN ** C 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 HIS A 508 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 GLN D 176 GLN D 372 HIS D 420 GLN D 470 GLN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 300 HIS H 420 GLN ** H 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25296 Z= 0.254 Angle : 0.605 9.733 34203 Z= 0.320 Chirality : 0.041 0.368 3849 Planarity : 0.004 0.050 4389 Dihedral : 4.340 51.162 3345 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.28 % Allowed : 8.05 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % 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: -0.33 (0.15), residues: 3059 helix: 0.39 (0.12), residues: 1827 sheet: -1.41 (0.62), residues: 63 loop : -1.01 (0.19), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 367 HIS 0.008 0.001 HIS D 372 PHE 0.029 0.002 PHE D 392 TYR 0.024 0.001 TYR D 163 ARG 0.007 0.001 ARG F 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 341 time to evaluate : 2.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 145 ASP cc_start: 0.8640 (t0) cc_final: 0.8427 (t0) REVERT: A 335 MET cc_start: 0.7951 (ttp) cc_final: 0.7742 (ttt) REVERT: A 480 MET cc_start: 0.8367 (tpp) cc_final: 0.8072 (tpp) REVERT: A 497 GLN cc_start: 0.6765 (tm-30) cc_final: 0.6520 (tm-30) REVERT: A 638 PHE cc_start: 0.8544 (m-80) cc_final: 0.8272 (m-10) REVERT: B 86 ARG cc_start: 0.7944 (ttm-80) cc_final: 0.7608 (mtp85) REVERT: E 99 ILE cc_start: 0.8771 (tt) cc_final: 0.8409 (tt) REVERT: D 350 ARG cc_start: 0.7686 (tpm170) cc_final: 0.7148 (mmt-90) REVERT: D 354 TYR cc_start: 0.6666 (t80) cc_final: 0.6371 (t80) REVERT: D 373 LEU cc_start: 0.8883 (mt) cc_final: 0.8609 (tt) REVERT: D 386 LEU cc_start: 0.9231 (tt) cc_final: 0.8838 (mt) REVERT: I 47 SER cc_start: 0.8854 (t) cc_final: 0.8390 (m) REVERT: K 53 ASP cc_start: 0.6711 (t0) cc_final: 0.6487 (t0) REVERT: H 102 GLU cc_start: 0.6137 (pm20) cc_final: 0.5698 (pm20) REVERT: H 304 ASN cc_start: 0.7219 (m-40) cc_final: 0.6851 (p0) REVERT: H 336 LEU cc_start: 0.4042 (mt) cc_final: 0.3801 (mp) REVERT: H 367 TRP cc_start: 0.8279 (m-10) cc_final: 0.8051 (m-10) outliers start: 35 outliers final: 21 residues processed: 358 average time/residue: 0.3522 time to fit residues: 197.8141 Evaluate side-chains 320 residues out of total 2741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 299 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain D residue 153 TYR Chi-restraints excluded: chain D residue 453 ILE Chi-restraints exclu------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 GLN C 521 GLN C 546 GLN ** C 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 300 HIS H 362 GLN ** H 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25296 Z= 0.184 Angle : 0.562 10.332 34203 Z= 0.295 Chirality : 0.040 0.341 3849 Planarity : 0.004 0.048 4389 Dihedral : 4.289 51.508 3345 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.17 % Allowed : 10.76 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % 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: -0.18 (0.15), residues: 3059 helix: 0.50 (0.12), residues: 1865 sheet: -1.75 (0.62), residues: 54 loop : -0.97 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 33 HIS 0.008 0.001 HIS H 300 PHE 0.027 0.001 PHE C 527 TYR 0.040 0.002 TYR D 163 ARG 0.007 0.000 ARG F 29 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 326 time to evaluate : 2.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 297 MET cc_start: 0.8083 (ttm) cc_final: 0.7863 (ttm) REVERT: A 236 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8181 (mtt) REVERT: A 427 ASP cc_start: 0.7587 (t70) cc_final: 0.7382 (t70) REVERT: A 438 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7637 (mtt) REVERT: A 480 MET cc_start: 0.8218 (tpp) cc_final: 0.8014 (tpp) REVERT: A 497 GLN cc_start: 0.6729 (tm-30) cc_final: 0.6427 (tm-30) REVERT: A 638 PHE cc_start: 0.8508 (m-80) cc_final: 0.8214 (m-10) REVERT: B 86 ARG cc_start: 0.7907 (ttm-80) cc_final: 0.7585 (mtp85) REVERT: E 99 ILE cc_start: 0.8732 (tt) cc_final: 0.8364 (tt) REVERT: F 22 SER cc_start: 0.8001 (p) cc_final: 0.7769 (t) REVERT: F 29 ARG cc_start: 0.7791 (ttp-110) cc_final: 0.7459 (ptm160) REVERT: D 350 ARG cc_start: 0.7772 (tpm170) cc_final: 0.7336 (mmp-170) REVERT: D 354 TYR cc_start: 0.6711 (t80) cc_final: 0.6378 (t80) REVERT: D 373 LEU cc_start: 0.8835 (mt) cc_final: 0.8586 (tt) REVERT: D 386 LEU cc_start: 0.9197 (tt) cc_final: 0.8819 (mt) REVERT: D 440 TYR cc_start: 0.7087 (t80) cc_final: 0.6389 (t80) REVERT: I 47 SER cc_start: 0.8722 (t) cc_final: 0.8186 (m) REVERT: H 102 GLU cc_start: 0.6172 (pm20) cc_final: 0.5727 (pm20) REVERT: H 304 ASN cc_start: 0.7200 (m-40) cc_final: 0.6857 (p0) REVERT: H 367 TRP cc_start: 0.8350 (m-10) cc_final: 0.7838 (m-10) REVERT: H 369 HIS cc_start: 0.7897 (t70) cc_final: 0.7625 (t-90) REVERT: H 388 PHE cc_start: 0.7706 (t80) cc_final: 0.7121 (t80) REVERT: H 555 ILE cc_start: 0.8425 (mt) cc_final: 0.8209 (mt) outliers start: 32 outliers final: 20 residues processed: 344 average time/residue: 0.3398 time to fit residues: 182.3342 Evaluate side-chains 312 residues out of total 2741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 290 time to evaluate : 2.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain D residue 153 TYR Chi-restraints excluded: chain I residue 23 SER Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain H residue 300 HIS Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 513 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 271 optimal weight: 0.6980 chunk 206 optimal weight: 0.9980 chunk 142 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 131 optimal weight: 9.9990 chunk 184 optimal weight: 9.9990 chunk 275 optimal weight: 2.9990 chunk 291 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 GLN ** C 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 ASN ** D 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLEvaluate side-chains 314 residues out of total 2741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 284 time to evaluate : 2.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 139 TYR Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain I residue 23 SER Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain H residue 300 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 243 optimal weight: 10.0000 chunk 165 optimal weight: 20.0000 chunk 4 optimal weight: 0.5980 chunk 217 optimal weight: 0.9980 chunk 120 optimal weight: 0.5980 chunk 249 optimal weight: 20.0000 chunk 201 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 149 optimal weight: 0.0970 chunk 262 optimal weight: 8.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: