Starting phenix.real_space_refine on Wed Apr 8 18:15:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rhp_19178/04_2026/8rhp_19178.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rhp_19178/04_2026/8rhp_19178.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8rhp_19178/04_2026/8rhp_19178.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rhp_19178/04_2026/8rhp_19178.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rhp_19178/04_2026/8rhp_19178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rhp_19178/04_2026/8rhp_19178.map" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 7 Type Number sf(0) Gaussians Mo 4 10.26 5 Ca 4 9.91 5 Fe 72 7.16 5 S 384 5.16 5 C 26986 2.51 5 N 7216 2.21 5 O 8062 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42728 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 456} Chain: "B" Number of atoms: 4179 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 522, 4173 Classifications: {'peptide': 522} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Conformer: "B" Number of residues, atoms: 522, 4173 Classifications: {'peptide': 522} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} bond proxies already assigned to first conformer: 4272 Chain: "C" Number of atoms: 4190 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 522, 4173 Classifications: {'peptide': 522} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Conformer: "B" Number of residues, atoms: 522, 4173 Classifications: {'peptide': 522} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} bond proxies already assigned to first conformer: 4260 Chain: "D" Number of atoms: 3805 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Conformer: "B" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} bond proxies already assigned to first conformer: 3863 Conformer: "C" Number of residues, atoms: 477, 3781 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Unresolved chain link angles: 4 Unresolved chain link dihedrals: 8 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 bond proxies already assigned to first conformer: 3863 Chain: "E" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 918 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain: "F" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2187 Classifications: {'peptide': 289} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 280} Chain: "G" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2187 Classifications: {'peptide': 289} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 280} Chain: "H" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 456} Chain: "I" Number of atoms: 4179 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 522, 4173 Classifications: {'peptide': 522} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Conformer: "B" Number of residues, atoms: 522, 4173 Classifications: {'peptide': 522} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} bond proxies already assigned to first conformer: 4272 Chain: "J" Number of atoms: 4190 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 522, 4173 Classifications: {'peptide': 522} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Conformer: "B" Number of residues, atoms: 522, 4173 Classifications: {'peptide': 522} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} bond proxies already assigned to first conformer: 4260 Chain: "K" Number of atoms: 3805 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Conformer: "B" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} bond proxies already assigned to first conformer: 3863 Conformer: "C" Number of residues, atoms: 477, 3781 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Unresolved chain link angles: 4 Unresolved chain link dihedrals: 8 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 bond proxies already assigned to first conformer: 3863 Chain: "L" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 918 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain: "M" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2187 Classifications: {'peptide': 289} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 280} Chain: "N" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2187 Classifications: {'peptide': 289} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 280} Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 47 Unusual residues: {'CLF': 1, 'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 2, 16 Unusual residues: {' CA': 1, 'CLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 2, 16 Unusual residues: {' CA': 1, 'CLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 16 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 2, 16 Unusual residues: {' CA': 1, 'CLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1170 SG CYS A 154 36.584 33.295 40.938 1.00123.08 S ATOM 4549 SG CYS B 95 40.893 34.714 43.833 1.00 97.36 S ATOM 465 SG CYS A 62 39.764 38.659 38.763 1.00114.86 S ATOM 652 SG CYS A 88 35.829 38.048 44.549 1.00111.83 S ATOM 652 SG CYS A 88 35.829 38.048 44.549 1.00111.83 S ATOM 5008 SG CYS B 153 36.097 32.904 45.553 1.00138.21 S ATOM 4369 SG CYS B 70 39.772 37.095 50.095 1.00124.61 S ATOM 4549 SG CYS B 95 40.893 34.714 43.833 1.00 97.36 S ATOM 2089 SG CYS A 275 43.411 49.876 26.141 1.00116.93 S ATOM 13335 SG CYS D 154 67.084 90.695 87.429 1.00 87.15 S ATOM 8728 SG CYS C 95 67.053 85.395 86.502 1.00 78.88 S ATOM 12624 SG CYS D 62 61.294 88.449 87.364 1.00118.03 S ATOM 12817 SG CYS D 88 65.275 88.706 81.788 1.00 91.06 S ATOM 12817 SG CYS D 88 65.275 88.706 81.788 1.00 91.06 S ATOM 9181 SG CYS C 153 70.246 88.764 83.510 1.00 93.61 S ATOM 8548 SG CYS C 70 68.226 82.676 80.422 1.00 87.47 S ATOM 8728 SG CYS C 95 67.053 85.395 86.502 1.00 78.88 S ATOM 14263 SG CYS D 275 44.953 90.578 92.287 1.00114.08 S ATOM 16274 SG CYS E 42 78.698 100.663 106.590 1.00123.62 S ATOM 16309 SG CYS E 47 77.992 103.056 109.312 1.00109.80 S ATOM 16325 SG CYS E 50 73.730 105.287 105.643 1.00114.94 S ATOM 16736 SG CYS E 102 74.706 102.375 103.637 1.00102.22 S ATOM 19758 SG CYS G 98 78.251 113.501 117.794 1.00 66.76 S ATOM 17571 SG CYS F 98 75.480 107.342 118.724 1.00 88.42 S ATOM 17842 SG CYS F 133 77.231 110.642 123.620 1.00125.95 S ATOM 20029 SG CYS G 133 81.396 108.193 119.485 1.00 82.26 S ATOM 23345 SG CYS H 275 79.689 190.828 25.975 1.00119.82 S ATOM 22426 SG CYS H 154 86.308 207.339 41.026 1.00124.37 S ATOM 25805 SG CYS I 95 82.182 205.928 43.719 1.00 97.92 S ATOM 21721 SG CYS H 62 83.078 202.035 38.745 1.00115.72 S ATOM 21908 SG CYS H 88 87.088 202.502 44.539 1.00113.63 S ATOM 21908 SG CYS H 88 87.088 202.502 44.539 1.00113.63 S ATOM 26264 SG CYS I 153 86.869 207.636 45.743 1.00140.13 S ATOM 25625 SG CYS I 70 83.136 203.469 50.087 1.00128.18 S ATOM 25805 SG CYS I 95 82.182 205.928 43.719 1.00 97.92 S ATOM 34591 SG CYS K 154 55.834 149.880 87.428 1.00 88.50 S ATOM 29984 SG CYS J 95 55.865 155.179 86.502 1.00 83.15 S ATOM 33880 SG CYS K 62 61.626 152.122 87.365 1.00118.53 S ATOM 34073 SG CYS K 88 57.645 151.867 81.789 1.00 93.06 S ATOM 34073 SG CYS K 88 57.645 151.867 81.789 1.00 93.06 S ATOM 30437 SG CYS J 153 52.807 151.709 83.498 1.00 97.15 S ATOM 29804 SG CYS J 70 54.695 157.895 80.422 1.00 90.80 S ATOM 29984 SG CYS J 95 55.865 155.179 86.502 1.00 83.15 S ATOM 35519 SG CYS K 275 77.968 149.996 92.289 1.00115.89 S ATOM 37530 SG CYS L 42 44.290 139.643 106.943 1.00125.67 S ATOM 37565 SG CYS L 47 45.124 137.237 109.317 1.00111.36 S ATOM 37581 SG CYS L 50 49.048 135.215 105.400 1.00117.90 S ATOM 37992 SG CYS L 102 48.468 137.877 103.376 1.00104.64 S ATOM 41014 SG CYS N 98 44.675 127.070 117.805 1.00 68.03 S ATOM 38827 SG CYS M 98 47.442 133.230 118.731 1.00 89.95 S ATOM 39098 SG CYS M 133 45.693 129.934 123.628 1.00128.13 S ATOM 41285 SG CYS N 133 41.534 132.390 119.477 1.00 80.94 S Residues with excluded nonbonded symmetry interactions: 10 residue: pdb=" N ASER B 101 " occ=0.65 ... (10 atoms not shown) pdb=" OG BSER B 101 " occ=0.35 residue: pdb=" N ASER C 252 " occ=0.62 ... (10 atoms not shown) pdb=" OG BSER C 252 " occ=0.38 residue: pdb=" N AARG C 453 " occ=0.51 ... (20 atoms not shown) pdb=" NH2BARG C 453 " occ=0.49 residue: pdb=" N ASER I 101 " occ=0.72 ... (10 atoms not shown) pdb=" OG BSER I 101 " occ=0.28 residue: pdb=" N ASER J 252 " occ=0.60 ... (10 atoms not shown) pdb=" OG BSER J 252 " occ=0.40 residue: pdb=" N AARG J 453 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG J 453 " occ=0.50 residue: pdb="CA CA B 601 " occ=0.49 residue: pdb=" S1 BCLF C 602 " occ=0.93 ... (13 atoms not shown) pdb="FE8 BCLF C 602 " occ=0.93 residue: pdb="CA CA I 602 " occ=0.55 residue: pdb=" S1 BCLF J 602 " occ=0.82 ... (13 atoms not shown) pdb="FE8 BCLF J 602 " occ=0.82 Time building chain proxies: 14.92, per 1000 atoms: 0.35 Number of scatterers: 42728 At special positions: 0 Unit cell: (123.798, 241.45, 168.576, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mo 4 41.97 Fe 72 26.01 Ca 4 19.99 S 384 16.00 O 8062 8.00 N 7216 7.00 C 26986 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=32, symmetry=0 Number of additional bonds: simple=32, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.83 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 47 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 102 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 50 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 42 " pdb=" FES L 201 " pdb="FE1 FES L 201 " - pdb=" SG CYS L 47 " pdb="FE1 FES L 201 " - pdb=" SG CYS L 42 " pdb="FE2 FES L 201 " - pdb=" SG CYS L 50 " pdb="FE2 FES L 201 " - pdb=" SG CYS L 102 " pdb=" SF4 F 301 " pdb="FE3 SF4 F 301 " - pdb=" SG CYS F 133 " pdb="FE4 SF4 F 301 " - pdb=" SG CYS G 133 " pdb="FE2 SF4 F 301 " - pdb=" SG CYS F 98 " pdb="FE1 SF4 F 301 " - pdb=" SG CYS G 98 " pdb=" SF4 M 301 " pdb="FE3 SF4 M 301 " - pdb=" SG CYS M 133 " pdb="FE4 SF4 M 301 " - pdb=" SG CYS N 133 " pdb="FE1 SF4 M 301 " - pdb=" SG CYS N 98 " pdb="FE2 SF4 M 301 " - pdb=" SG CYS M 98 " Number of angles added : 36 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9884 Finding SS restraints... Secondary structure from input PDB file: 269 helices and 32 sheets defined 54.3% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 21 through 30 removed outlier: 3.943A pdb=" N LYS A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 85 through 92 removed outlier: 4.675A pdb=" N GLY A 89 " --> pdb=" O PRO A 85 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 92 " --> pdb=" O CYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.853A pdb=" N GLY A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.763A pdb=" N VAL A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A 172 " --> pdb=" O LYS A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 206 removed outlier: 3.671A pdb=" N HIS A 196 " --> pdb=" O SER A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 233 through 245 Processing helix chain 'A' and resid 258 through 265 removed outlier: 3.647A pdb=" N ILE A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 275 through 291 removed outlier: 3.562A pdb=" N MET A 279 " --> pdb=" O CYS A 275 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N TYR A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 315 removed outlier: 3.576A pdb=" N LYS A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 343 removed outlier: 3.504A pdb=" N GLN A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 344 through 347 removed outlier: 3.877A pdb=" N GLU A 347 " --> pdb=" O PRO A 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 344 through 347' Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 383 through 392 removed outlier: 3.874A pdb=" N LYS A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 424 through 434 removed outlier: 4.531A pdb=" N PHE A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ILE A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 451 through 468 Processing helix chain 'A' and resid 469 through 474 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 17 through 31 Processing helix chain 'B' and resid 36 through 48 Processing helix chain 'B' and resid 49 through 57 Processing helix chain 'B' and resid 70 through 80 removed outlier: 3.940A pdb=" N GLY B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 4.076A pdb=" N VAL B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 removed outlier: 3.888A pdb=" N VAL B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 142 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 161 through 172 Processing helix chain 'B' and resid 192 through 210 Processing helix chain 'B' and resid 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'B' and resid 233 through 248 removed outlier: 3.752A pdb=" N PHE B 237 " --> pdb=" O TYR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 removed outlier: 4.085A pdb=" N THR B 263 " --> pdb=" O VAL B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 341 through 363 removed outlier: 3.639A pdb=" N THR B 345 " --> pdb=" O PRO B 341 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N THR B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N TRP B 361 " --> pdb=" O ASP B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 387 Processing helix chain 'B' and resid 399 through 412 Processing helix chain 'B' and resid 426 through 437 Processing helix chain 'B' and resid 447 through 459 removed outlier: 4.182A pdb=" N ILE B 451 " --> pdb=" O TYR B 447 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG B 453 " --> pdb=" O LYS B 449 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY B 459 " --> pdb=" O THR B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 463 Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 485 through 509 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.683A pdb=" N ASN B 518 " --> pdb=" O THR B 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 15 removed outlier: 3.701A pdb=" N PHE C 15 " --> pdb=" O SER C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 31 Processing helix chain 'C' and resid 36 through 48 Processing helix chain 'C' and resid 49 through 57 removed outlier: 3.666A pdb=" N GLN C 53 " --> pdb=" O THR C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 81 removed outlier: 4.066A pdb=" N GLY C 74 " --> pdb=" O CYS C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 108 removed outlier: 4.508A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 152 through 159 removed outlier: 3.547A pdb=" N GLU C 156 " --> pdb=" O THR C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 172 Processing helix chain 'C' and resid 192 through 210 Processing helix chain 'C' and resid 211 through 213 No H-bonds generated for 'chain 'C' and resid 211 through 213' Processing helix chain 'C' and resid 233 through 248 removed outlier: 3.566A pdb=" N PHE C 237 " --> pdb=" O TYR C 233 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU C 244 " --> pdb=" O ILE C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 284 Processing helix chain 'C' and resid 285 through 287 No H-bonds generated for 'chain 'C' and resid 285 through 287' Processing helix chain 'C' and resid 298 through 308 Processing helix chain 'C' and resid 322 through 337 Processing helix chain 'C' and resid 341 through 358 removed outlier: 3.674A pdb=" N THR C 345 " --> pdb=" O PRO C 341 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU C 347 " --> pdb=" O SER C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 363 removed outlier: 3.541A pdb=" N LEU C 362 " --> pdb=" O SER C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 387 Processing helix chain 'C' and resid 399 through 412 Processing helix chain 'C' and resid 426 through 437 Processing helix chain 'C' and resid 445 through 447 No H-bonds generated for 'chain 'C' and resid 445 through 447' Processing helix chain 'C' and resid 448 through 459 removed outlier: 3.696A pdb=" N LYS C 458 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 463 Processing helix chain 'C' and resid 478 through 482 removed outlier: 3.623A pdb=" N ARG C 481 " --> pdb=" O HIS C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 509 removed outlier: 3.562A pdb=" N GLY C 489 " --> pdb=" O LEU C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.527A pdb=" N ASN C 518 " --> pdb=" O THR C 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 18 Processing helix chain 'D' and resid 21 through 31 removed outlier: 3.865A pdb=" N LYS D 30 " --> pdb=" O LYS D 26 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N HIS D 31 " --> pdb=" O ASP D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 45 Processing helix chain 'D' and resid 62 through 68 Processing helix chain 'D' and resid 85 through 92 removed outlier: 4.715A pdb=" N GLY D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 Processing helix chain 'D' and resid 127 through 142 removed outlier: 3.596A pdb=" N ALA D 132 " --> pdb=" O ASP D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 159 removed outlier: 4.131A pdb=" N GLY D 157 " --> pdb=" O GLU D 153 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU D 158 " --> pdb=" O CYS D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 175 removed outlier: 3.930A pdb=" N VAL D 166 " --> pdb=" O ASP D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 206 removed outlier: 4.175A pdb=" N GLY D 194 " --> pdb=" O SER D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 211 removed outlier: 4.394A pdb=" N ARG D 210 " --> pdb=" O LEU D 207 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP D 211 " --> pdb=" O GLY D 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 207 through 211' Processing helix chain 'D' and resid 230 through 232 No H-bonds generated for 'chain 'D' and resid 230 through 232' Processing helix chain 'D' and resid 233 through 244 removed outlier: 3.912A pdb=" N LEU D 241 " --> pdb=" O SER D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 265 Processing helix chain 'D' and resid 266 through 268 No H-bonds generated for 'chain 'D' and resid 266 through 268' Processing helix chain 'D' and resid 275 through 291 removed outlier: 5.798A pdb=" N TYR D 281 " --> pdb=" O ARG D 277 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ILE D 282 " --> pdb=" O SER D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 315 Processing helix chain 'D' and resid 317 through 343 Proline residue: D 333 - end of helix Processing helix chain 'D' and resid 358 through 363 Processing helix chain 'D' and resid 363 through 370 removed outlier: 3.562A pdb=" N LEU D 370 " --> pdb=" O ALA D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 392 removed outlier: 4.140A pdb=" N LYS D 392 " --> pdb=" O ASP D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 417 Processing helix chain 'D' and resid 424 through 433 removed outlier: 4.553A pdb=" N PHE D 429 " --> pdb=" O ILE D 425 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ILE D 430 " --> pdb=" O LYS D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 468 removed outlier: 4.001A pdb=" N ALA D 457 " --> pdb=" O PHE D 453 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE D 458 " --> pdb=" O ASP D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 474 removed outlier: 3.616A pdb=" N TRP D 472 " --> pdb=" O ASN D 469 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS D 473 " --> pdb=" O PRO D 470 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS D 474 " --> pdb=" O CYS D 471 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 469 through 474' Processing helix chain 'E' and resid 27 through 34 Processing helix chain 'E' and resid 68 through 79 Processing helix chain 'E' and resid 82 through 93 Processing helix chain 'F' and resid 15 through 30 removed outlier: 3.606A pdb=" N MET F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 65 Processing helix chain 'F' and resid 67 through 71 Processing helix chain 'F' and resid 72 through 77 removed outlier: 3.530A pdb=" N VAL F 76 " --> pdb=" O GLU F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.861A pdb=" N VAL F 84 " --> pdb=" O TYR F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 114 removed outlier: 3.826A pdb=" N ILE F 104 " --> pdb=" O GLY F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 142 Processing helix chain 'F' and resid 155 through 172 removed outlier: 3.513A pdb=" N MET F 159 " --> pdb=" O GLU F 155 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR F 172 " --> pdb=" O GLY F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 202 removed outlier: 3.512A pdb=" N ILE F 197 " --> pdb=" O GLU F 193 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE F 198 " --> pdb=" O ASP F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 223 removed outlier: 3.939A pdb=" N GLN F 219 " --> pdb=" O ASP F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 232 Processing helix chain 'F' and resid 235 through 250 Processing helix chain 'F' and resid 261 through 272 Processing helix chain 'G' and resid 15 through 30 Processing helix chain 'G' and resid 46 through 51 removed outlier: 3.854A pdb=" N LEU G 50 " --> pdb=" O THR G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 65 removed outlier: 3.519A pdb=" N ALA G 65 " --> pdb=" O MET G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 76 removed outlier: 3.924A pdb=" N VAL G 76 " --> pdb=" O GLU G 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 72 through 76' Processing helix chain 'G' and resid 81 through 83 No H-bonds generated for 'chain 'G' and resid 81 through 83' Processing helix chain 'G' and resid 100 through 114 removed outlier: 3.508A pdb=" N ILE G 104 " --> pdb=" O GLY G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 142 Processing helix chain 'G' and resid 155 through 172 removed outlier: 3.596A pdb=" N MET G 159 " --> pdb=" O GLU G 155 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR G 172 " --> pdb=" O GLY G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 204 Processing helix chain 'G' and resid 215 through 224 removed outlier: 3.962A pdb=" N GLN G 219 " --> pdb=" O ASP G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 232 Processing helix chain 'G' and resid 235 through 250 Processing helix chain 'G' and resid 261 through 272 Processing helix chain 'H' and resid 5 through 18 Processing helix chain 'H' and resid 21 through 30 removed outlier: 3.944A pdb=" N LYS H 30 " --> pdb=" O LYS H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 45 Processing helix chain 'H' and resid 62 through 68 Processing helix chain 'H' and resid 85 through 92 removed outlier: 4.674A pdb=" N GLY H 89 " --> pdb=" O PRO H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 126 Processing helix chain 'H' and resid 127 through 142 Processing helix chain 'H' and resid 153 through 159 removed outlier: 3.855A pdb=" N GLY H 157 " --> pdb=" O GLU H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 175 removed outlier: 3.767A pdb=" N VAL H 166 " --> pdb=" O ASP H 162 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA H 172 " --> pdb=" O LYS H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 206 removed outlier: 3.672A pdb=" N HIS H 196 " --> pdb=" O SER H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 232 No H-bonds generated for 'chain 'H' and resid 230 through 232' Processing helix chain 'H' and resid 233 through 245 Processing helix chain 'H' and resid 258 through 265 removed outlier: 3.643A pdb=" N ILE H 262 " --> pdb=" O SER H 258 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU H 263 " --> pdb=" O ILE H 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 266 through 268 No H-bonds generated for 'chain 'H' and resid 266 through 268' Processing helix chain 'H' and resid 275 through 291 removed outlier: 3.578A pdb=" N MET H 279 " --> pdb=" O CYS H 275 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR H 281 " --> pdb=" O ARG H 277 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ILE H 282 " --> pdb=" O SER H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 315 removed outlier: 3.580A pdb=" N LYS H 315 " --> pdb=" O ALA H 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 317 through 347 removed outlier: 3.500A pdb=" N GLN H 321 " --> pdb=" O ASP H 317 " (cutoff:3.500A) Proline residue: H 333 - end of helix Proline residue: H 344 - end of helix Processing helix chain 'H' and resid 358 through 363 Processing helix chain 'H' and resid 363 through 370 Processing helix chain 'H' and resid 383 through 392 removed outlier: 3.873A pdb=" N LYS H 392 " --> pdb=" O ASP H 388 " (cutoff:3.500A) Processing helix chain 'H' and resid 405 through 417 Processing helix chain 'H' and resid 424 through 434 removed outlier: 4.532A pdb=" N PHE H 429 " --> pdb=" O ILE H 425 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ILE H 430 " --> pdb=" O LYS H 426 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET H 434 " --> pdb=" O ILE H 430 " (cutoff:3.500A) Processing helix chain 'H' and resid 443 through 447 Processing helix chain 'H' and resid 451 through 468 Processing helix chain 'H' and resid 469 through 474 removed outlier: 3.501A pdb=" N LYS H 474 " --> pdb=" O CYS H 471 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 15 Processing helix chain 'I' and resid 17 through 31 Processing helix chain 'I' and resid 36 through 48 Processing helix chain 'I' and resid 49 through 57 Processing helix chain 'I' and resid 70 through 80 removed outlier: 3.945A pdb=" N GLY I 74 " --> pdb=" O CYS I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 108 removed outlier: 4.100A pdb=" N VAL I 96 " --> pdb=" O SER I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 126 removed outlier: 3.894A pdb=" N VAL I 124 " --> pdb=" O GLU I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 142 Processing helix chain 'I' and resid 152 through 159 Processing helix chain 'I' and resid 161 through 172 Processing helix chain 'I' and resid 192 through 210 Processing helix chain 'I' and resid 211 through 213 No H-bonds generated for 'chain 'I' and resid 211 through 213' Processing helix chain 'I' and resid 233 through 248 removed outlier: 3.750A pdb=" N PHE I 237 " --> pdb=" O TYR I 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 259 through 263 removed outlier: 4.086A pdb=" N THR I 263 " --> pdb=" O VAL I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 277 through 284 Processing helix chain 'I' and resid 285 through 287 No H-bonds generated for 'chain 'I' and resid 285 through 287' Processing helix chain 'I' and resid 298 through 308 Processing helix chain 'I' and resid 322 through 337 Processing helix chain 'I' and resid 341 through 363 removed outlier: 3.639A pdb=" N THR I 345 " --> pdb=" O PRO I 341 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N THR I 360 " --> pdb=" O THR I 356 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N TRP I 361 " --> pdb=" O ASP I 357 " (cutoff:3.500A) Processing helix chain 'I' and resid 372 through 387 Processing helix chain 'I' and resid 399 through 412 Processing helix chain 'I' and resid 426 through 437 removed outlier: 3.570A pdb=" N LEU I 430 " --> pdb=" O ASP I 426 " (cutoff:3.500A) Processing helix chain 'I' and resid 447 through 459 removed outlier: 4.181A pdb=" N ILE I 451 " --> pdb=" O TYR I 447 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG I 453 " --> pdb=" O LYS I 449 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY I 459 " --> pdb=" O THR I 455 " (cutoff:3.500A) Processing helix chain 'I' and resid 460 through 463 Processing helix chain 'I' and resid 478 through 482 removed outlier: 3.512A pdb=" N ARG I 481 " --> pdb=" O HIS I 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 485 through 509 removed outlier: 3.537A pdb=" N GLY I 489 " --> pdb=" O LEU I 485 " (cutoff:3.500A) Processing helix chain 'I' and resid 515 through 519 removed outlier: 3.668A pdb=" N ASN I 518 " --> pdb=" O THR I 515 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 15 removed outlier: 3.714A pdb=" N PHE J 15 " --> pdb=" O SER J 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 31 Processing helix chain 'J' and resid 36 through 48 Processing helix chain 'J' and resid 49 through 57 removed outlier: 3.668A pdb=" N GLN J 53 " --> pdb=" O THR J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 81 removed outlier: 4.066A pdb=" N GLY J 74 " --> pdb=" O CYS J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 108 removed outlier: 4.496A pdb=" N VAL J 96 " --> pdb=" O SER J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 119 through 126 Processing helix chain 'J' and resid 127 through 142 Processing helix chain 'J' and resid 152 through 159 removed outlier: 3.519A pdb=" N GLU J 156 " --> pdb=" O THR J 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 192 through 210 Processing helix chain 'J' and resid 211 through 213 No H-bonds generated for 'chain 'J' and resid 211 through 213' Processing helix chain 'J' and resid 233 through 248 removed outlier: 3.566A pdb=" N PHE J 237 " --> pdb=" O TYR J 233 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU J 244 " --> pdb=" O ILE J 240 " (cutoff:3.500A) Processing helix chain 'J' and resid 277 through 284 Processing helix chain 'J' and resid 285 through 287 No H-bonds generated for 'chain 'J' and resid 285 through 287' Processing helix chain 'J' and resid 298 through 308 Processing helix chain 'J' and resid 322 through 337 Processing helix chain 'J' and resid 341 through 358 removed outlier: 3.678A pdb=" N THR J 345 " --> pdb=" O PRO J 341 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU J 347 " --> pdb=" O SER J 343 " (cutoff:3.500A) Processing helix chain 'J' and resid 358 through 363 removed outlier: 3.539A pdb=" N LEU J 362 " --> pdb=" O SER J 358 " (cutoff:3.500A) Processing helix chain 'J' and resid 372 through 387 Processing helix chain 'J' and resid 399 through 412 Processing helix chain 'J' and resid 426 through 437 removed outlier: 3.503A pdb=" N LEU J 430 " --> pdb=" O ASP J 426 " (cutoff:3.500A) Processing helix chain 'J' and resid 445 through 447 No H-bonds generated for 'chain 'J' and resid 445 through 447' Processing helix chain 'J' and resid 448 through 459 removed outlier: 3.697A pdb=" N LYS J 458 " --> pdb=" O ASP J 454 " (cutoff:3.500A) Processing helix chain 'J' and resid 460 through 463 Processing helix chain 'J' and resid 478 through 482 removed outlier: 3.624A pdb=" N ARG J 481 " --> pdb=" O HIS J 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 485 through 509 removed outlier: 3.567A pdb=" N GLY J 489 " --> pdb=" O LEU J 485 " (cutoff:3.500A) Processing helix chain 'J' and resid 515 through 519 removed outlier: 3.581A pdb=" N ASN J 518 " --> pdb=" O THR J 515 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 18 Processing helix chain 'K' and resid 21 through 31 removed outlier: 3.872A pdb=" N LYS K 30 " --> pdb=" O LYS K 26 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N HIS K 31 " --> pdb=" O ASP K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 45 Processing helix chain 'K' and resid 62 through 68 Processing helix chain 'K' and resid 85 through 92 removed outlier: 4.712A pdb=" N GLY K 89 " --> pdb=" O PRO K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 119 through 126 Processing helix chain 'K' and resid 127 through 142 removed outlier: 3.599A pdb=" N ALA K 132 " --> pdb=" O ASP K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 160 removed outlier: 4.132A pdb=" N GLY K 157 " --> pdb=" O GLU K 153 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU K 158 " --> pdb=" O CYS K 154 " (cutoff:3.500A) Processing helix chain 'K' and resid 162 through 175 removed outlier: 3.926A pdb=" N VAL K 166 " --> pdb=" O ASP K 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 206 removed outlier: 4.177A pdb=" N GLY K 194 " --> pdb=" O SER K 190 " (cutoff:3.500A) Processing helix chain 'K' and resid 207 through 211 removed outlier: 4.395A pdb=" N ARG K 210 " --> pdb=" O LEU K 207 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP K 211 " --> pdb=" O GLY K 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 207 through 211' Processing helix chain 'K' and resid 230 through 232 No H-bonds generated for 'chain 'K' and resid 230 through 232' Processing helix chain 'K' and resid 233 through 244 removed outlier: 3.913A pdb=" N LEU K 241 " --> pdb=" O SER K 237 " (cutoff:3.500A) Processing helix chain 'K' and resid 258 through 265 Processing helix chain 'K' and resid 266 through 268 No H-bonds generated for 'chain 'K' and resid 266 through 268' Processing helix chain 'K' and resid 275 through 291 removed outlier: 5.795A pdb=" N TYR K 281 " --> pdb=" O ARG K 277 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ILE K 282 " --> pdb=" O SER K 278 " (cutoff:3.500A) Processing helix chain 'K' and resid 301 through 315 Processing helix chain 'K' and resid 317 through 343 Proline residue: K 333 - end of helix Processing helix chain 'K' and resid 358 through 363 Processing helix chain 'K' and resid 363 through 370 removed outlier: 3.562A pdb=" N LEU K 370 " --> pdb=" O ALA K 366 " (cutoff:3.500A) Processing helix chain 'K' and resid 385 through 392 removed outlier: 3.517A pdb=" N ARG K 389 " --> pdb=" O ASP K 385 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS K 392 " --> pdb=" O ASP K 388 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 417 Processing helix chain 'K' and resid 424 through 433 removed outlier: 4.554A pdb=" N PHE K 429 " --> pdb=" O ILE K 425 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ILE K 430 " --> pdb=" O LYS K 426 " (cutoff:3.500A) Processing helix chain 'K' and resid 451 through 468 removed outlier: 3.999A pdb=" N ALA K 457 " --> pdb=" O PHE K 453 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE K 458 " --> pdb=" O ASP K 454 " (cutoff:3.500A) Processing helix chain 'K' and resid 469 through 474 removed outlier: 3.617A pdb=" N TRP K 472 " --> pdb=" O ASN K 469 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS K 473 " --> pdb=" O PRO K 470 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS K 474 " --> pdb=" O CYS K 471 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 469 through 474' Processing helix chain 'L' and resid 27 through 34 Processing helix chain 'L' and resid 68 through 79 Processing helix chain 'L' and resid 82 through 93 Processing helix chain 'M' and resid 15 through 30 removed outlier: 3.608A pdb=" N MET M 30 " --> pdb=" O ALA M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 65 Processing helix chain 'M' and resid 67 through 71 Processing helix chain 'M' and resid 72 through 77 removed outlier: 3.525A pdb=" N VAL M 76 " --> pdb=" O GLU M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 84 removed outlier: 3.838A pdb=" N VAL M 84 " --> pdb=" O TYR M 81 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 114 removed outlier: 3.825A pdb=" N ILE M 104 " --> pdb=" O GLY M 100 " (cutoff:3.500A) Processing helix chain 'M' and resid 137 through 142 Processing helix chain 'M' and resid 155 through 172 removed outlier: 3.514A pdb=" N MET M 159 " --> pdb=" O GLU M 155 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR M 172 " --> pdb=" O GLY M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 192 through 202 removed outlier: 3.535A pdb=" N ILE M 197 " --> pdb=" O GLU M 193 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE M 198 " --> pdb=" O ASP M 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 215 through 223 removed outlier: 3.936A pdb=" N GLN M 219 " --> pdb=" O ASP M 215 " (cutoff:3.500A) Processing helix chain 'M' and resid 227 through 232 Processing helix chain 'M' and resid 235 through 250 Processing helix chain 'M' and resid 261 through 272 Processing helix chain 'N' and resid 15 through 30 Processing helix chain 'N' and resid 46 through 51 removed outlier: 3.840A pdb=" N LEU N 50 " --> pdb=" O THR N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 65 removed outlier: 3.521A pdb=" N ALA N 65 " --> pdb=" O MET N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 76 removed outlier: 3.910A pdb=" N VAL N 76 " --> pdb=" O GLU N 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 72 through 76' Processing helix chain 'N' and resid 81 through 83 No H-bonds generated for 'chain 'N' and resid 81 through 83' Processing helix chain 'N' and resid 100 through 114 removed outlier: 3.502A pdb=" N ILE N 104 " --> pdb=" O GLY N 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 142 Processing helix chain 'N' and resid 155 through 172 removed outlier: 3.601A pdb=" N MET N 159 " --> pdb=" O GLU N 155 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR N 172 " --> pdb=" O GLY N 168 " (cutoff:3.500A) Processing helix chain 'N' and resid 192 through 204 Processing helix chain 'N' and resid 215 through 224 removed outlier: 3.959A pdb=" N GLN N 219 " --> pdb=" O ASP N 215 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 232 Processing helix chain 'N' and resid 235 through 250 Processing helix chain 'N' and resid 261 through 272 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 181 removed outlier: 4.145A pdb=" N PHE A 114 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 251 removed outlier: 7.621A pdb=" N VAL A 223 " --> pdb=" O VAL A 250 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 373 through 374 removed outlier: 6.657A pdb=" N ARG A 350 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N GLY A 422 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N MET A 352 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE A 421 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 114 through 115 Processing sheet with id=AA6, first strand: chain 'B' and resid 251 through 253 removed outlier: 6.370A pdb=" N ASN B 225 " --> pdb=" O VAL B 291 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 420 through 423 removed outlier: 8.422A pdb=" N THR B 420 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL B 391 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N TYR B 422 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE B 393 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N PHE B 367 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE B 393 " --> pdb=" O PHE B 367 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU B 369 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N CYS B 395 " --> pdb=" O LEU B 369 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 63 through 64 removed outlier: 4.095A pdb=" N PHE D 114 " --> pdb=" O HIS D 80 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE D 79 " --> pdb=" O SER D 149 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N GLN D 151 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE D 81 " --> pdb=" O GLN D 151 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE D 148 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL D 181 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL D 150 " --> pdb=" O VAL D 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 114 through 115 Processing sheet with id=AB1, first strand: chain 'C' and resid 251 through 253 removed outlier: 6.427A pdb=" N ILE C 224 " --> pdb=" O ASER C 252 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ASN C 225 " --> pdb=" O VAL C 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 420 through 423 removed outlier: 7.594A pdb=" N LEU C 369 " --> pdb=" O VAL C 391 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ILE C 393 " --> pdb=" O LEU C 369 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG C 366 " --> pdb=" O PHE C 441 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ILE C 443 " --> pdb=" O ARG C 366 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA C 368 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N MET C 442 " --> pdb=" O ILE C 467 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 32 through 34 removed outlier: 6.056A pdb=" N VAL D 351 " --> pdb=" O VAL D 374 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY D 376 " --> pdb=" O VAL D 351 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARG D 350 " --> pdb=" O LEU D 420 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N GLY D 422 " --> pdb=" O ARG D 350 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N MET D 352 " --> pdb=" O GLY D 422 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE D 421 " --> pdb=" O ARG D 439 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 248 through 254 removed outlier: 7.816A pdb=" N VAL D 223 " --> pdb=" O VAL D 250 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLN D 252 " --> pdb=" O VAL D 223 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE D 225 " --> pdb=" O GLN D 252 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N SER D 254 " --> pdb=" O ILE D 225 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N GLY D 227 " --> pdb=" O SER D 254 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 15 through 18 Processing sheet with id=AB6, first strand: chain 'F' and resid 85 through 88 removed outlier: 6.847A pdb=" N VAL F 34 " --> pdb=" O LYS F 85 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N VAL F 87 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE F 36 " --> pdb=" O VAL F 87 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA F 7 " --> pdb=" O TYR F 149 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N VAL F 151 " --> pdb=" O ALA F 7 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N TYR F 9 " --> pdb=" O VAL F 151 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE F 148 " --> pdb=" O GLY F 182 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ILE F 184 " --> pdb=" O ILE F 148 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ILE F 150 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ASN F 186 " --> pdb=" O ILE F 150 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N CYS F 152 " --> pdb=" O ASN F 186 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE F 209 " --> pdb=" O GLY F 181 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU F 183 " --> pdb=" O ILE F 209 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N PHE F 211 " --> pdb=" O LEU F 183 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N CYS F 185 " --> pdb=" O PHE F 211 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 77 through 79 removed outlier: 6.930A pdb=" N VAL G 34 " --> pdb=" O LYS G 85 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N VAL G 87 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE G 36 " --> pdb=" O VAL G 87 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARG G 4 " --> pdb=" O VAL G 123 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N TYR G 125 " --> pdb=" O ARG G 4 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N CYS G 6 " --> pdb=" O TYR G 125 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL G 127 " --> pdb=" O CYS G 6 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ILE G 8 " --> pdb=" O VAL G 127 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLN G 5 " --> pdb=" O GLU G 147 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N TYR G 149 " --> pdb=" O GLN G 5 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ALA G 7 " --> pdb=" O TYR G 149 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N VAL G 151 " --> pdb=" O ALA G 7 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N TYR G 9 " --> pdb=" O VAL G 151 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE G 148 " --> pdb=" O LEU G 180 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY G 182 " --> pdb=" O ILE G 148 " (cutoff:3.500A) removed outlier: 12.725A pdb=" N MET G 208 " --> pdb=" O ARG G 179 " (cutoff:3.500A) removed outlier: 10.709A pdb=" N GLY G 181 " --> pdb=" O MET G 208 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N HIS G 210 " --> pdb=" O GLY G 181 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU G 183 " --> pdb=" O HIS G 210 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N VAL G 212 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N CYS G 185 " --> pdb=" O VAL G 212 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 32 through 34 Processing sheet with id=AB9, first strand: chain 'H' and resid 178 through 181 removed outlier: 4.150A pdb=" N PHE H 114 " --> pdb=" O HIS H 80 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 248 through 251 removed outlier: 7.641A pdb=" N VAL H 223 " --> pdb=" O VAL H 250 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 373 through 374 removed outlier: 6.661A pdb=" N ARG H 350 " --> pdb=" O LEU H 420 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N GLY H 422 " --> pdb=" O ARG H 350 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N MET H 352 " --> pdb=" O GLY H 422 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE H 421 " --> pdb=" O ARG H 439 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 114 through 115 Processing sheet with id=AC4, first strand: chain 'I' and resid 251 through 253 removed outlier: 6.369A pdb=" N ASN I 225 " --> pdb=" O VAL I 291 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 420 through 423 removed outlier: 8.430A pdb=" N THR I 420 " --> pdb=" O GLU I 389 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL I 391 " --> pdb=" O THR I 420 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N TYR I 422 " --> pdb=" O VAL I 391 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE I 393 " --> pdb=" O TYR I 422 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N PHE I 367 " --> pdb=" O VAL I 391 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ILE I 393 " --> pdb=" O PHE I 367 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ARG I 366 " --> pdb=" O PHE I 441 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ILE I 443 " --> pdb=" O ARG I 366 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA I 368 " --> pdb=" O ILE I 443 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 63 through 64 removed outlier: 4.098A pdb=" N PHE K 114 " --> pdb=" O HIS K 80 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE K 79 " --> pdb=" O SER K 149 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N GLN K 151 " --> pdb=" O ILE K 79 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE K 81 " --> pdb=" O GLN K 151 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE K 148 " --> pdb=" O VAL K 179 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N VAL K 181 " --> pdb=" O ILE K 148 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL K 150 " --> pdb=" O VAL K 181 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 114 through 115 Processing sheet with id=AC8, first strand: chain 'J' and resid 251 through 253 removed outlier: 6.429A pdb=" N ILE J 224 " --> pdb=" O ASER J 252 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASN J 225 " --> pdb=" O VAL J 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'J' and resid 420 through 423 removed outlier: 6.050A pdb=" N PHE J 367 " --> pdb=" O PRO J 390 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS J 392 " --> pdb=" O PHE J 367 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ARG J 366 " --> pdb=" O PHE J 441 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE J 443 " --> pdb=" O ARG J 366 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ALA J 368 " --> pdb=" O ILE J 443 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N MET J 442 " --> pdb=" O ILE J 467 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 32 through 34 removed outlier: 6.050A pdb=" N VAL K 351 " --> pdb=" O VAL K 374 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY K 376 " --> pdb=" O VAL K 351 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG K 350 " --> pdb=" O LEU K 420 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N GLY K 422 " --> pdb=" O ARG K 350 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N MET K 352 " --> pdb=" O GLY K 422 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE K 421 " --> pdb=" O ARG K 439 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 248 through 254 removed outlier: 7.818A pdb=" N VAL K 223 " --> pdb=" O VAL K 250 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLN K 252 " --> pdb=" O VAL K 223 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE K 225 " --> pdb=" O GLN K 252 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N SER K 254 " --> pdb=" O ILE K 225 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N GLY K 227 " --> pdb=" O SER K 254 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 15 through 18 Processing sheet with id=AD4, first strand: chain 'M' and resid 85 through 88 removed outlier: 6.835A pdb=" N VAL M 34 " --> pdb=" O LYS M 85 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N VAL M 87 " --> pdb=" O VAL M 34 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE M 36 " --> pdb=" O VAL M 87 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL M 123 " --> pdb=" O ARG M 4 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLN M 5 " --> pdb=" O GLU M 147 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N TYR M 149 " --> pdb=" O GLN M 5 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA M 7 " --> pdb=" O TYR M 149 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N VAL M 151 " --> pdb=" O ALA M 7 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N TYR M 9 " --> pdb=" O VAL M 151 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE M 148 " --> pdb=" O GLY M 182 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ILE M 184 " --> pdb=" O ILE M 148 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE M 150 " --> pdb=" O ILE M 184 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ASN M 186 " --> pdb=" O ILE M 150 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N CYS M 152 " --> pdb=" O ASN M 186 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE M 209 " --> pdb=" O GLY M 181 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU M 183 " --> pdb=" O ILE M 209 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N PHE M 211 " --> pdb=" O LEU M 183 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N CYS M 185 " --> pdb=" O PHE M 211 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 77 through 79 removed outlier: 6.708A pdb=" N ARG N 4 " --> pdb=" O VAL N 123 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N TYR N 125 " --> pdb=" O ARG N 4 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N CYS N 6 " --> pdb=" O TYR N 125 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N VAL N 127 " --> pdb=" O CYS N 6 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ILE N 8 " --> pdb=" O VAL N 127 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLN N 5 " --> pdb=" O GLU N 147 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N TYR N 149 " --> pdb=" O GLN N 5 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ALA N 7 " --> pdb=" O TYR N 149 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL N 151 " --> pdb=" O ALA N 7 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N TYR N 9 " --> pdb=" O VAL N 151 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ILE N 148 " --> pdb=" O LEU N 180 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY N 182 " --> pdb=" O ILE N 148 " (cutoff:3.500A) removed outlier: 12.736A pdb=" N MET N 208 " --> pdb=" O ARG N 179 " (cutoff:3.500A) removed outlier: 10.726A pdb=" N GLY N 181 " --> pdb=" O MET N 208 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N HIS N 210 " --> pdb=" O GLY N 181 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU N 183 " --> pdb=" O HIS N 210 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N VAL N 212 " --> pdb=" O LEU N 183 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N CYS N 185 " --> pdb=" O VAL N 212 " (cutoff:3.500A) 1920 hydrogen bonds defined for protein. 5591 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.46 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.53: 40773 1.53 - 1.88: 2703 1.88 - 2.24: 83 2.24 - 2.59: 185 2.59 - 2.95: 36 Bond restraints: 43780 Sorted by residual: bond pdb="FE4 BCLF C 602 " pdb="FE5 BCLF C 602 " ideal model delta sigma weight residual 2.200 2.946 -0.746 2.00e-02 2.50e+03 1.39e+03 bond pdb="FE4 BCLF J 602 " pdb="FE5 BCLF J 602 " ideal model delta sigma weight residual 2.200 2.945 -0.745 2.00e-02 2.50e+03 1.39e+03 bond pdb="FE2 BCLF C 602 " pdb="FE8 BCLF C 602 " ideal model delta sigma weight residual 2.200 2.929 -0.729 2.00e-02 2.50e+03 1.33e+03 bond pdb="FE4 BCLF I 601 " pdb="FE5 BCLF I 601 " ideal model delta sigma weight residual 2.200 2.928 -0.728 2.00e-02 2.50e+03 1.33e+03 bond pdb="FE4 BCLF A 501 " pdb="FE5 BCLF A 501 " ideal model delta sigma weight residual 2.200 2.928 -0.728 2.00e-02 2.50e+03 1.33e+03 ... (remaining 43775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.69: 59027 6.69 - 13.39: 35 13.39 - 20.08: 10 20.08 - 26.77: 0 26.77 - 33.46: 8 Bond angle restraints: 59080 Sorted by residual: angle pdb=" N LEU E 28 " pdb=" CA LEU E 28 " pdb=" C LEU E 28 " ideal model delta sigma weight residual 111.56 93.86 17.70 1.53e+00 4.27e-01 1.34e+02 angle pdb=" S1 FES E 201 " pdb="FE1 FES E 201 " pdb=" S2 FES E 201 " ideal model delta sigma weight residual 104.33 90.45 13.88 1.20e+00 6.94e-01 1.34e+02 angle pdb=" S1 FES L 201 " pdb="FE1 FES L 201 " pdb=" S2 FES L 201 " ideal model delta sigma weight residual 104.33 90.46 13.87 1.20e+00 6.94e-01 1.34e+02 angle pdb=" N LEU L 28 " pdb=" CA LEU L 28 " pdb=" C LEU L 28 " ideal model delta sigma weight residual 111.56 93.97 17.59 1.53e+00 4.27e-01 1.32e+02 angle pdb=" S1 BCLF I 601 " pdb="FE2 BCLF I 601 " pdb="FE4 BCLF I 601 " ideal model delta sigma weight residual 90.00 56.54 33.46 3.00e+00 1.11e-01 1.24e+02 ... (remaining 59075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 25512 17.18 - 34.35: 1117 34.35 - 51.53: 201 51.53 - 68.71: 38 68.71 - 85.89: 14 Dihedral angle restraints: 26882 sinusoidal: 11398 harmonic: 15484 Sorted by residual: dihedral pdb=" C LEU C 369 " pdb=" N LEU C 369 " pdb=" CA LEU C 369 " pdb=" CB LEU C 369 " ideal model delta harmonic sigma weight residual -122.60 -112.35 -10.25 0 2.50e+00 1.60e-01 1.68e+01 dihedral pdb=" C LEU B 369 " pdb=" N LEU B 369 " pdb=" CA LEU B 369 " pdb=" CB LEU B 369 " ideal model delta harmonic sigma weight residual -122.60 -112.48 -10.12 0 2.50e+00 1.60e-01 1.64e+01 dihedral pdb=" CA SER E 25 " pdb=" C SER E 25 " pdb=" N THR E 26 " pdb=" CA THR E 26 " ideal model delta harmonic sigma weight residual -180.00 -159.82 -20.18 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 26879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 5215 0.054 - 0.109: 1010 0.109 - 0.163: 112 0.163 - 0.217: 10 0.217 - 0.271: 3 Chirality restraints: 6350 Sorted by residual: chirality pdb=" CA CYS L 42 " pdb=" N CYS L 42 " pdb=" C CYS L 42 " pdb=" CB CYS L 42 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C3 HCA H 501 " pdb=" C4 HCA H 501 " pdb=" C7 HCA H 501 " pdb=" O7 HCA H 501 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" C3 HCA A 502 " pdb=" C4 HCA A 502 " pdb=" C7 HCA A 502 " pdb=" O7 HCA A 502 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 6347 not shown) Planarity restraints: 7630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 250 " 0.028 2.00e-02 2.50e+03 5.55e-02 3.08e+01 pdb=" C VAL A 250 " -0.096 2.00e-02 2.50e+03 pdb=" O VAL A 250 " 0.036 2.00e-02 2.50e+03 pdb=" N ALA A 251 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA L 101 " 0.020 2.00e-02 2.50e+03 3.79e-02 1.43e+01 pdb=" C ALA L 101 " -0.066 2.00e-02 2.50e+03 pdb=" O ALA L 101 " 0.023 2.00e-02 2.50e+03 pdb=" N CYS L 102 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 101 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C ALA E 101 " 0.059 2.00e-02 2.50e+03 pdb=" O ALA E 101 " -0.021 2.00e-02 2.50e+03 pdb=" N CYS E 102 " -0.020 2.00e-02 2.50e+03 ... (remaining 7627 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 855 2.67 - 3.23: 41400 3.23 - 3.79: 69091 3.79 - 4.34: 99683 4.34 - 4.90: 161908 Nonbonded interactions: 372937 Sorted by model distance: nonbonded pdb=" O7 HCA H 501 " pdb="MO1 ICS H 502 " model vdw 2.115 3.190 nonbonded pdb=" O6 HCA D 501 " pdb="MO1 ICS D 502 " model vdw 2.191 3.190 nonbonded pdb=" OH TYR I 102 " pdb=" OH TYR I 447 " model vdw 2.198 3.040 nonbonded pdb=" OH TYR B 102 " pdb=" OH TYR B 447 " model vdw 2.198 3.040 nonbonded pdb=" OD1 ASP B 353 " pdb="CA CA B 601 " model vdw 2.201 2.510 ... (remaining 372932 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' and (resid 4 through 75 or resid 77 through 164 or resid 166 through \ 236 or resid 238 through 480)) selection = (chain 'D' and (resid 4 through 75 or resid 77 through 164 or resid 166 through \ 236 or resid 238 through 480)) selection = (chain 'H' and (resid 4 through 75 or resid 77 through 164 or resid 166 through \ 236 or resid 238 through 480)) selection = (chain 'K' and (resid 4 through 75 or resid 77 through 164 or resid 166 through \ 236 or resid 238 through 480)) } ncs_group { reference = (chain 'B' and (resid 2 through 100 or resid 102 through 251 or resid 253 throug \ h 452 or resid 454 through 523)) selection = (chain 'C' and (resid 2 through 100 or resid 102 through 251 or resid 253 throug \ h 452 or resid 454 through 523)) selection = (chain 'I' and (resid 2 through 100 or resid 102 through 251 or resid 253 throug \ h 452 or resid 454 through 523)) selection = (chain 'J' and (resid 2 through 100 or resid 102 through 251 or resid 253 throug \ h 452 or resid 454 through 523)) } ncs_group { reference = chain 'E' selection = chain 'L' } ncs_group { reference = (chain 'F' and resid 2 through 290) selection = chain 'G' selection = (chain 'M' and resid 2 through 290) selection = chain 'N' } 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=0.00 max=1.00 mean=0.99 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: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 50.000 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 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 : 0.020 0.746 43828 Z= 1.039 Angle : 0.815 33.463 59116 Z= 0.441 Chirality : 0.043 0.271 6350 Planarity : 0.004 0.056 7630 Dihedral : 10.119 85.887 16998 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.55 % Favored : 97.37 % Rotamer: Outliers : 0.89 % Allowed : 5.27 % Favored : 93.84 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.12), residues: 5392 helix: 1.35 (0.11), residues: 2476 sheet: -0.84 (0.21), residues: 600 loop : -0.77 (0.13), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 277 TYR 0.012 0.001 TYR D 379 PHE 0.016 0.001 PHE L 40 TRP 0.033 0.001 TRP I 370 HIS 0.005 0.001 HIS H 442 Details of bonding type rmsd covalent geometry : bond 0.02026 (43780) covalent geometry : angle 0.79026 (59080) hydrogen bonds : bond 0.17501 ( 1920) hydrogen bonds : angle 6.80604 ( 5591) metal coordination : bond 0.03555 ( 16) metal coordination : angle 8.14353 ( 36) Misc. bond : bond 0.06823 ( 32) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 4568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 596 time to evaluate : 1.549 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: A 36 ASP cc_start: 0.8098 (t0) cc_final: 0.7847 (t0) REVERT: A 50 LYS cc_start: 0.9113 (mmtt) cc_final: 0.8910 (mmmm) REVERT: A 245 MET cc_start: 0.8777 (ttp) cc_final: 0.8162 (tpp) REVERT: A 391 MET cc_start: 0.7666 (mtt) cc_final: 0.7422 (mtt) REVERT: A 401 TYR cc_start: 0.8290 (OUTLIER) cc_final: 0.8083 (p90) REVERT: A 407 TYR cc_start: 0.8281 (t80) cc_final: 0.7967 (t80) REVERT: A 413 VAL cc_start: 0.9252 (t) cc_final: 0.9004 (m) REVERT: B 161 ASP cc_start: 0.8877 (t0) cc_final: 0.8376 (t0) REVERT: B 491 MET cc_start: 0.9120 (mtp) cc_final: 0.8837 (mtt) REVERT: B 503 GLU cc_start: 0.9218 (tt0) cc_final: 0.8786 (tp30) REVERT: C 262 ASP cc_start: 0.8367 (t0) cc_final: 0.8002 (t0) REVERT: D 57 MET cc_start: 0.9367 (ttm) cc_final: 0.9133 (ttp) REVERT: D 307 GLU cc_start: 0.8518 (tt0) cc_final: 0.8302 (tt0) REVERT: D 403 ASP cc_start: 0.9049 (t0) cc_final: 0.8780 (t0) REVERT: E 108 ASP cc_start: 0.9111 (t0) cc_final: 0.8889 (t70) REVERT: F 116 TYR cc_start: 0.8225 (m-80) cc_final: 0.7986 (m-10) REVERT: F 138 MET cc_start: 0.9004 (tmt) cc_final: 0.8686 (tmt) REVERT: F 159 MET cc_start: 0.8944 (mpt) cc_final: 0.8702 (mpp) REVERT: F 226 MET cc_start: 0.8736 (ttm) cc_final: 0.8407 (ttm) REVERT: F 270 MET cc_start: 0.8557 (mmt) cc_final: 0.8216 (mmp) REVERT: F 290 VAL cc_start: 0.7247 (t) cc_final: 0.6918 (t) REVERT: G 187 SER cc_start: 0.8225 (t) cc_final: 0.7867 (m) REVERT: G 275 MET cc_start: 0.8575 (ttm) cc_final: 0.8117 (ttp) REVERT: H 10 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8376 (tp30) REVERT: H 36 ASP cc_start: 0.8029 (t0) cc_final: 0.7754 (t0) REVERT: H 50 LYS cc_start: 0.9125 (mmtt) cc_final: 0.8876 (mmmm) REVERT: H 245 MET cc_start: 0.8770 (ttp) cc_final: 0.8118 (tpp) REVERT: H 401 TYR cc_start: 0.8262 (OUTLIER) cc_final: 0.8059 (p90) REVERT: H 413 VAL cc_start: 0.9256 (t) cc_final: 0.9021 (m) REVERT: I 161 ASP cc_start: 0.8833 (t0) cc_final: 0.8289 (t0) REVERT: I 271 MET cc_start: 0.9104 (ttm) cc_final: 0.8876 (ttp) REVERT: I 491 MET cc_start: 0.9146 (mtp) cc_final: 0.8867 (mtt) REVERT: I 503 GLU cc_start: 0.9223 (tt0) cc_final: 0.8841 (tp30) REVERT: J 262 ASP cc_start: 0.8368 (t0) cc_final: 0.7982 (t0) REVERT: K 57 MET cc_start: 0.9331 (ttm) cc_final: 0.9094 (ttp) REVERT: K 307 GLU cc_start: 0.8430 (tt0) cc_final: 0.8219 (tt0) REVERT: K 403 ASP cc_start: 0.9022 (t0) cc_final: 0.8755 (t0) REVERT: L 108 ASP cc_start: 0.9130 (t0) cc_final: 0.8875 (t70) REVERT: M 116 TYR cc_start: 0.8262 (m-80) cc_final: 0.7907 (m-80) REVERT: M 138 MET cc_start: 0.8979 (tmt) cc_final: 0.8667 (tmt) REVERT: M 226 MET cc_start: 0.8703 (ttm) cc_final: 0.8371 (ttm) REVERT: M 270 MET cc_start: 0.8526 (mmt) cc_final: 0.8055 (mmp) REVERT: M 290 VAL cc_start: 0.7242 (t) cc_final: 0.6883 (t) REVERT: N 61 MET cc_start: 0.9062 (mmm) cc_final: 0.8861 (mmp) REVERT: N 275 MET cc_start: 0.8553 (ttm) cc_final: 0.8075 (ttp) outliers start: 41 outliers final: 20 residues processed: 635 average time/residue: 0.8464 time to fit residues: 642.2645 Evaluate side-chains 404 residues out of total 4568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 382 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 362 HIS Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain H residue 362 HIS Chi-restraints excluded: chain H residue 401 TYR Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 153 CYS Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 362 HIS Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 84 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 394 optimal weight: 4.9990 chunk 430 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 265 optimal weight: 30.0000 chunk 523 optimal weight: 8.9990 chunk 497 optimal weight: 9.9990 chunk 414 optimal weight: 3.9990 chunk 310 optimal weight: 0.6980 chunk 488 optimal weight: 1.9990 chunk 366 optimal weight: 1.9990 chunk 223 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 ASN ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN A 468 ASN ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 GLN B 71 GLN B 225 ASN B 286 ASN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 HIS B 429 HIS C 45 GLN C 225 ASN C 268 GLN C 286 ASN ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 338 GLN C 363 HIS C 429 HIS C 499 ASN D 98 ASN D 119 GLN D 274 HIS D 468 ASN F 51 HIS F 146 GLN H 83 HIS ** H 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 ASN ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 252 GLN H 271 ASN H 468 ASN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 GLN I 71 GLN I 225 ASN I 268 GLN I 286 ASN ** I 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 363 HIS I 429 HIS J 45 GLN J 225 ASN J 268 GLN J 286 ASN ** J 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 338 GLN J 363 HIS J 429 HIS J 499 ASN K 41 GLN K 98 ASN K 119 GLN K 199 ASN K 274 HIS K 468 ASN M 51 HIS M 146 GLN N 55 GLN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.085360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.056975 restraints weight = 313054.429| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 4.92 r_work: 0.2605 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 222 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 225 | |-----------------------------------------------------------------------------| r_final: 0.2587 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.192 43828 Z= 0.155 Angle : 0.709 28.976 59116 Z= 0.328 Chirality : 0.043 0.165 6350 Planarity : 0.004 0.044 7630 Dihedral : 5.170 81.366 6594 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.94 % Favored : 97.02 % Rotamer: Outliers : 1.46 % Allowed : 10.84 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.12), residues: 5392 helix: 1.50 (0.11), residues: 2556 sheet: -0.73 (0.22), residues: 564 loop : -0.70 (0.13), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 206 TYR 0.024 0.001 TYR M 172 PHE 0.015 0.001 PHE A 431 TRP 0.011 0.001 TRP B 296 HIS 0.004 0.001 HIS C 429 Details of bonding type rmsd covalent geometry : bond 0.00333 (43780) covalent geometry : angle 0.68794 (59080) hydrogen bonds : bond 0.04142 ( 1920) hydrogen bonds : angle 5.25641 ( 5591) metal coordination : bond 0.01935 ( 16) metal coordination : angle 7.05650 ( 36) Misc. bond : bond 0.08893 ( 32) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 4568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 416 time to evaluate : 1.294 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: A 8 GLU cc_start: 0.9506 (mt-10) cc_final: 0.9133 (mt-10) REVERT: A 36 ASP cc_start: 0.8155 (t0) cc_final: 0.7888 (t0) REVERT: A 50 LYS cc_start: 0.9059 (mmtt) cc_final: 0.8788 (mmmm) REVERT: A 78 MET cc_start: 0.9171 (mtp) cc_final: 0.8825 (mtp) REVERT: A 245 MET cc_start: 0.8588 (ttp) cc_final: 0.7986 (tpp) REVERT: A 407 TYR cc_start: 0.7947 (t80) cc_final: 0.7729 (t80) REVERT: B 23 MET cc_start: 0.8732 (ttp) cc_final: 0.8290 (tmt) REVERT: B 161 ASP cc_start: 0.8838 (t0) cc_final: 0.8306 (t0) REVERT: B 503 GLU cc_start: 0.8820 (tt0) cc_final: 0.8587 (tp30) REVERT: C 120 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8260 (mt-10) REVERT: C 262 ASP cc_start: 0.8352 (t0) cc_final: 0.7815 (t70) REVERT: D 57 MET cc_start: 0.9336 (ttm) cc_final: 0.8948 (ttm) REVERT: D 307 GLU cc_start: 0.8683 (tt0) cc_final: 0.8463 (tt0) REVERT: D 403 ASP cc_start: 0.9184 (t0) cc_final: 0.8945 (t0) REVERT: E 41 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8305 (pt0) REVERT: E 85 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8467 (mt-10) REVERT: E 92 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8086 (mtm110) REVERT: E 108 ASP cc_start: 0.9148 (t0) cc_final: 0.8869 (t70) REVERT: F 3 MET cc_start: 0.8583 (ttp) cc_final: 0.8281 (ttp) REVERT: F 138 MET cc_start: 0.8348 (tmt) cc_final: 0.8086 (tmm) REVERT: F 159 MET cc_start: 0.9111 (mpt) cc_final: 0.8594 (mpp) REVERT: F 208 MET cc_start: 0.8828 (tmm) cc_final: 0.8522 (tmm) REVERT: F 210 HIS cc_start: 0.8078 (t-170) cc_final: 0.7760 (t-90) REVERT: F 226 MET cc_start: 0.8372 (ttm) cc_final: 0.7941 (ttm) REVERT: G 187 SER cc_start: 0.8163 (t) cc_final: 0.7785 (m) REVERT: G 226 MET cc_start: 0.8342 (mtp) cc_final: 0.8111 (mtp) REVERT: H 36 ASP cc_start: 0.8161 (t0) cc_final: 0.7893 (t0) REVERT: H 50 LYS cc_start: 0.9019 (mmtt) cc_final: 0.8773 (mmmm) REVERT: H 78 MET cc_start: 0.9155 (mtp) cc_final: 0.8855 (mtp) REVERT: H 245 MET cc_start: 0.8623 (ttp) cc_final: 0.7991 (tpp) REVERT: H 407 TYR cc_start: 0.7865 (t80) cc_final: 0.7308 (t80) REVERT: I 23 MET cc_start: 0.8746 (ttp) cc_final: 0.8350 (tmt) REVERT: I 161 ASP cc_start: 0.8836 (t0) cc_final: 0.8307 (t0) REVERT: I 503 GLU cc_start: 0.8826 (tt0) cc_final: 0.8592 (tp30) REVERT: J 120 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8257 (mt-10) REVERT: J 262 ASP cc_start: 0.8338 (t0) cc_final: 0.7801 (t70) REVERT: K 57 MET cc_start: 0.9331 (ttm) cc_final: 0.8947 (ttm) REVERT: K 279 MET cc_start: 0.9031 (mmt) cc_final: 0.8829 (mmt) REVERT: K 307 GLU cc_start: 0.8695 (tt0) cc_final: 0.8475 (tt0) REVERT: K 403 ASP cc_start: 0.9188 (t0) cc_final: 0.8953 (t0) REVERT: L 41 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8303 (pt0) REVERT: L 85 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8439 (mt-10) REVERT: L 108 ASP cc_start: 0.9166 (t0) cc_final: 0.8884 (t70) REVERT: M 3 MET cc_start: 0.8688 (ttm) cc_final: 0.8400 (ttp) REVERT: M 152 CYS cc_start: 0.7750 (t) cc_final: 0.7130 (p) REVERT: M 208 MET cc_start: 0.8792 (tmm) cc_final: 0.8517 (tmm) REVERT: M 210 HIS cc_start: 0.8616 (t-90) cc_final: 0.8200 (t-90) REVERT: M 226 MET cc_start: 0.8378 (ttm) cc_final: 0.7943 (ttm) REVERT: N 55 GLN cc_start: 0.7100 (tt0) cc_final: 0.6307 (tt0) REVERT: N 61 MET cc_start: 0.8479 (mmm) cc_final: 0.8250 (mmt) REVERT: N 86 CYS cc_start: 0.7406 (OUTLIER) cc_final: 0.7080 (p) REVERT: N 226 MET cc_start: 0.8385 (mtp) cc_final: 0.8035 (mtp) outliers start: 67 outliers final: 37 residues processed: 463 average time/residue: 0.7794 time to fit residues: 439.8605 Evaluate side-chains 414 residues out of total 4568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 373 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain C residue 153 CYS Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 362 HIS Chi-restraints excluded: chain D residue 465 MET Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 92 ARG Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 362 HIS Chi-restraints excluded: chain I residue 153 CYS Chi-restraints excluded: chain I residue 154 MET Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 362 HIS Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 465 MET Chi-restraints excluded: chain L residue 41 GLU Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 282 ILE Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 86 CYS Chi-restraints excluded: chain N residue 175 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 65 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 189 optimal weight: 4.9990 chunk 288 optimal weight: 6.9990 chunk 207 optimal weight: 0.0980 chunk 458 optimal weight: 8.9990 chunk 271 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 364 optimal weight: 7.9990 chunk 382 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 overall best weight: 4.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 294 GLN B 513 GLN C 128 GLN C 294 GLN D 41 GLN D 98 ASN D 199 ASN E 32 GLN H 98 ASN H 432 GLN I 294 GLN J 128 GLN J 294 GLN K 41 GLN K 98 ASN K 199 ASN L 32 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.082121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.053047 restraints weight = 323048.656| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 4.54 r_work: 0.2534 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2527 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2527 r_free = 0.2527 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 225 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2526 r_free = 0.2526 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 227 | |-----------------------------------------------------------------------------| r_final: 0.2526 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.153 43828 Z= 0.273 Angle : 0.750 29.142 59116 Z= 0.342 Chirality : 0.046 0.157 6350 Planarity : 0.004 0.048 7630 Dihedral : 5.034 80.556 6578 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.34 % Favored : 96.63 % Rotamer: Outliers : 2.15 % Allowed : 10.91 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.12), residues: 5392 helix: 1.41 (0.11), residues: 2548 sheet: -0.75 (0.21), residues: 564 loop : -0.78 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 206 TYR 0.018 0.002 TYR H 229 PHE 0.014 0.001 PHE H 431 TRP 0.019 0.002 TRP C 370 HIS 0.005 0.001 HIS J 297 Details of bonding type rmsd covalent geometry : bond 0.00631 (43780) covalent geometry : angle 0.71957 (59080) hydrogen bonds : bond 0.04428 ( 1920) hydrogen bonds : angle 5.13999 ( 5591) metal coordination : bond 0.02469 ( 16) metal coordination : angle 8.60066 ( 36) Misc. bond : bond 0.07042 ( 32) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 4568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 369 time to evaluate : 1.682 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: A 8 GLU cc_start: 0.9515 (mt-10) cc_final: 0.9148 (mt-10) REVERT: A 10 GLU cc_start: 0.9199 (OUTLIER) cc_final: 0.8946 (mp0) REVERT: A 36 ASP cc_start: 0.8160 (t0) cc_final: 0.7895 (t0) REVERT: A 50 LYS cc_start: 0.9064 (mmtt) cc_final: 0.8799 (mmmm) REVERT: A 78 MET cc_start: 0.9296 (mtp) cc_final: 0.8880 (mtp) REVERT: A 245 MET cc_start: 0.8611 (ttp) cc_final: 0.8061 (tpp) REVERT: A 277 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7025 (tpp80) REVERT: A 407 TYR cc_start: 0.7992 (t80) cc_final: 0.7749 (t80) REVERT: B 23 MET cc_start: 0.8778 (ttp) cc_final: 0.8474 (ppp) REVERT: B 161 ASP cc_start: 0.8833 (t0) cc_final: 0.8297 (t0) REVERT: B 503 GLU cc_start: 0.8843 (tt0) cc_final: 0.8625 (tp30) REVERT: C 262 ASP cc_start: 0.8533 (t0) cc_final: 0.8005 (t70) REVERT: C 491 MET cc_start: 0.8667 (mtt) cc_final: 0.8426 (mtt) REVERT: D 27 ASP cc_start: 0.8779 (t0) cc_final: 0.8485 (t0) REVERT: D 57 MET cc_start: 0.9291 (ttm) cc_final: 0.9039 (ttp) REVERT: D 307 GLU cc_start: 0.8752 (tt0) cc_final: 0.8518 (tt0) REVERT: D 403 ASP cc_start: 0.9236 (t0) cc_final: 0.8979 (t0) REVERT: E 16 LYS cc_start: 0.9434 (OUTLIER) cc_final: 0.8941 (ttmt) REVERT: E 37 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.9010 (mtpp) REVERT: E 41 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8336 (pt0) REVERT: E 85 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8508 (mt-10) REVERT: E 108 ASP cc_start: 0.9149 (t0) cc_final: 0.8851 (t70) REVERT: F 3 MET cc_start: 0.8613 (ttp) cc_final: 0.8340 (ttp) REVERT: F 116 TYR cc_start: 0.7986 (m-10) cc_final: 0.7785 (m-80) REVERT: F 159 MET cc_start: 0.9141 (mpt) cc_final: 0.8557 (mpp) REVERT: F 208 MET cc_start: 0.8748 (tmm) cc_final: 0.7989 (tmm) REVERT: F 210 HIS cc_start: 0.8223 (t-170) cc_final: 0.7766 (t-90) REVERT: F 226 MET cc_start: 0.8492 (ttm) cc_final: 0.8074 (ttm) REVERT: F 262 MET cc_start: 0.8533 (tpp) cc_final: 0.8304 (tpp) REVERT: F 270 MET cc_start: 0.9250 (mmp) cc_final: 0.8846 (mmp) REVERT: G 187 SER cc_start: 0.8144 (t) cc_final: 0.7822 (m) REVERT: G 226 MET cc_start: 0.8226 (mtp) cc_final: 0.7954 (mtp) REVERT: G 270 MET cc_start: 0.8890 (mmm) cc_final: 0.8503 (mmm) REVERT: G 275 MET cc_start: 0.8524 (ttp) cc_final: 0.8024 (ptp) REVERT: H 8 GLU cc_start: 0.9499 (mt-10) cc_final: 0.9164 (mt-10) REVERT: H 10 GLU cc_start: 0.9193 (OUTLIER) cc_final: 0.8935 (mp0) REVERT: H 36 ASP cc_start: 0.8133 (t0) cc_final: 0.7851 (t0) REVERT: H 50 LYS cc_start: 0.9023 (mmtt) cc_final: 0.8777 (mmmm) REVERT: H 78 MET cc_start: 0.9280 (mtp) cc_final: 0.8902 (mtp) REVERT: H 245 MET cc_start: 0.8627 (ttp) cc_final: 0.8131 (tpp) REVERT: H 277 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.6958 (tpp80) REVERT: I 23 MET cc_start: 0.8761 (ttp) cc_final: 0.8442 (ppp) REVERT: I 161 ASP cc_start: 0.8837 (t0) cc_final: 0.8298 (t0) REVERT: I 503 GLU cc_start: 0.8849 (tt0) cc_final: 0.8631 (tp30) REVERT: J 120 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8276 (mt-10) REVERT: J 262 ASP cc_start: 0.8516 (t0) cc_final: 0.7989 (t70) REVERT: J 491 MET cc_start: 0.8658 (mtt) cc_final: 0.8415 (mtt) REVERT: K 27 ASP cc_start: 0.8806 (t0) cc_final: 0.8493 (t0) REVERT: K 57 MET cc_start: 0.9286 (ttm) cc_final: 0.9035 (ttp) REVERT: K 307 GLU cc_start: 0.8771 (tt0) cc_final: 0.8550 (tt0) REVERT: K 403 ASP cc_start: 0.9231 (t0) cc_final: 0.8980 (t0) REVERT: L 16 LYS cc_start: 0.9431 (OUTLIER) cc_final: 0.8941 (ttmt) REVERT: L 37 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.9010 (mtpp) REVERT: L 85 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8479 (mt-10) REVERT: L 108 ASP cc_start: 0.9158 (t0) cc_final: 0.8870 (t70) REVERT: M 3 MET cc_start: 0.8683 (ttm) cc_final: 0.8440 (ttp) REVERT: M 61 MET cc_start: 0.8289 (mmm) cc_final: 0.7849 (mpm) REVERT: M 116 TYR cc_start: 0.8044 (m-10) cc_final: 0.7830 (m-80) REVERT: M 159 MET cc_start: 0.9170 (mpp) cc_final: 0.8966 (mpp) REVERT: M 210 HIS cc_start: 0.8668 (t70) cc_final: 0.8285 (t-90) REVERT: M 226 MET cc_start: 0.8515 (ttm) cc_final: 0.8066 (ttm) REVERT: M 262 MET cc_start: 0.8475 (tpp) cc_final: 0.8172 (tpp) REVERT: M 270 MET cc_start: 0.9233 (mmp) cc_final: 0.8930 (mmp) REVERT: N 159 MET cc_start: 0.9401 (mtm) cc_final: 0.9199 (mtm) REVERT: N 226 MET cc_start: 0.8194 (mtp) cc_final: 0.7919 (mtp) REVERT: N 275 MET cc_start: 0.8458 (ttp) cc_final: 0.8150 (ptp) outliers start: 99 outliers final: 43 residues processed: 445 average time/residue: 0.7844 time to fit residues: 424.2958 Evaluate side-chains 405 residues out of total 4568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 353 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 153 CYS Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 362 HIS Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 286 THR Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 277 ARG Chi-restraints excluded: chain H residue 362 HIS Chi-restraints excluded: chain H residue 445 ASP Chi-restraints excluded: chain I residue 153 CYS Chi-restraints excluded: chain I residue 320 MET Chi-restraints excluded: chain J residue 38 ASP Chi-restraints excluded: chain J residue 153 CYS Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 362 HIS Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 152 CYS Chi-restraints excluded: chain M residue 282 ILE Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 152 CYS Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain N residue 286 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 342 optimal weight: 4.9990 chunk 231 optimal weight: 8.9990 chunk 45 optimal weight: 8.9990 chunk 346 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 399 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 438 optimal weight: 5.9990 chunk 329 optimal weight: 7.9990 chunk 475 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN D 98 ASN ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN K 98 ASN K 199 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.081981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.053084 restraints weight = 299716.284| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 4.41 r_work: 0.2542 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2536 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2536 r_free = 0.2536 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 227 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2536 r_free = 0.2536 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 227 | |-----------------------------------------------------------------------------| r_final: 0.2536 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.140 43828 Z= 0.242 Angle : 0.734 29.056 59116 Z= 0.329 Chirality : 0.045 0.156 6350 Planarity : 0.004 0.047 7630 Dihedral : 4.990 80.465 6576 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.11 % Favored : 96.85 % Rotamer: Outliers : 2.09 % Allowed : 11.21 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.12), residues: 5392 helix: 1.42 (0.11), residues: 2548 sheet: -0.79 (0.22), residues: 524 loop : -0.74 (0.12), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 206 TYR 0.019 0.001 TYR N 160 PHE 0.011 0.001 PHE D 429 TRP 0.015 0.001 TRP C 370 HIS 0.005 0.001 HIS C 297 Details of bonding type rmsd covalent geometry : bond 0.00561 (43780) covalent geometry : angle 0.69550 (59080) hydrogen bonds : bond 0.04086 ( 1920) hydrogen bonds : angle 5.04633 ( 5591) metal coordination : bond 0.02115 ( 16) metal coordination : angle 9.52143 ( 36) Misc. bond : bond 0.06193 ( 32) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 4568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 368 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.9497 (mt-10) cc_final: 0.9147 (mt-10) REVERT: A 36 ASP cc_start: 0.8207 (t0) cc_final: 0.7930 (t0) REVERT: A 50 LYS cc_start: 0.9052 (mmtt) cc_final: 0.8788 (mmmm) REVERT: A 78 MET cc_start: 0.9308 (mtp) cc_final: 0.8802 (mtp) REVERT: A 407 TYR cc_start: 0.8003 (t80) cc_final: 0.7796 (t80) REVERT: B 23 MET cc_start: 0.8798 (ttp) cc_final: 0.8540 (ppp) REVERT: B 151 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.8146 (p) REVERT: B 161 ASP cc_start: 0.8834 (t0) cc_final: 0.8313 (t0) REVERT: B 491 MET cc_start: 0.8815 (mtp) cc_final: 0.8568 (mtm) REVERT: B 503 GLU cc_start: 0.8865 (tt0) cc_final: 0.8630 (tp30) REVERT: C 262 ASP cc_start: 0.8493 (t0) cc_final: 0.7975 (t70) REVERT: C 491 MET cc_start: 0.8674 (mtt) cc_final: 0.8437 (mtt) REVERT: D 27 ASP cc_start: 0.8776 (t0) cc_final: 0.8468 (t0) REVERT: D 57 MET cc_start: 0.9285 (ttm) cc_final: 0.9031 (ttp) REVERT: D 307 GLU cc_start: 0.8745 (tt0) cc_final: 0.8530 (tt0) REVERT: D 403 ASP cc_start: 0.9237 (t0) cc_final: 0.8990 (t0) REVERT: E 37 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.9004 (mtpp) REVERT: E 108 ASP cc_start: 0.9142 (t0) cc_final: 0.8844 (t70) REVERT: F 3 MET cc_start: 0.8586 (ttp) cc_final: 0.8292 (ttp) REVERT: F 61 MET cc_start: 0.8376 (mmm) cc_final: 0.7922 (mpm) REVERT: F 116 TYR cc_start: 0.7936 (m-10) cc_final: 0.7561 (m-80) REVERT: F 120 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8594 (mm) REVERT: F 159 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8578 (mpp) REVERT: F 226 MET cc_start: 0.8485 (ttm) cc_final: 0.8065 (ttm) REVERT: F 262 MET cc_start: 0.8540 (tpp) cc_final: 0.8322 (tpp) REVERT: G 86 CYS cc_start: 0.7375 (OUTLIER) cc_final: 0.7077 (p) REVERT: G 187 SER cc_start: 0.8194 (t) cc_final: 0.7885 (m) REVERT: G 226 MET cc_start: 0.8166 (mtp) cc_final: 0.7877 (mtp) REVERT: H 8 GLU cc_start: 0.9494 (mt-10) cc_final: 0.9158 (mt-10) REVERT: H 36 ASP cc_start: 0.8136 (t0) cc_final: 0.7848 (t0) REVERT: H 50 LYS cc_start: 0.9012 (mmtt) cc_final: 0.8767 (mmmm) REVERT: H 78 MET cc_start: 0.9296 (mtp) cc_final: 0.8900 (mtp) REVERT: H 245 MET cc_start: 0.8544 (ttp) cc_final: 0.8082 (tpp) REVERT: H 277 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7511 (tpp80) REVERT: H 401 TYR cc_start: 0.7717 (p90) cc_final: 0.7442 (p90) REVERT: I 23 MET cc_start: 0.8774 (ttp) cc_final: 0.8505 (ppp) REVERT: I 131 MET cc_start: 0.8525 (tpp) cc_final: 0.7424 (tpp) REVERT: I 151 THR cc_start: 0.8438 (OUTLIER) cc_final: 0.8174 (p) REVERT: I 161 ASP cc_start: 0.8823 (t0) cc_final: 0.8309 (t0) REVERT: I 442 MET cc_start: 0.9212 (mtm) cc_final: 0.8916 (mtm) REVERT: I 503 GLU cc_start: 0.8856 (tt0) cc_final: 0.8621 (tp30) REVERT: J 120 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8023 (mm-30) REVERT: J 262 ASP cc_start: 0.8483 (t0) cc_final: 0.7961 (t70) REVERT: J 491 MET cc_start: 0.8653 (mtt) cc_final: 0.8416 (mtt) REVERT: K 27 ASP cc_start: 0.8808 (t0) cc_final: 0.8500 (t0) REVERT: K 57 MET cc_start: 0.9284 (ttm) cc_final: 0.9033 (ttp) REVERT: K 307 GLU cc_start: 0.8758 (tt0) cc_final: 0.8543 (tt0) REVERT: K 403 ASP cc_start: 0.9239 (t0) cc_final: 0.8995 (t0) REVERT: L 37 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.9015 (mtpp) REVERT: L 108 ASP cc_start: 0.9136 (t0) cc_final: 0.8848 (t70) REVERT: M 3 MET cc_start: 0.8644 (ttm) cc_final: 0.8356 (ttp) REVERT: M 61 MET cc_start: 0.8257 (mmm) cc_final: 0.7853 (mpm) REVERT: M 116 TYR cc_start: 0.7956 (m-10) cc_final: 0.7588 (m-80) REVERT: M 120 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8646 (mm) REVERT: M 152 CYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7216 (p) REVERT: M 159 MET cc_start: 0.9248 (mpp) cc_final: 0.8789 (mpp) REVERT: M 208 MET cc_start: 0.8564 (tmm) cc_final: 0.8093 (tmt) REVERT: M 210 HIS cc_start: 0.8543 (t70) cc_final: 0.8190 (t-90) REVERT: M 226 MET cc_start: 0.8514 (ttm) cc_final: 0.8076 (ttm) REVERT: M 262 MET cc_start: 0.8492 (tpp) cc_final: 0.8197 (tpp) REVERT: N 86 CYS cc_start: 0.7554 (OUTLIER) cc_final: 0.7277 (p) REVERT: N 159 MET cc_start: 0.9381 (mtm) cc_final: 0.9044 (mtm) REVERT: N 208 MET cc_start: 0.8447 (tmm) cc_final: 0.8236 (tmm) REVERT: N 226 MET cc_start: 0.8137 (mtp) cc_final: 0.7844 (mtp) REVERT: N 270 MET cc_start: 0.8961 (mmt) cc_final: 0.8577 (mmm) REVERT: N 275 MET cc_start: 0.8488 (ttp) cc_final: 0.8146 (ptp) outliers start: 96 outliers final: 48 residues processed: 445 average time/residue: 0.7467 time to fit residues: 405.6055 Evaluate side-chains 407 residues out of total 4568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 348 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 153 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 362 HIS Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 152 CYS Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 286 THR Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 277 ARG Chi-restraints excluded: chain H residue 362 HIS Chi-restraints excluded: chain H residue 404 VAL Chi-restraints excluded: chain H residue 463 MET Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 153 CYS Chi-restraints excluded: chain J residue 38 ASP Chi-restraints excluded: chain J residue 153 CYS Chi-restraints excluded: chain J residue 263 THR Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 98 ASN Chi-restraints excluded: chain K residue 362 HIS Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain M residue 17 SER Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 152 CYS Chi-restraints excluded: chain M residue 282 ILE Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 86 CYS Chi-restraints excluded: chain N residue 152 CYS Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain N residue 286 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 237 optimal weight: 4.9990 chunk 396 optimal weight: 0.9990 chunk 355 optimal weight: 0.8980 chunk 73 optimal weight: 0.0670 chunk 209 optimal weight: 1.9990 chunk 263 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 59 optimal weight: 0.4980 chunk 430 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 3 optimal weight: 40.0000 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 ASN ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 GLN D 41 GLN D 98 ASN D 271 ASN H 98 ASN ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN K 271 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.084010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.054966 restraints weight = 289147.792| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 4.44 r_work: 0.2591 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2603 r_free = 0.2603 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 227 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2603 r_free = 0.2603 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 227 | |-----------------------------------------------------------------------------| r_final: 0.2603 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.123 43828 Z= 0.115 Angle : 0.674 29.091 59116 Z= 0.300 Chirality : 0.042 0.188 6350 Planarity : 0.004 0.043 7630 Dihedral : 4.769 80.940 6576 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.78 % Favored : 97.19 % Rotamer: Outliers : 1.70 % Allowed : 12.12 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.12), residues: 5392 helix: 1.69 (0.11), residues: 2524 sheet: -0.63 (0.21), residues: 564 loop : -0.67 (0.12), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 97 TYR 0.022 0.001 TYR M 172 PHE 0.013 0.001 PHE H 431 TRP 0.011 0.001 TRP A 335 HIS 0.005 0.001 HIS C 297 Details of bonding type rmsd covalent geometry : bond 0.00251 (43780) covalent geometry : angle 0.64410 (59080) hydrogen bonds : bond 0.03318 ( 1920) hydrogen bonds : angle 4.87262 ( 5591) metal coordination : bond 0.00963 ( 16) metal coordination : angle 8.11131 ( 36) Misc. bond : bond 0.05168 ( 32) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 4568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 384 time to evaluate : 1.822 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 8 GLU cc_start: 0.9497 (mt-10) cc_final: 0.9129 (mt-10) REVERT: A 14 GLN cc_start: 0.9331 (OUTLIER) cc_final: 0.9099 (mp10) REVERT: A 36 ASP cc_start: 0.8218 (t0) cc_final: 0.7930 (t0) REVERT: A 50 LYS cc_start: 0.9044 (mmtt) cc_final: 0.8766 (mmmm) REVERT: A 78 MET cc_start: 0.9320 (mtp) cc_final: 0.8914 (mtp) REVERT: A 245 MET cc_start: 0.8434 (ttp) cc_final: 0.7895 (tpp) REVERT: B 23 MET cc_start: 0.8841 (ttp) cc_final: 0.8558 (ppp) REVERT: B 151 THR cc_start: 0.8501 (OUTLIER) cc_final: 0.8228 (p) REVERT: B 161 ASP cc_start: 0.8829 (t0) cc_final: 0.8317 (t0) REVERT: B 503 GLU cc_start: 0.8945 (tt0) cc_final: 0.8715 (tp30) REVERT: C 262 ASP cc_start: 0.8484 (t0) cc_final: 0.7946 (t70) REVERT: C 491 MET cc_start: 0.8733 (mtt) cc_final: 0.8524 (mtt) REVERT: D 57 MET cc_start: 0.9370 (ttm) cc_final: 0.9166 (ttm) REVERT: D 307 GLU cc_start: 0.8745 (tt0) cc_final: 0.8529 (tt0) REVERT: D 403 ASP cc_start: 0.9156 (t0) cc_final: 0.8891 (t0) REVERT: E 16 LYS cc_start: 0.9479 (OUTLIER) cc_final: 0.9021 (ttmt) REVERT: E 37 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8998 (mtpp) REVERT: E 41 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8258 (pt0) REVERT: E 108 ASP cc_start: 0.9163 (t0) cc_final: 0.8897 (t70) REVERT: F 3 MET cc_start: 0.8638 (ttp) cc_final: 0.8355 (ttp) REVERT: F 61 MET cc_start: 0.8389 (mmm) cc_final: 0.7989 (mpm) REVERT: F 116 TYR cc_start: 0.7819 (m-10) cc_final: 0.7577 (m-10) REVERT: F 120 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8592 (mm) REVERT: F 208 MET cc_start: 0.8548 (tmm) cc_final: 0.8093 (tmm) REVERT: F 210 HIS cc_start: 0.8397 (t-170) cc_final: 0.7991 (t-90) REVERT: F 226 MET cc_start: 0.8467 (ttm) cc_final: 0.8077 (ttm) REVERT: F 240 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8355 (tt0) REVERT: F 262 MET cc_start: 0.8601 (tpp) cc_final: 0.8344 (tpp) REVERT: G 86 CYS cc_start: 0.7427 (OUTLIER) cc_final: 0.7118 (p) REVERT: G 187 SER cc_start: 0.8149 (t) cc_final: 0.7846 (m) REVERT: G 226 MET cc_start: 0.8205 (mtp) cc_final: 0.7832 (mtp) REVERT: G 270 MET cc_start: 0.8825 (mmm) cc_final: 0.8532 (mmm) REVERT: G 275 MET cc_start: 0.8492 (ttp) cc_final: 0.8142 (ptp) REVERT: H 8 GLU cc_start: 0.9502 (mt-10) cc_final: 0.9125 (mt-10) REVERT: H 36 ASP cc_start: 0.8188 (t0) cc_final: 0.7888 (t0) REVERT: H 50 LYS cc_start: 0.9041 (mmtt) cc_final: 0.8790 (mmmm) REVERT: H 78 MET cc_start: 0.9316 (mtp) cc_final: 0.8923 (mtp) REVERT: H 245 MET cc_start: 0.8478 (ttp) cc_final: 0.8117 (tpp) REVERT: I 23 MET cc_start: 0.8821 (ttp) cc_final: 0.8584 (ppp) REVERT: I 151 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8272 (p) REVERT: I 161 ASP cc_start: 0.8836 (t0) cc_final: 0.8323 (t0) REVERT: I 442 MET cc_start: 0.9274 (mtm) cc_final: 0.8948 (mtm) REVERT: I 503 GLU cc_start: 0.8949 (tt0) cc_final: 0.8718 (tp30) REVERT: J 262 ASP cc_start: 0.8480 (t0) cc_final: 0.7957 (t70) REVERT: J 491 MET cc_start: 0.8727 (mtt) cc_final: 0.8517 (mtt) REVERT: K 307 GLU cc_start: 0.8759 (tt0) cc_final: 0.8544 (tt0) REVERT: K 403 ASP cc_start: 0.9189 (t0) cc_final: 0.8908 (t0) REVERT: L 16 LYS cc_start: 0.9491 (OUTLIER) cc_final: 0.9013 (ttmt) REVERT: L 37 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.9008 (mtpp) REVERT: L 108 ASP cc_start: 0.9156 (t0) cc_final: 0.8920 (t70) REVERT: M 3 MET cc_start: 0.8681 (ttm) cc_final: 0.8411 (ttp) REVERT: M 61 MET cc_start: 0.8296 (mmm) cc_final: 0.7919 (mpm) REVERT: M 120 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8612 (mm) REVERT: M 152 CYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7246 (p) REVERT: M 159 MET cc_start: 0.9302 (mpp) cc_final: 0.8945 (mpp) REVERT: M 208 MET cc_start: 0.8410 (tmm) cc_final: 0.8124 (tmt) REVERT: M 210 HIS cc_start: 0.8596 (t70) cc_final: 0.8062 (t70) REVERT: M 226 MET cc_start: 0.8459 (ttm) cc_final: 0.8034 (ttm) REVERT: M 262 MET cc_start: 0.8542 (tpp) cc_final: 0.8244 (tpp) REVERT: N 55 GLN cc_start: 0.7040 (tt0) cc_final: 0.6583 (tt0) REVERT: N 86 CYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7337 (p) REVERT: N 208 MET cc_start: 0.8499 (tmm) cc_final: 0.8256 (tmm) REVERT: N 226 MET cc_start: 0.8204 (mtp) cc_final: 0.7820 (mtp) REVERT: N 270 MET cc_start: 0.8972 (mmt) cc_final: 0.8593 (mmm) REVERT: N 275 MET cc_start: 0.8555 (ttp) cc_final: 0.8245 (ptp) outliers start: 78 outliers final: 42 residues processed: 436 average time/residue: 0.7555 time to fit residues: 403.6716 Evaluate side-chains 410 residues out of total 4568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 355 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 153 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 362 HIS Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 240 GLU Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 152 CYS Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 286 THR Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 362 HIS Chi-restraints excluded: chain H residue 463 MET Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 153 CYS Chi-restraints excluded: chain I residue 171 LYS Chi-restraints excluded: chain J residue 38 ASP Chi-restraints excluded: chain J residue 153 CYS Chi-restraints excluded: chain J residue 263 THR Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 362 HIS Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 152 CYS Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 86 CYS Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain N residue 286 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 215 optimal weight: 5.9990 chunk 437 optimal weight: 6.9990 chunk 368 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 296 optimal weight: 0.9990 chunk 212 optimal weight: 7.9990 chunk 166 optimal weight: 0.0980 chunk 447 optimal weight: 4.9990 chunk 245 optimal weight: 7.9990 chunk 91 optimal weight: 0.6980 chunk 503 optimal weight: 30.0000 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN C 168 ASN D 98 ASN H 98 ASN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 GLN J 168 ASN K 98 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.084968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.056191 restraints weight = 273233.478| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 4.36 r_work: 0.2620 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2632 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 227 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 227 | |-----------------------------------------------------------------------------| r_final: 0.2632 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 43828 Z= 0.110 Angle : 0.665 29.109 59116 Z= 0.295 Chirality : 0.042 0.205 6350 Planarity : 0.004 0.042 7630 Dihedral : 4.568 80.444 6576 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.63 % Favored : 97.34 % Rotamer: Outliers : 1.76 % Allowed : 12.43 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.12), residues: 5392 helix: 1.83 (0.11), residues: 2512 sheet: -0.54 (0.21), residues: 564 loop : -0.60 (0.12), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 359 TYR 0.017 0.001 TYR G 160 PHE 0.015 0.001 PHE L 40 TRP 0.011 0.001 TRP A 335 HIS 0.005 0.001 HIS C 297 Details of bonding type rmsd covalent geometry : bond 0.00243 (43780) covalent geometry : angle 0.63909 (59080) hydrogen bonds : bond 0.03072 ( 1920) hydrogen bonds : angle 4.75385 ( 5591) metal coordination : bond 0.00937 ( 16) metal coordination : angle 7.42881 ( 36) Misc. bond : bond 0.04690 ( 32) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 4568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 375 time to evaluate : 1.685 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: A 8 GLU cc_start: 0.9498 (mt-10) cc_final: 0.9131 (mt-10) REVERT: A 14 GLN cc_start: 0.9327 (OUTLIER) cc_final: 0.9096 (mp10) REVERT: A 36 ASP cc_start: 0.8225 (t0) cc_final: 0.7912 (t0) REVERT: A 50 LYS cc_start: 0.9037 (mmtt) cc_final: 0.8743 (mmmm) REVERT: A 245 MET cc_start: 0.8305 (ttp) cc_final: 0.7927 (tpp) REVERT: B 23 MET cc_start: 0.8830 (ttp) cc_final: 0.8567 (ppp) REVERT: B 151 THR cc_start: 0.8534 (OUTLIER) cc_final: 0.8261 (p) REVERT: B 161 ASP cc_start: 0.8860 (t0) cc_final: 0.8350 (t0) REVERT: B 491 MET cc_start: 0.8836 (mtp) cc_final: 0.8571 (mtm) REVERT: B 503 GLU cc_start: 0.8962 (tt0) cc_final: 0.8716 (tp30) REVERT: C 262 ASP cc_start: 0.8428 (t0) cc_final: 0.7898 (t70) REVERT: C 516 ASP cc_start: 0.8453 (p0) cc_final: 0.7632 (t0) REVERT: D 57 MET cc_start: 0.9384 (ttm) cc_final: 0.9161 (ttm) REVERT: D 307 GLU cc_start: 0.8735 (tt0) cc_final: 0.8509 (tt0) REVERT: D 403 ASP cc_start: 0.9152 (t0) cc_final: 0.8854 (t0) REVERT: E 37 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8994 (mtpp) REVERT: E 41 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8221 (pt0) REVERT: E 108 ASP cc_start: 0.9208 (t0) cc_final: 0.8978 (t70) REVERT: F 3 MET cc_start: 0.8647 (ttp) cc_final: 0.8371 (ttp) REVERT: F 61 MET cc_start: 0.8336 (mmm) cc_final: 0.7961 (mpm) REVERT: F 116 TYR cc_start: 0.7726 (m-10) cc_final: 0.7472 (m-10) REVERT: F 120 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8638 (mm) REVERT: F 159 MET cc_start: 0.8921 (mmm) cc_final: 0.8175 (mpp) REVERT: F 210 HIS cc_start: 0.8355 (t-170) cc_final: 0.7853 (t-90) REVERT: F 226 MET cc_start: 0.8438 (ttm) cc_final: 0.8056 (ttm) REVERT: F 262 MET cc_start: 0.8570 (tpp) cc_final: 0.8314 (tpp) REVERT: G 55 GLN cc_start: 0.6802 (tt0) cc_final: 0.5965 (tt0) REVERT: G 86 CYS cc_start: 0.7424 (OUTLIER) cc_final: 0.7102 (p) REVERT: G 187 SER cc_start: 0.8097 (t) cc_final: 0.7794 (m) REVERT: G 270 MET cc_start: 0.8823 (mmt) cc_final: 0.8528 (mmm) REVERT: G 275 MET cc_start: 0.8553 (ttp) cc_final: 0.8183 (ptp) REVERT: H 8 GLU cc_start: 0.9497 (mt-10) cc_final: 0.9131 (mt-10) REVERT: H 36 ASP cc_start: 0.8210 (t0) cc_final: 0.7901 (t0) REVERT: H 50 LYS cc_start: 0.9031 (mmtt) cc_final: 0.8709 (mmmm) REVERT: H 229 TYR cc_start: 0.7958 (m-10) cc_final: 0.7579 (m-10) REVERT: H 401 TYR cc_start: 0.8055 (p90) cc_final: 0.7819 (p90) REVERT: I 23 MET cc_start: 0.8834 (ttp) cc_final: 0.8612 (ppp) REVERT: I 131 MET cc_start: 0.8592 (tpp) cc_final: 0.7566 (tpp) REVERT: I 151 THR cc_start: 0.8551 (OUTLIER) cc_final: 0.8286 (p) REVERT: I 161 ASP cc_start: 0.8845 (t0) cc_final: 0.8373 (t0) REVERT: I 442 MET cc_start: 0.9247 (mtm) cc_final: 0.8972 (mtm) REVERT: I 503 GLU cc_start: 0.8970 (tt0) cc_final: 0.8719 (tp30) REVERT: J 262 ASP cc_start: 0.8449 (t0) cc_final: 0.7897 (t70) REVERT: K 307 GLU cc_start: 0.8745 (tt0) cc_final: 0.8520 (tt0) REVERT: K 403 ASP cc_start: 0.9159 (t0) cc_final: 0.8878 (t0) REVERT: L 37 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.9014 (mtpp) REVERT: L 41 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8202 (pt0) REVERT: L 92 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7868 (mtm110) REVERT: L 108 ASP cc_start: 0.9201 (t0) cc_final: 0.8937 (t70) REVERT: M 3 MET cc_start: 0.8695 (ttm) cc_final: 0.8445 (ttp) REVERT: M 61 MET cc_start: 0.8298 (mmm) cc_final: 0.7934 (mpm) REVERT: M 120 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8617 (mm) REVERT: M 152 CYS cc_start: 0.7927 (t) cc_final: 0.7245 (p) REVERT: M 159 MET cc_start: 0.9329 (mpp) cc_final: 0.8999 (mpp) REVERT: M 184 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.8050 (mt) REVERT: M 208 MET cc_start: 0.8284 (tmm) cc_final: 0.7891 (tmm) REVERT: M 210 HIS cc_start: 0.8607 (t70) cc_final: 0.8099 (t70) REVERT: M 226 MET cc_start: 0.8430 (ttm) cc_final: 0.7994 (ttm) REVERT: M 262 MET cc_start: 0.8502 (tpp) cc_final: 0.8219 (tpp) REVERT: N 55 GLN cc_start: 0.6918 (tt0) cc_final: 0.6468 (tt0) REVERT: N 86 CYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7370 (p) REVERT: N 208 MET cc_start: 0.8498 (tmm) cc_final: 0.8219 (tmm) REVERT: N 226 MET cc_start: 0.8112 (mtp) cc_final: 0.7827 (mtp) REVERT: N 270 MET cc_start: 0.8897 (mmt) cc_final: 0.8560 (mmm) REVERT: N 275 MET cc_start: 0.8545 (ttp) cc_final: 0.8304 (ptp) outliers start: 81 outliers final: 43 residues processed: 435 average time/residue: 0.7694 time to fit residues: 408.9697 Evaluate side-chains 411 residues out of total 4568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 357 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 153 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 362 HIS Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 152 CYS Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 286 THR Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 362 HIS Chi-restraints excluded: chain H residue 404 VAL Chi-restraints excluded: chain H residue 463 MET Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 153 CYS Chi-restraints excluded: chain I residue 320 MET Chi-restraints excluded: chain J residue 38 ASP Chi-restraints excluded: chain J residue 153 CYS Chi-restraints excluded: chain J residue 263 THR Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 362 HIS Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 92 ARG Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 184 ILE Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 86 CYS Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain N residue 286 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 38 optimal weight: 0.8980 chunk 137 optimal weight: 0.6980 chunk 158 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 289 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 127 optimal weight: 8.9990 chunk 233 optimal weight: 40.0000 chunk 107 optimal weight: 0.4980 chunk 113 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 ASN H 98 ASN ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 513 GLN K 41 GLN K 98 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.085169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.056436 restraints weight = 279782.765| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 4.39 r_work: 0.2628 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 227 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 227 | |-----------------------------------------------------------------------------| r_final: 0.2638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 43828 Z= 0.110 Angle : 0.666 29.098 59116 Z= 0.296 Chirality : 0.042 0.240 6350 Planarity : 0.003 0.042 7630 Dihedral : 4.486 80.741 6576 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.76 % Favored : 97.20 % Rotamer: Outliers : 1.33 % Allowed : 13.34 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.12), residues: 5392 helix: 1.86 (0.11), residues: 2512 sheet: -0.49 (0.22), residues: 524 loop : -0.55 (0.12), residues: 2356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 359 TYR 0.018 0.001 TYR H 229 PHE 0.014 0.001 PHE H 431 TRP 0.012 0.001 TRP A 335 HIS 0.005 0.001 HIS C 297 Details of bonding type rmsd covalent geometry : bond 0.00246 (43780) covalent geometry : angle 0.64201 (59080) hydrogen bonds : bond 0.03013 ( 1920) hydrogen bonds : angle 4.70549 ( 5591) metal coordination : bond 0.00853 ( 16) metal coordination : angle 7.26516 ( 36) Misc. bond : bond 0.04433 ( 32) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 4568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 366 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.9504 (mt-10) cc_final: 0.9132 (mt-10) REVERT: A 14 GLN cc_start: 0.9338 (OUTLIER) cc_final: 0.9105 (mp10) REVERT: A 36 ASP cc_start: 0.8229 (t0) cc_final: 0.7878 (t0) REVERT: A 50 LYS cc_start: 0.9023 (mmtt) cc_final: 0.8700 (mmmm) REVERT: A 78 MET cc_start: 0.9310 (mtp) cc_final: 0.8894 (mtp) REVERT: A 245 MET cc_start: 0.8270 (ttp) cc_final: 0.7954 (tpp) REVERT: A 391 MET cc_start: 0.7347 (mtt) cc_final: 0.7039 (mtp) REVERT: B 23 MET cc_start: 0.8850 (ttp) cc_final: 0.8647 (ppp) REVERT: B 131 MET cc_start: 0.8441 (ttm) cc_final: 0.8135 (tpp) REVERT: B 151 THR cc_start: 0.8487 (OUTLIER) cc_final: 0.8218 (p) REVERT: B 161 ASP cc_start: 0.8888 (t0) cc_final: 0.8395 (t0) REVERT: B 491 MET cc_start: 0.8804 (mtp) cc_final: 0.8581 (mtm) REVERT: B 503 GLU cc_start: 0.8922 (tt0) cc_final: 0.8684 (tp30) REVERT: C 262 ASP cc_start: 0.8412 (t0) cc_final: 0.7859 (t70) REVERT: D 57 MET cc_start: 0.9371 (ttm) cc_final: 0.9165 (ttp) REVERT: D 307 GLU cc_start: 0.8728 (tt0) cc_final: 0.8501 (tt0) REVERT: D 394 MET cc_start: 0.8877 (mmm) cc_final: 0.8655 (mmm) REVERT: D 403 ASP cc_start: 0.9120 (t0) cc_final: 0.8827 (t0) REVERT: E 41 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8155 (pt0) REVERT: E 108 ASP cc_start: 0.9215 (t0) cc_final: 0.8965 (t70) REVERT: F 3 MET cc_start: 0.8645 (ttp) cc_final: 0.8385 (ttp) REVERT: F 61 MET cc_start: 0.8315 (mmm) cc_final: 0.7939 (mpm) REVERT: F 120 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8539 (mm) REVERT: F 159 MET cc_start: 0.8909 (mmm) cc_final: 0.8124 (mpp) REVERT: F 210 HIS cc_start: 0.8364 (t-170) cc_final: 0.8095 (t-90) REVERT: F 226 MET cc_start: 0.8414 (ttm) cc_final: 0.7972 (ttm) REVERT: F 262 MET cc_start: 0.8563 (tpp) cc_final: 0.8358 (tpp) REVERT: G 86 CYS cc_start: 0.7406 (OUTLIER) cc_final: 0.7173 (p) REVERT: G 187 SER cc_start: 0.8040 (t) cc_final: 0.7766 (m) REVERT: G 208 MET cc_start: 0.8455 (tmm) cc_final: 0.8172 (tmm) REVERT: G 226 MET cc_start: 0.8158 (mtp) cc_final: 0.7723 (mtp) REVERT: G 270 MET cc_start: 0.8837 (mmt) cc_final: 0.8480 (mmm) REVERT: G 275 MET cc_start: 0.8577 (ttp) cc_final: 0.8335 (ptp) REVERT: H 8 GLU cc_start: 0.9514 (mt-10) cc_final: 0.9148 (mt-10) REVERT: H 14 GLN cc_start: 0.9322 (OUTLIER) cc_final: 0.9079 (mp10) REVERT: H 36 ASP cc_start: 0.8190 (t0) cc_final: 0.7825 (t0) REVERT: H 50 LYS cc_start: 0.9036 (mmtt) cc_final: 0.8688 (mmmm) REVERT: H 245 MET cc_start: 0.8392 (ttp) cc_final: 0.8020 (tpp) REVERT: H 368 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8695 (mp0) REVERT: H 391 MET cc_start: 0.7287 (mtt) cc_final: 0.6938 (mtp) REVERT: H 401 TYR cc_start: 0.8019 (p90) cc_final: 0.7765 (p90) REVERT: I 23 MET cc_start: 0.8842 (ttp) cc_final: 0.8629 (ppp) REVERT: I 131 MET cc_start: 0.8589 (tpp) cc_final: 0.7502 (tpp) REVERT: I 151 THR cc_start: 0.8532 (OUTLIER) cc_final: 0.8271 (p) REVERT: I 161 ASP cc_start: 0.8885 (t0) cc_final: 0.8424 (t0) REVERT: I 442 MET cc_start: 0.9218 (mtm) cc_final: 0.8900 (mtm) REVERT: I 503 GLU cc_start: 0.8931 (tt0) cc_final: 0.8686 (tp30) REVERT: J 262 ASP cc_start: 0.8418 (t0) cc_final: 0.7838 (t0) REVERT: J 491 MET cc_start: 0.8645 (mtt) cc_final: 0.8443 (mtt) REVERT: K 307 GLU cc_start: 0.8739 (tt0) cc_final: 0.8512 (tt0) REVERT: K 403 ASP cc_start: 0.9126 (t0) cc_final: 0.8831 (t0) REVERT: L 41 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8126 (pt0) REVERT: L 92 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7832 (mtm110) REVERT: L 108 ASP cc_start: 0.9202 (t0) cc_final: 0.8970 (t70) REVERT: M 3 MET cc_start: 0.8693 (ttm) cc_final: 0.8452 (ttp) REVERT: M 61 MET cc_start: 0.8260 (mmm) cc_final: 0.7900 (mpm) REVERT: M 120 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8595 (mm) REVERT: M 152 CYS cc_start: 0.7909 (t) cc_final: 0.7245 (p) REVERT: M 159 MET cc_start: 0.9335 (mpp) cc_final: 0.8961 (mpp) REVERT: M 210 HIS cc_start: 0.8647 (t70) cc_final: 0.8157 (t70) REVERT: M 226 MET cc_start: 0.8397 (ttm) cc_final: 0.7964 (ttm) REVERT: M 262 MET cc_start: 0.8558 (tpp) cc_final: 0.8319 (tpp) REVERT: N 55 GLN cc_start: 0.6901 (tt0) cc_final: 0.6422 (tt0) REVERT: N 86 CYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7371 (p) REVERT: N 208 MET cc_start: 0.8525 (tmm) cc_final: 0.8247 (tmm) REVERT: N 226 MET cc_start: 0.8150 (mtp) cc_final: 0.7869 (mtp) REVERT: N 270 MET cc_start: 0.8885 (mmt) cc_final: 0.8532 (mmm) outliers start: 61 outliers final: 42 residues processed: 414 average time/residue: 0.7950 time to fit residues: 400.4935 Evaluate side-chains 408 residues out of total 4568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 357 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 153 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain D residue 362 HIS Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 152 CYS Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 286 THR Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 362 HIS Chi-restraints excluded: chain H residue 404 VAL Chi-restraints excluded: chain H residue 463 MET Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 153 CYS Chi-restraints excluded: chain I residue 320 MET Chi-restraints excluded: chain J residue 38 ASP Chi-restraints excluded: chain J residue 153 CYS Chi-restraints excluded: chain J residue 263 THR Chi-restraints excluded: chain K residue 77 ASP Chi-restraints excluded: chain K residue 98 ASN Chi-restraints excluded: chain K residue 362 HIS Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain L residue 92 ARG Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 86 CYS Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain N residue 286 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 422 optimal weight: 2.9990 chunk 335 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 429 optimal weight: 10.0000 chunk 292 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 275 optimal weight: 6.9990 chunk 495 optimal weight: 20.0000 chunk 186 optimal weight: 2.9990 chunk 400 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 HIS D 41 GLN D 98 ASN ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 457 HIS I 513 GLN K 98 ASN ** K 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.085013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.056265 restraints weight = 291584.448| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 4.47 r_work: 0.2620 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 227 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 227 | |-----------------------------------------------------------------------------| r_final: 0.2630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.248 43828 Z= 0.185 Angle : 0.848 59.196 59116 Z= 0.425 Chirality : 0.044 0.537 6350 Planarity : 0.005 0.215 7630 Dihedral : 4.521 80.805 6574 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.81 % Favored : 97.13 % Rotamer: Outliers : 1.46 % Allowed : 13.50 % Favored : 85.05 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.12), residues: 5392 helix: 1.84 (0.11), residues: 2512 sheet: -0.47 (0.22), residues: 524 loop : -0.57 (0.12), residues: 2356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 206 TYR 0.012 0.001 TYR K 99 PHE 0.014 0.001 PHE H 431 TRP 0.011 0.001 TRP A 335 HIS 0.005 0.001 HIS C 297 Details of bonding type rmsd covalent geometry : bond 0.00396 (43780) covalent geometry : angle 0.82861 (59080) hydrogen bonds : bond 0.03056 ( 1920) hydrogen bonds : angle 4.70156 ( 5591) metal coordination : bond 0.00977 ( 16) metal coordination : angle 7.25931 ( 36) Misc. bond : bond 0.04353 ( 32) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 4568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 358 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.9498 (mt-10) cc_final: 0.9130 (mt-10) REVERT: A 14 GLN cc_start: 0.9338 (OUTLIER) cc_final: 0.9104 (mp10) REVERT: A 36 ASP cc_start: 0.8236 (t0) cc_final: 0.7886 (t0) REVERT: A 50 LYS cc_start: 0.9025 (mmtt) cc_final: 0.8700 (mmmm) REVERT: A 78 MET cc_start: 0.9314 (mtp) cc_final: 0.8903 (mtp) REVERT: A 245 MET cc_start: 0.8273 (ttp) cc_final: 0.7958 (tpp) REVERT: A 391 MET cc_start: 0.7344 (mtt) cc_final: 0.7029 (mtp) REVERT: B 23 MET cc_start: 0.8853 (ttp) cc_final: 0.8647 (ppp) REVERT: B 131 MET cc_start: 0.8440 (ttm) cc_final: 0.8131 (tpp) REVERT: B 151 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8227 (p) REVERT: B 161 ASP cc_start: 0.8895 (t0) cc_final: 0.8404 (t0) REVERT: B 491 MET cc_start: 0.8831 (mtp) cc_final: 0.8627 (mtm) REVERT: B 503 GLU cc_start: 0.8925 (tt0) cc_final: 0.8690 (tp30) REVERT: C 262 ASP cc_start: 0.8412 (t0) cc_final: 0.7860 (t70) REVERT: D 57 MET cc_start: 0.9371 (ttm) cc_final: 0.9167 (ttp) REVERT: D 307 GLU cc_start: 0.8738 (tt0) cc_final: 0.8512 (tt0) REVERT: D 403 ASP cc_start: 0.9128 (t0) cc_final: 0.8837 (t0) REVERT: E 41 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8153 (pt0) REVERT: E 108 ASP cc_start: 0.9216 (t0) cc_final: 0.8965 (t70) REVERT: F 3 MET cc_start: 0.8643 (ttp) cc_final: 0.8383 (ttp) REVERT: F 61 MET cc_start: 0.8318 (mmm) cc_final: 0.7952 (mpm) REVERT: F 120 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8538 (mm) REVERT: F 159 MET cc_start: 0.8911 (mmm) cc_final: 0.8127 (mpp) REVERT: F 226 MET cc_start: 0.8422 (ttm) cc_final: 0.7982 (ttm) REVERT: G 86 CYS cc_start: 0.7433 (OUTLIER) cc_final: 0.7194 (p) REVERT: G 187 SER cc_start: 0.8045 (t) cc_final: 0.7773 (m) REVERT: G 208 MET cc_start: 0.8459 (tmm) cc_final: 0.8184 (tmm) REVERT: G 226 MET cc_start: 0.8167 (mtp) cc_final: 0.7739 (mtp) REVERT: G 270 MET cc_start: 0.8844 (mmt) cc_final: 0.8487 (mmm) REVERT: G 275 MET cc_start: 0.8583 (ttp) cc_final: 0.8339 (ptp) REVERT: H 8 GLU cc_start: 0.9513 (mt-10) cc_final: 0.9133 (mt-10) REVERT: H 14 GLN cc_start: 0.9322 (OUTLIER) cc_final: 0.9079 (mp10) REVERT: H 36 ASP cc_start: 0.8201 (t0) cc_final: 0.7832 (t0) REVERT: H 50 LYS cc_start: 0.9037 (mmtt) cc_final: 0.8685 (mmmm) REVERT: H 245 MET cc_start: 0.8366 (ttp) cc_final: 0.7983 (tpp) REVERT: H 368 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8700 (mp0) REVERT: H 391 MET cc_start: 0.7182 (mtt) cc_final: 0.6900 (mtp) REVERT: H 401 TYR cc_start: 0.8015 (p90) cc_final: 0.7768 (p90) REVERT: I 23 MET cc_start: 0.8840 (ttp) cc_final: 0.8625 (ppp) REVERT: I 131 MET cc_start: 0.8591 (tpp) cc_final: 0.7500 (tpp) REVERT: I 151 THR cc_start: 0.8542 (OUTLIER) cc_final: 0.8283 (p) REVERT: I 161 ASP cc_start: 0.8888 (t0) cc_final: 0.8428 (t0) REVERT: I 442 MET cc_start: 0.9219 (mtm) cc_final: 0.8897 (mtm) REVERT: I 503 GLU cc_start: 0.8930 (tt0) cc_final: 0.8689 (tp30) REVERT: J 262 ASP cc_start: 0.8420 (t0) cc_final: 0.7863 (t70) REVERT: K 307 GLU cc_start: 0.8748 (tt0) cc_final: 0.8522 (tt0) REVERT: K 403 ASP cc_start: 0.9132 (t0) cc_final: 0.8841 (t0) REVERT: L 41 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8130 (pt0) REVERT: L 92 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7845 (mtm110) REVERT: L 108 ASP cc_start: 0.9206 (t0) cc_final: 0.8974 (t70) REVERT: M 3 MET cc_start: 0.8695 (ttm) cc_final: 0.8457 (ttp) REVERT: M 61 MET cc_start: 0.8265 (mmm) cc_final: 0.7903 (mpm) REVERT: M 120 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8599 (mm) REVERT: M 152 CYS cc_start: 0.7911 (t) cc_final: 0.7237 (p) REVERT: M 159 MET cc_start: 0.9343 (mpp) cc_final: 0.9024 (mpp) REVERT: M 184 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.8077 (mt) REVERT: M 210 HIS cc_start: 0.8594 (t70) cc_final: 0.8181 (t70) REVERT: M 226 MET cc_start: 0.8402 (ttm) cc_final: 0.7970 (ttm) REVERT: M 262 MET cc_start: 0.8560 (tpp) cc_final: 0.8319 (tpp) REVERT: N 55 GLN cc_start: 0.6894 (tt0) cc_final: 0.6410 (tt0) REVERT: N 86 CYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7393 (p) REVERT: N 208 MET cc_start: 0.8529 (tmm) cc_final: 0.8253 (tmm) REVERT: N 226 MET cc_start: 0.8171 (mtp) cc_final: 0.7888 (mtp) outliers start: 67 outliers final: 45 residues processed: 411 average time/residue: 0.7801 time to fit residues: 390.7730 Evaluate side-chains 405 residues out of total 4568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 350 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 153 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 362 HIS Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 465 MET Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 152 CYS Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 286 THR Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 362 HIS Chi-restraints excluded: chain H residue 404 VAL Chi-restraints excluded: chain H residue 463 MET Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 153 CYS Chi-restraints excluded: chain I residue 320 MET Chi-restraints excluded: chain J residue 38 ASP Chi-restraints excluded: chain J residue 153 CYS Chi-restraints excluded: chain J residue 263 THR Chi-restraints excluded: chain K residue 362 HIS Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain L residue 92 ARG Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 184 ILE Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 86 CYS Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain N residue 286 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 391 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 525 optimal weight: 7.9990 chunk 292 optimal weight: 0.0060 chunk 512 optimal weight: 10.0000 chunk 310 optimal weight: 0.8980 chunk 314 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 452 optimal weight: 1.9990 chunk 420 optimal weight: 9.9990 chunk 294 optimal weight: 2.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 513 GLN ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.085648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.057707 restraints weight = 295836.828| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 4.32 r_work: 0.2707 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2714 r_free = 0.2714 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 227 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2714 r_free = 0.2714 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 227 | |-----------------------------------------------------------------------------| r_final: 0.2714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.248 43828 Z= 0.185 Angle : 0.848 59.196 59116 Z= 0.425 Chirality : 0.044 0.537 6350 Planarity : 0.005 0.215 7630 Dihedral : 4.521 80.805 6574 Min Nonbonded Distance : 1.525 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.81 % Favored : 97.13 % Rotamer: Outliers : 1.24 % Allowed : 13.80 % Favored : 84.96 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.12), residues: 5392 helix: 1.84 (0.11), residues: 2512 sheet: -0.47 (0.22), residues: 524 loop : -0.57 (0.12), residues: 2356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 206 TYR 0.012 0.001 TYR K 99 PHE 0.014 0.001 PHE H 431 TRP 0.011 0.001 TRP A 335 HIS 0.005 0.001 HIS C 297 Details of bonding type rmsd covalent geometry : bond 0.00396 (43780) covalent geometry : angle 0.82861 (59080) hydrogen bonds : bond 0.03056 ( 1920) hydrogen bonds : angle 4.70156 ( 5591) metal coordination : bond 0.00977 ( 16) metal coordination : angle 7.25931 ( 36) Misc. bond : bond 0.04353 ( 32) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 4568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 350 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.9488 (mt-10) cc_final: 0.9113 (mt-10) REVERT: A 14 GLN cc_start: 0.9365 (OUTLIER) cc_final: 0.9105 (mp10) REVERT: A 36 ASP cc_start: 0.8237 (t0) cc_final: 0.7884 (t0) REVERT: A 50 LYS cc_start: 0.9106 (mmtt) cc_final: 0.8773 (mmmm) REVERT: A 78 MET cc_start: 0.9419 (mtp) cc_final: 0.9068 (mtp) REVERT: A 245 MET cc_start: 0.8431 (ttp) cc_final: 0.8106 (tpp) REVERT: A 391 MET cc_start: 0.7494 (mtt) cc_final: 0.7162 (mtp) REVERT: B 23 MET cc_start: 0.8992 (ttp) cc_final: 0.8776 (ppp) REVERT: B 131 MET cc_start: 0.8554 (ttm) cc_final: 0.8240 (tpp) REVERT: B 151 THR cc_start: 0.8659 (OUTLIER) cc_final: 0.8387 (p) REVERT: B 161 ASP cc_start: 0.8858 (t0) cc_final: 0.8348 (t0) REVERT: B 503 GLU cc_start: 0.9134 (tt0) cc_final: 0.8891 (tp30) REVERT: C 262 ASP cc_start: 0.8486 (t0) cc_final: 0.8041 (t70) REVERT: D 307 GLU cc_start: 0.8774 (tt0) cc_final: 0.8559 (tt0) REVERT: D 403 ASP cc_start: 0.9112 (t0) cc_final: 0.8800 (t0) REVERT: E 41 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8283 (pt0) REVERT: E 108 ASP cc_start: 0.9275 (t0) cc_final: 0.9056 (t70) REVERT: F 3 MET cc_start: 0.8699 (ttp) cc_final: 0.8459 (ttp) REVERT: F 61 MET cc_start: 0.8459 (mmm) cc_final: 0.8101 (mpm) REVERT: F 120 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8624 (mm) REVERT: F 159 MET cc_start: 0.8956 (mmm) cc_final: 0.8155 (mpp) REVERT: F 226 MET cc_start: 0.8575 (ttm) cc_final: 0.8129 (ttm) REVERT: G 86 CYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7428 (p) REVERT: G 187 SER cc_start: 0.8148 (t) cc_final: 0.7868 (m) REVERT: G 208 MET cc_start: 0.8567 (tmm) cc_final: 0.8299 (tmm) REVERT: G 226 MET cc_start: 0.8263 (mtp) cc_final: 0.7845 (mtp) REVERT: G 270 MET cc_start: 0.8887 (mmt) cc_final: 0.8530 (mmm) REVERT: H 8 GLU cc_start: 0.9500 (mt-10) cc_final: 0.9123 (mt-10) REVERT: H 14 GLN cc_start: 0.9351 (OUTLIER) cc_final: 0.9077 (mp10) REVERT: H 36 ASP cc_start: 0.8192 (t0) cc_final: 0.7827 (t0) REVERT: H 50 LYS cc_start: 0.9123 (mmtt) cc_final: 0.8763 (mmmm) REVERT: H 245 MET cc_start: 0.8535 (ttp) cc_final: 0.8124 (tpp) REVERT: H 368 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8753 (mp0) REVERT: H 391 MET cc_start: 0.7326 (mtt) cc_final: 0.7028 (mtp) REVERT: H 401 TYR cc_start: 0.8214 (p90) cc_final: 0.7980 (p90) REVERT: I 23 MET cc_start: 0.8980 (ttp) cc_final: 0.8754 (ppp) REVERT: I 131 MET cc_start: 0.8698 (tpp) cc_final: 0.7617 (tpp) REVERT: I 151 THR cc_start: 0.8703 (OUTLIER) cc_final: 0.8440 (p) REVERT: I 161 ASP cc_start: 0.8854 (t0) cc_final: 0.8374 (t0) REVERT: I 442 MET cc_start: 0.9232 (mtm) cc_final: 0.9003 (mtm) REVERT: I 503 GLU cc_start: 0.9146 (tt0) cc_final: 0.8899 (tp30) REVERT: J 262 ASP cc_start: 0.8506 (t0) cc_final: 0.8049 (t70) REVERT: K 307 GLU cc_start: 0.8787 (tt0) cc_final: 0.8573 (tt0) REVERT: K 403 ASP cc_start: 0.9124 (t0) cc_final: 0.8814 (t0) REVERT: L 41 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8263 (pt0) REVERT: L 92 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.7947 (mtm110) REVERT: M 3 MET cc_start: 0.8714 (ttm) cc_final: 0.8512 (ttp) REVERT: M 61 MET cc_start: 0.8402 (mmm) cc_final: 0.8048 (mpm) REVERT: M 120 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8672 (mm) REVERT: M 152 CYS cc_start: 0.8068 (t) cc_final: 0.7430 (p) REVERT: M 159 MET cc_start: 0.9362 (mpp) cc_final: 0.9062 (mpp) REVERT: M 210 HIS cc_start: 0.8624 (t70) cc_final: 0.8248 (t70) REVERT: M 226 MET cc_start: 0.8560 (ttm) cc_final: 0.8124 (ttm) REVERT: M 262 MET cc_start: 0.8597 (tpp) cc_final: 0.8345 (tpp) REVERT: N 55 GLN cc_start: 0.7155 (tt0) cc_final: 0.6721 (tt0) REVERT: N 86 CYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7610 (p) REVERT: N 208 MET cc_start: 0.8664 (tmm) cc_final: 0.8395 (tmm) REVERT: N 226 MET cc_start: 0.8302 (mtp) cc_final: 0.8029 (mtp) outliers start: 57 outliers final: 45 residues processed: 397 average time/residue: 0.7956 time to fit residues: 384.3577 Evaluate side-chains 404 residues out of total 4568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 350 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 153 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 362 HIS Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 465 MET Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 152 CYS Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 286 THR Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 362 HIS Chi-restraints excluded: chain H residue 404 VAL Chi-restraints excluded: chain H residue 463 MET Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 153 CYS Chi-restraints excluded: chain I residue 320 MET Chi-restraints excluded: chain J residue 38 ASP Chi-restraints excluded: chain J residue 153 CYS Chi-restraints excluded: chain J residue 263 THR Chi-restraints excluded: chain K residue 362 HIS Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain L residue 92 ARG Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 86 CYS Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain N residue 286 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 200 optimal weight: 10.0000 chunk 268 optimal weight: 20.0000 chunk 321 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 473 optimal weight: 0.4980 chunk 338 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 508 optimal weight: 3.9990 chunk 451 optimal weight: 5.9990 chunk 441 optimal weight: 5.9990 chunk 400 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 513 GLN ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.085669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.057921 restraints weight = 252867.487| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 4.01 r_work: 0.2725 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 227 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 228 | |-----------------------------------------------------------------------------| r_final: 0.2727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.248 43828 Z= 0.185 Angle : 0.848 59.196 59116 Z= 0.425 Chirality : 0.044 0.537 6350 Planarity : 0.005 0.215 7630 Dihedral : 4.521 80.805 6574 Min Nonbonded Distance : 1.525 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.81 % Favored : 97.13 % Rotamer: Outliers : 1.22 % Allowed : 13.84 % Favored : 84.94 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.12), residues: 5392 helix: 1.84 (0.11), residues: 2512 sheet: -0.47 (0.22), residues: 524 loop : -0.57 (0.12), residues: 2356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 206 TYR 0.012 0.001 TYR K 99 PHE 0.014 0.001 PHE H 431 TRP 0.011 0.001 TRP A 335 HIS 0.005 0.001 HIS C 297 Details of bonding type rmsd covalent geometry : bond 0.00396 (43780) covalent geometry : angle 0.82861 (59080) hydrogen bonds : bond 0.03056 ( 1920) hydrogen bonds : angle 4.70156 ( 5591) metal coordination : bond 0.00977 ( 16) metal coordination : angle 7.25931 ( 36) Misc. bond : bond 0.04353 ( 32) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 4568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 350 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.9491 (mt-10) cc_final: 0.9116 (mt-10) REVERT: A 14 GLN cc_start: 0.9361 (OUTLIER) cc_final: 0.9104 (mp10) REVERT: A 36 ASP cc_start: 0.8238 (t0) cc_final: 0.7886 (t0) REVERT: A 50 LYS cc_start: 0.9104 (mmtt) cc_final: 0.8769 (mmmm) REVERT: A 78 MET cc_start: 0.9416 (mtp) cc_final: 0.9061 (mtp) REVERT: A 245 MET cc_start: 0.8429 (ttp) cc_final: 0.8108 (tpp) REVERT: A 391 MET cc_start: 0.7471 (mtt) cc_final: 0.7142 (mtp) REVERT: B 23 MET cc_start: 0.8987 (ttp) cc_final: 0.8772 (ppp) REVERT: B 131 MET cc_start: 0.8553 (ttm) cc_final: 0.8240 (tpp) REVERT: B 151 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8384 (p) REVERT: B 161 ASP cc_start: 0.8850 (t0) cc_final: 0.8340 (t0) REVERT: B 503 GLU cc_start: 0.9130 (tt0) cc_final: 0.8890 (tp30) REVERT: C 262 ASP cc_start: 0.8460 (t0) cc_final: 0.8017 (t70) REVERT: D 307 GLU cc_start: 0.8759 (tt0) cc_final: 0.8545 (tt0) REVERT: D 403 ASP cc_start: 0.9098 (t0) cc_final: 0.8782 (t0) REVERT: E 41 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8265 (pt0) REVERT: E 108 ASP cc_start: 0.9270 (t0) cc_final: 0.9049 (t70) REVERT: F 3 MET cc_start: 0.8688 (ttp) cc_final: 0.8449 (ttp) REVERT: F 61 MET cc_start: 0.8455 (mmm) cc_final: 0.8095 (mpm) REVERT: F 120 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8626 (mm) REVERT: F 159 MET cc_start: 0.8950 (mmm) cc_final: 0.8147 (mpp) REVERT: F 226 MET cc_start: 0.8557 (ttm) cc_final: 0.8107 (ttm) REVERT: G 86 CYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7416 (p) REVERT: G 187 SER cc_start: 0.8151 (t) cc_final: 0.7870 (m) REVERT: G 208 MET cc_start: 0.8559 (tmm) cc_final: 0.8291 (tmm) REVERT: G 226 MET cc_start: 0.8233 (mtp) cc_final: 0.7814 (mtp) REVERT: H 8 GLU cc_start: 0.9503 (mt-10) cc_final: 0.9126 (mt-10) REVERT: H 14 GLN cc_start: 0.9347 (OUTLIER) cc_final: 0.9075 (mp10) REVERT: H 36 ASP cc_start: 0.8194 (t0) cc_final: 0.7827 (t0) REVERT: H 50 LYS cc_start: 0.9119 (mmtt) cc_final: 0.8758 (mmmm) REVERT: H 245 MET cc_start: 0.8535 (ttp) cc_final: 0.8127 (tpp) REVERT: H 368 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8735 (mp0) REVERT: H 391 MET cc_start: 0.7295 (mtt) cc_final: 0.7002 (mtp) REVERT: H 401 TYR cc_start: 0.8200 (p90) cc_final: 0.7965 (p90) REVERT: I 23 MET cc_start: 0.8977 (ttp) cc_final: 0.8750 (ppp) REVERT: I 131 MET cc_start: 0.8694 (tpp) cc_final: 0.7611 (tpp) REVERT: I 151 THR cc_start: 0.8700 (OUTLIER) cc_final: 0.8438 (p) REVERT: I 161 ASP cc_start: 0.8847 (t0) cc_final: 0.8367 (t0) REVERT: I 442 MET cc_start: 0.9220 (mtm) cc_final: 0.8993 (mtm) REVERT: I 503 GLU cc_start: 0.9139 (tt0) cc_final: 0.8896 (tp30) REVERT: J 262 ASP cc_start: 0.8481 (t0) cc_final: 0.8023 (t70) REVERT: K 307 GLU cc_start: 0.8773 (tt0) cc_final: 0.8559 (tt0) REVERT: K 403 ASP cc_start: 0.9108 (t0) cc_final: 0.8796 (t0) REVERT: L 41 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8245 (pt0) REVERT: L 92 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.7928 (mtm110) REVERT: M 3 MET cc_start: 0.8706 (ttm) cc_final: 0.8506 (ttp) REVERT: M 61 MET cc_start: 0.8395 (mmm) cc_final: 0.8043 (mpm) REVERT: M 120 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8675 (mm) REVERT: M 152 CYS cc_start: 0.8036 (t) cc_final: 0.7408 (p) REVERT: M 159 MET cc_start: 0.9359 (mpp) cc_final: 0.9058 (mpp) REVERT: M 210 HIS cc_start: 0.8636 (t70) cc_final: 0.8238 (t70) REVERT: M 226 MET cc_start: 0.8544 (ttm) cc_final: 0.8107 (ttm) REVERT: M 262 MET cc_start: 0.8587 (tpp) cc_final: 0.8335 (tpp) REVERT: N 55 GLN cc_start: 0.7129 (tt0) cc_final: 0.6692 (tt0) REVERT: N 86 CYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7593 (p) REVERT: N 208 MET cc_start: 0.8653 (tmm) cc_final: 0.8383 (tmm) REVERT: N 226 MET cc_start: 0.8272 (mtp) cc_final: 0.7996 (mtp) outliers start: 56 outliers final: 45 residues processed: 396 average time/residue: 0.8077 time to fit residues: 388.7154 Evaluate side-chains 404 residues out of total 4568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 350 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 153 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 362 HIS Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 465 MET Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 152 CYS Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 286 THR Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 362 HIS Chi-restraints excluded: chain H residue 404 VAL Chi-restraints excluded: chain H residue 463 MET Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 153 CYS Chi-restraints excluded: chain I residue 320 MET Chi-restraints excluded: chain J residue 38 ASP Chi-restraints excluded: chain J residue 153 CYS Chi-restraints excluded: chain J residue 263 THR Chi-restraints excluded: chain K residue 362 HIS Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain L residue 92 ARG Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 86 CYS Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain N residue 286 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 109 optimal weight: 0.8980 chunk 326 optimal weight: 8.9990 chunk 175 optimal weight: 10.0000 chunk 477 optimal weight: 0.7980 chunk 181 optimal weight: 1.9990 chunk 272 optimal weight: 0.9990 chunk 345 optimal weight: 0.0370 chunk 423 optimal weight: 0.9980 chunk 392 optimal weight: 10.0000 chunk 487 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 513 GLN ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.085650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.057765 restraints weight = 279831.736| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 4.19 r_work: 0.2715 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 228 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 229 | |-----------------------------------------------------------------------------| r_final: 0.2719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.248 43828 Z= 0.185 Angle : 0.848 59.196 59116 Z= 0.425 Chirality : 0.044 0.537 6350 Planarity : 0.005 0.215 7630 Dihedral : 4.521 80.805 6574 Min Nonbonded Distance : 1.525 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.81 % Favored : 97.13 % Rotamer: Outliers : 1.22 % Allowed : 13.82 % Favored : 84.96 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.12), residues: 5392 helix: 1.84 (0.11), residues: 2512 sheet: -0.47 (0.22), residues: 524 loop : -0.57 (0.12), residues: 2356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 206 TYR 0.012 0.001 TYR K 99 PHE 0.014 0.001 PHE H 431 TRP 0.011 0.001 TRP A 335 HIS 0.005 0.001 HIS C 297 Details of bonding type rmsd covalent geometry : bond 0.00396 (43780) covalent geometry : angle 0.82861 (59080) hydrogen bonds : bond 0.03056 ( 1920) hydrogen bonds : angle 4.70156 ( 5591) metal coordination : bond 0.00977 ( 16) metal coordination : angle 7.25931 ( 36) Misc. bond : bond 0.04353 ( 32) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16702.68 seconds wall clock time: 284 minutes 55.16 seconds (17095.16 seconds total)