Starting phenix.real_space_refine on Tue Mar 12 23:40:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tug_41623/03_2024/8tug_41623_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tug_41623/03_2024/8tug_41623.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tug_41623/03_2024/8tug_41623_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tug_41623/03_2024/8tug_41623_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tug_41623/03_2024/8tug_41623_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tug_41623/03_2024/8tug_41623.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tug_41623/03_2024/8tug_41623.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tug_41623/03_2024/8tug_41623_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tug_41623/03_2024/8tug_41623_trim_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.138 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: 8 Type Number sf(0) Gaussians Zn 8 6.06 5 P 104 5.49 5 Mg 1 5.21 5 S 179 5.16 5 C 21331 2.51 5 N 6051 2.21 5 O 6762 1.98 5 H 31001 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 826": "OD1" <-> "OD2" Residue "A ASP 992": "OD1" <-> "OD2" Residue "A ASP 1334": "OD1" <-> "OD2" Residue "A GLU 1403": "OE1" <-> "OE2" Residue "B PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 866": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1132": "OE1" <-> "OE2" Residue "D ASP 156": "OD1" <-> "OD2" Residue "F ASP 110": "OD1" <-> "OD2" Residue "G GLU 33": "OE1" <-> "OE2" Residue "G ASP 52": "OD1" <-> "OD2" Residue "H GLU 45": "OE1" <-> "OE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 61": "OD1" <-> "OD2" Residue "I ASP 94": "OD1" <-> "OD2" Residue "K ASP 22": "OD1" <-> "OD2" Residue "L TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 65437 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 21594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1367, 21594 Classifications: {'peptide': 1367} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1304} Chain breaks: 6 Chain: "B" Number of atoms: 16596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 16596 Classifications: {'peptide': 1041} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 45, 'TRANS': 995} Chain breaks: 10 Chain: "C" Number of atoms: 4146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 4146 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "D" Number of atoms: 2276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2276 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 139} Chain breaks: 1 Chain: "E" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3548 Classifications: {'peptide': 215} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1330 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 75} Chain: "G" Number of atoms: 2687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 2687 Classifications: {'peptide': 171} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 2090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2090 Classifications: {'peptide': 133} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 2 Chain: "I" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1862 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "J" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1075 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1674 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "L" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 751 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "M" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 2516 Classifications: {'peptide': 503} Incomplete info: {'truncation_to_alanine': 502} Link IDs: {'CIS': 1, 'TRANS': 501} Chain breaks: 3 Unresolved non-hydrogen bonds: 1005 Unresolved non-hydrogen angles: 1507 Unresolved non-hydrogen dihedrals: 503 Planarities with less than four sites: {'UNK:plan-1': 502} Unresolved non-hydrogen planarities: 502 Chain: "N" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 1496 Classifications: {'DNA': 47} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 46} Chain: "T" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 1457 Unusual residues: {'TTD': 1} Classifications: {'DNA': 45, 'undetermined': 1} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 43, None: 2} Not linked: pdbres=" DC T 17 " pdbres="TTD T 18 " Not linked: pdbres="TTD T 18 " pdbres=" DT T 19 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "R" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 330 Classifications: {'RNA': 10} Modifications used: {'3*END': 1, 'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} 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: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2450 SG CYS A 167 94.790 73.431 122.135 1.00166.92 S ATOM 946 SG CYS A 70 47.998 74.162 108.269 1.00139.29 S ATOM 1041 SG CYS A 77 48.058 73.172 104.501 1.00127.44 S ATOM 37197 SG CYS B1163 57.453 84.914 112.585 1.00116.38 S ATOM 37233 SG CYS B1166 60.172 82.484 111.252 1.00116.47 S ATOM 37483 SG CYS B1182 56.943 81.325 113.052 1.00127.47 S ATOM 37522 SG CYS B1185 59.934 82.923 114.868 1.00125.90 S ATOM 39497 SG CYS C 86 10.638 69.795 49.203 1.00131.15 S ATOM 39527 SG CYS C 88 12.070 66.889 51.205 1.00136.51 S ATOM 39581 SG CYS C 92 10.355 66.234 47.955 1.00125.27 S ATOM 39625 SG CYS C 95 13.819 68.051 48.077 1.00122.68 S ATOM 54292 SG CYS I 7 130.742 43.274 71.139 1.00216.83 S ATOM 54338 SG CYS I 10 128.804 41.443 73.460 1.00216.80 S ATOM 55348 SG CYS I 75 116.530 59.012 29.461 1.00195.27 S ATOM 55395 SG CYS I 78 117.205 55.370 27.991 1.00196.86 S ATOM 55819 SG CYS I 103 113.849 56.458 29.788 1.00188.38 S ATOM 55859 SG CYS I 106 117.151 55.711 31.447 1.00191.25 S ATOM 56243 SG CYS J 7 41.808 67.306 33.680 1.00 86.75 S ATOM 56284 SG CYS J 10 41.717 69.843 31.319 1.00 88.08 S ATOM 56840 SG CYS J 45 42.938 69.345 30.949 1.00 88.30 S ATOM 58988 SG CYS L 31 37.148 31.619 60.290 1.00149.63 S ATOM 59023 SG CYS L 34 37.061 30.667 58.813 1.00152.87 S ATOM 59282 SG CYS L 51 39.015 28.214 59.183 1.00152.08 S Time building chain proxies: 22.11, per 1000 atoms: 0.34 Number of scatterers: 65437 At special positions: 0 Unit cell: (154.28, 157.76, 169.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 8 29.99 S 179 16.00 P 104 15.00 Mg 1 11.99 O 6762 8.00 N 6051 7.00 C 21331 6.00 H 31001 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 45.22 Conformation dependent library (CDL) restraints added in 5.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " Number of angles added : 18 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8046 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 164 helices and 40 sheets defined 41.2% alpha, 14.5% beta 37 base pairs and 64 stacking pairs defined. Time for finding SS restraints: 27.67 Creating SS restraints... Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 93 through 103 removed outlier: 4.678A pdb=" N ALA A 97 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N CYS A 103 " --> pdb=" O LYS A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 131 through 144 removed outlier: 3.541A pdb=" N PHE A 135 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N THR A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 212 removed outlier: 3.510A pdb=" N LEU A 208 " --> pdb=" O THR A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 222 removed outlier: 3.536A pdb=" N THR A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 261 through 281 Processing helix chain 'A' and resid 286 through 304 removed outlier: 3.522A pdb=" N MET A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 385 through 394 Processing helix chain 'A' and resid 419 through 422 removed outlier: 3.566A pdb=" N GLY A 422 " --> pdb=" O LYS A 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 419 through 422' Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 475 through 478 No H-bonds generated for 'chain 'A' and resid 475 through 478' Processing helix chain 'A' and resid 495 through 503 Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 525 through 534 removed outlier: 3.552A pdb=" N ILE A 531 " --> pdb=" O LEU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 551 removed outlier: 3.817A pdb=" N ASN A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 581 removed outlier: 3.572A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 622 No H-bonds generated for 'chain 'A' and resid 619 through 622' Processing helix chain 'A' and resid 629 through 636 removed outlier: 3.989A pdb=" N ARG A 635 " --> pdb=" O HIS A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 660 removed outlier: 4.097A pdb=" N LYS A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 673 through 699 Processing helix chain 'A' and resid 710 through 736 Processing helix chain 'A' and resid 742 through 749 Processing helix chain 'A' and resid 755 through 762 Processing helix chain 'A' and resid 795 through 797 No H-bonds generated for 'chain 'A' and resid 795 through 797' Processing helix chain 'A' and resid 810 through 844 removed outlier: 3.683A pdb=" N GLY A 819 " --> pdb=" O PHE A 815 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLY A 835 " --> pdb=" O THR A 831 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA A 844 " --> pdb=" O ARG A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 870 No H-bonds generated for 'chain 'A' and resid 868 through 870' Processing helix chain 'A' and resid 875 through 877 No H-bonds generated for 'chain 'A' and resid 875 through 877' Processing helix chain 'A' and resid 890 through 897 Processing helix chain 'A' and resid 910 through 912 No H-bonds generated for 'chain 'A' and resid 910 through 912' Processing helix chain 'A' and resid 923 through 946 removed outlier: 3.638A pdb=" N LEU A 928 " --> pdb=" O LYS A 924 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU A 945 " --> pdb=" O LYS A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 970 Processing helix chain 'A' and resid 983 through 996 removed outlier: 3.620A pdb=" N GLU A 995 " --> pdb=" O LYS A 991 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN A 996 " --> pdb=" O ASP A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1014 Processing helix chain 'A' and resid 1016 through 1025 Processing helix chain 'A' and resid 1028 through 1032 Processing helix chain 'A' and resid 1039 through 1056 Processing helix chain 'A' and resid 1064 through 1077 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1099 through 1105 Processing helix chain 'A' and resid 1128 through 1138 Processing helix chain 'A' and resid 1143 through 1145 No H-bonds generated for 'chain 'A' and resid 1143 through 1145' Processing helix chain 'A' and resid 1199 through 1204 Processing helix chain 'A' and resid 1209 through 1219 Processing helix chain 'A' and resid 1258 through 1269 removed outlier: 3.617A pdb=" N LEU A1268 " --> pdb=" O GLU A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1318 removed outlier: 4.473A pdb=" N THR A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1338 removed outlier: 3.544A pdb=" N GLU A1337 " --> pdb=" O ILE A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1341 through 1358 removed outlier: 3.597A pdb=" N ASN A1354 " --> pdb=" O LYS A1350 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1376 Processing helix chain 'A' and resid 1396 through 1401 removed outlier: 4.066A pdb=" N SER A1401 " --> pdb=" O LEU A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1406 through 1414 Processing helix chain 'A' and resid 1424 through 1429 Processing helix chain 'A' and resid 1437 through 1439 No H-bonds generated for 'chain 'A' and resid 1437 through 1439' Processing helix chain 'A' and resid 1447 through 1452 Processing helix chain 'B' and resid 28 through 41 Processing helix chain 'B' and resid 45 through 56 removed outlier: 3.623A pdb=" N SER B 50 " --> pdb=" O GLN B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 64 Processing helix chain 'B' and resid 114 through 120 Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 282 through 288 Processing helix chain 'B' and resid 294 through 301 Processing helix chain 'B' and resid 308 through 323 Proline residue: B 316 - end of helix removed outlier: 4.779A pdb=" N VAL B 323 " --> pdb=" O GLU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 338 Processing helix chain 'B' and resid 349 through 358 removed outlier: 3.575A pdb=" N GLN B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 390 removed outlier: 3.939A pdb=" N GLU B 371 " --> pdb=" O GLU B 368 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N LYS B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE B 382 " --> pdb=" O GLY B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 403 No H-bonds generated for 'chain 'B' and resid 401 through 403' Processing helix chain 'B' and resid 409 through 434 removed outlier: 3.591A pdb=" N THR B 419 " --> pdb=" O GLN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 463 removed outlier: 3.839A pdb=" N THR B 452 " --> pdb=" O ILE B 448 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE B 453 " --> pdb=" O ASN B 449 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 460 " --> pdb=" O GLY B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 495 Processing helix chain 'B' and resid 516 through 518 No H-bonds generated for 'chain 'B' and resid 516 through 518' Processing helix chain 'B' and resid 530 through 532 No H-bonds generated for 'chain 'B' and resid 530 through 532' Processing helix chain 'B' and resid 552 through 560 removed outlier: 3.627A pdb=" N PHE B 557 " --> pdb=" O PRO B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 606 Processing helix chain 'B' and resid 655 through 670 Processing helix chain 'B' and resid 681 through 687 Processing helix chain 'B' and resid 695 through 700 removed outlier: 3.800A pdb=" N GLU B 699 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER B 700 " --> pdb=" O GLU B 696 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 695 through 700' Processing helix chain 'B' and resid 707 through 709 No H-bonds generated for 'chain 'B' and resid 707 through 709' Processing helix chain 'B' and resid 712 through 715 No H-bonds generated for 'chain 'B' and resid 712 through 715' Processing helix chain 'B' and resid 745 through 748 Processing helix chain 'B' and resid 759 through 761 No H-bonds generated for 'chain 'B' and resid 759 through 761' Processing helix chain 'B' and resid 764 through 775 removed outlier: 3.760A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 812 removed outlier: 3.629A pdb=" N GLU B 810 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 847 Processing helix chain 'B' and resid 996 through 998 No H-bonds generated for 'chain 'B' and resid 996 through 998' Processing helix chain 'B' and resid 1014 through 1020 Proline residue: B1018 - end of helix Processing helix chain 'B' and resid 1023 through 1038 Processing helix chain 'B' and resid 1052 through 1062 removed outlier: 3.659A pdb=" N HIS B1062 " --> pdb=" O LEU B1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 1099 through 1101 No H-bonds generated for 'chain 'B' and resid 1099 through 1101' Processing helix chain 'B' and resid 1132 through 1141 removed outlier: 3.612A pdb=" N MET B1138 " --> pdb=" O GLU B1134 " (cutoff:3.500A) Processing helix chain 'B' and resid 1144 through 1151 Processing helix chain 'B' and resid 1198 through 1209 Processing helix chain 'C' and resid 27 through 39 Processing helix chain 'C' and resid 60 through 69 removed outlier: 3.523A pdb=" N LEU C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 79 No H-bonds generated for 'chain 'C' and resid 77 through 79' Processing helix chain 'C' and resid 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 197 through 200 No H-bonds generated for 'chain 'C' and resid 197 through 200' Processing helix chain 'C' and resid 205 through 209 removed outlier: 3.969A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 266 Processing helix chain 'D' and resid 52 through 72 Processing helix chain 'D' and resid 119 through 133 Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 157 through 170 removed outlier: 4.025A pdb=" N ALA D 162 " --> pdb=" O GLU D 158 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL D 163 " --> pdb=" O THR D 159 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN D 165 " --> pdb=" O GLY D 161 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 182 Processing helix chain 'D' and resid 188 through 194 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 204 through 219 Processing helix chain 'E' and resid 7 through 26 Processing helix chain 'E' and resid 32 through 35 No H-bonds generated for 'chain 'E' and resid 32 through 35' Processing helix chain 'E' and resid 39 through 46 Processing helix chain 'E' and resid 56 through 58 No H-bonds generated for 'chain 'E' and resid 56 through 58' Processing helix chain 'E' and resid 66 through 71 Processing helix chain 'E' and resid 90 through 103 Processing helix chain 'E' and resid 118 through 124 Processing helix chain 'E' and resid 139 through 141 No H-bonds generated for 'chain 'E' and resid 139 through 141' Processing helix chain 'E' and resid 144 through 146 No H-bonds generated for 'chain 'E' and resid 144 through 146' Processing helix chain 'E' and resid 158 through 167 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'F' and resid 87 through 103 Processing helix chain 'F' and resid 117 through 126 Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 20 through 34 removed outlier: 4.476A pdb=" N LEU G 26 " --> pdb=" O LYS G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'I' and resid 117 through 121 Processing helix chain 'J' and resid 18 through 26 Processing helix chain 'J' and resid 32 through 39 Processing helix chain 'J' and resid 44 through 51 removed outlier: 3.852A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 60 No H-bonds generated for 'chain 'J' and resid 57 through 60' Processing helix chain 'K' and resid 40 through 52 removed outlier: 4.265A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 116 removed outlier: 4.062A pdb=" N ALA K 115 " --> pdb=" O LEU K 111 " (cutoff:3.500A) Processing helix chain 'M' and resid 233 through 248 Processing helix chain 'M' and resid 256 through 258 No H-bonds generated for 'chain 'M' and resid 256 through 258' Processing helix chain 'M' and resid 265 through 274 removed outlier: 4.383A pdb=" N UNK M 269 " --> pdb=" O UNK M 265 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N UNK M 270 " --> pdb=" O UNK M 266 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N UNK M 273 " --> pdb=" O UNK M 269 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N UNK M 274 " --> pdb=" O UNK M 270 " (cutoff:3.500A) Processing helix chain 'M' and resid 280 through 283 No H-bonds generated for 'chain 'M' and resid 280 through 283' Processing helix chain 'M' and resid 291 through 294 No H-bonds generated for 'chain 'M' and resid 291 through 294' Processing helix chain 'M' and resid 299 through 313 Processing helix chain 'M' and resid 329 through 339 removed outlier: 3.657A pdb=" N UNK M 333 " --> pdb=" O UNK M 329 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N UNK M 338 " --> pdb=" O UNK M 334 " (cutoff:3.500A) Processing helix chain 'M' and resid 355 through 368 Processing helix chain 'M' and resid 381 through 385 removed outlier: 3.627A pdb=" N UNK M 385 " --> pdb=" O UNK M 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 381 through 385' Processing helix chain 'M' and resid 448 through 454 Processing helix chain 'M' and resid 471 through 473 No H-bonds generated for 'chain 'M' and resid 471 through 473' Processing helix chain 'M' and resid 480 through 487 Processing helix chain 'M' and resid 505 through 515 removed outlier: 3.904A pdb=" N UNK M 510 " --> pdb=" O UNK M 506 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N UNK M 511 " --> pdb=" O UNK M 507 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N UNK M 513 " --> pdb=" O UNK M 509 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N UNK M 514 " --> pdb=" O UNK M 510 " (cutoff:3.500A) Processing helix chain 'M' and resid 523 through 529 removed outlier: 3.822A pdb=" N UNK M 528 " --> pdb=" O UNK M 524 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N UNK M 529 " --> pdb=" O UNK M 525 " (cutoff:3.500A) Processing helix chain 'M' and resid 531 through 537 Processing helix chain 'M' and resid 547 through 562 removed outlier: 3.606A pdb=" N UNK M 561 " --> pdb=" O UNK M 557 " (cutoff:3.500A) Processing helix chain 'M' and resid 591 through 601 Processing helix chain 'M' and resid 606 through 609 No H-bonds generated for 'chain 'M' and resid 606 through 609' Processing helix chain 'M' and resid 614 through 628 removed outlier: 3.569A pdb=" N UNK M 621 " --> pdb=" O UNK M 617 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N UNK M 627 " --> pdb=" O UNK M 623 " (cutoff:3.500A) Processing helix chain 'M' and resid 647 through 649 No H-bonds generated for 'chain 'M' and resid 647 through 649' Processing helix chain 'M' and resid 651 through 665 removed outlier: 3.545A pdb=" N UNK M 655 " --> pdb=" O UNK M 651 " (cutoff:3.500A) Processing helix chain 'M' and resid 677 through 688 Processing helix chain 'M' and resid 692 through 697 Processing helix chain 'M' and resid 708 through 719 removed outlier: 3.623A pdb=" N UNK M 716 " --> pdb=" O UNK M 712 " (cutoff:3.500A) Processing helix chain 'M' and resid 730 through 735 removed outlier: 3.689A pdb=" N UNK M 734 " --> pdb=" O UNK M 730 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N UNK M 735 " --> pdb=" O UNK M 731 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 730 through 735' Processing helix chain 'M' and resid 754 through 764 removed outlier: 4.762A pdb=" N UNK M 759 " --> pdb=" O UNK M 755 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N UNK M 760 " --> pdb=" O UNK M 756 " (cutoff:3.500A) Processing helix chain 'M' and resid 784 through 794 Processing sheet with id= A, first strand: chain 'A' and resid 151 through 153 Processing sheet with id= B, first strand: chain 'A' and resid 173 through 177 Processing sheet with id= C, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.700A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.153A pdb=" N PHE A 468 " --> pdb=" O SER A 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 363 through 367 removed outlier: 6.619A pdb=" N ARG A 459 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL A 366 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LYS A 461 " --> pdb=" O VAL A 366 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 375 through 379 Processing sheet with id= G, first strand: chain 'A' and resid 404 through 406 Processing sheet with id= H, first strand: chain 'A' and resid 587 through 590 Processing sheet with id= I, first strand: chain 'A' and resid 878 through 882 Processing sheet with id= J, first strand: chain 'A' and resid 1115 through 1119 Processing sheet with id= K, first strand: chain 'A' and resid 1147 through 1154 removed outlier: 6.833A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N SER A1150 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ARG A1194 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE A1152 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU A1192 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 68 through 71 removed outlier: 3.709A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 95 through 97 Processing sheet with id= N, first strand: chain 'B' and resid 203 through 205 Processing sheet with id= O, first strand: chain 'B' and resid 498 through 500 removed outlier: 6.035A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 224 through 227 Processing sheet with id= Q, first strand: chain 'B' and resid 255 through 258 removed outlier: 3.834A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 614 through 618 removed outlier: 6.533A pdb=" N ARG B 579 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ILE B 626 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE B 581 " --> pdb=" O ILE B 626 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 634 through 638 Processing sheet with id= T, first strand: chain 'B' and resid 793 through 796 removed outlier: 3.558A pdb=" N VAL B 968 " --> pdb=" O ARG B 857 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 1010 through 1012 Processing sheet with id= V, first strand: chain 'B' and resid 1157 through 1163 Processing sheet with id= W, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id= X, first strand: chain 'B' and resid 839 through 842 removed outlier: 7.503A pdb=" N MET B 841 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR B 993 " --> pdb=" O MET B 841 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 7 through 13 removed outlier: 6.823A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ALA C 13 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ASN C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 97 through 104 removed outlier: 5.916A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 111 through 114 Processing sheet with id= AB, first strand: chain 'E' and resid 60 through 62 removed outlier: 7.061A pdb=" N THR E 107 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N GLU E 81 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE E 109 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR E 131 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N PHE E 110 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLU E 133 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N TYR E 112 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N PHE E 135 " --> pdb=" O TYR E 112 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 152 through 156 removed outlier: 4.558A pdb=" N VAL E 195 " --> pdb=" O LEU E 156 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 133 through 137 Processing sheet with id= AE, first strand: chain 'G' and resid 2 through 13 removed outlier: 3.607A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'G' and resid 142 through 147 removed outlier: 3.594A pdb=" N GLU G 85 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'H' and resid 7 through 11 removed outlier: 6.559A pdb=" N TYR H 115 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N PHE H 104 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ALA H 113 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLU H 106 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LEU H 111 " --> pdb=" O GLU H 106 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'I' and resid 16 through 19 Processing sheet with id= AI, first strand: chain 'I' and resid 83 through 86 Processing sheet with id= AJ, first strand: chain 'K' and resid 19 through 23 Processing sheet with id= AK, first strand: chain 'L' and resid 29 through 31 Processing sheet with id= AL, first strand: chain 'M' and resid 318 through 320 removed outlier: 4.041A pdb=" N UNK M 318 " --> pdb=" O UNK M 493 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N UNK M 495 " --> pdb=" O UNK M 318 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N UNK M 468 " --> pdb=" O UNK M 494 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N UNK M 496 " --> pdb=" O UNK M 468 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'M' and resid 350 through 352 removed outlier: 6.265A pdb=" N UNK M 444 " --> pdb=" O UNK M 351 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N UNK M 375 " --> pdb=" O UNK M 445 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain 'M' and resid 582 through 587 removed outlier: 5.657A pdb=" N UNK M 775 " --> pdb=" O UNK M 583 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N UNK M 585 " --> pdb=" O UNK M 775 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N UNK M 777 " --> pdb=" O UNK M 585 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N UNK M 587 " --> pdb=" O UNK M 777 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N UNK M 779 " --> pdb=" O UNK M 587 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N UNK M 747 " --> pdb=" O UNK M 776 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N UNK M 778 " --> pdb=" O UNK M 747 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N UNK M 749 " --> pdb=" O UNK M 778 " (cutoff:3.500A) removed outlier: 11.929A pdb=" N UNK M 780 " --> pdb=" O UNK M 749 " (cutoff:3.500A) 1136 hydrogen bonds defined for protein. 3090 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 94 hydrogen bonds 188 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 64 stacking parallelities Total time for adding SS restraints: 24.15 Time building geometry restraints manager: 47.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 30951 1.03 - 1.23: 133 1.23 - 1.43: 14490 1.43 - 1.62: 20351 1.62 - 1.82: 286 Bond restraints: 66211 Sorted by residual: bond pdb=" C2 TTD T 18 " pdb=" N3 TTD T 18 " ideal model delta sigma weight residual 1.505 1.333 0.172 2.00e-02 2.50e+03 7.40e+01 bond pdb=" C2T TTD T 18 " pdb=" N3T TTD T 18 " ideal model delta sigma weight residual 1.496 1.330 0.166 2.00e-02 2.50e+03 6.89e+01 bond pdb=" C4T TTD T 18 " pdb=" N3T TTD T 18 " ideal model delta sigma weight residual 1.470 1.325 0.145 2.00e-02 2.50e+03 5.27e+01 bond pdb=" N1 TTD T 18 " pdb=" C2 TTD T 18 " ideal model delta sigma weight residual 1.475 1.332 0.143 2.00e-02 2.50e+03 5.10e+01 bond pdb=" C2' TTD T 18 " pdb=" C3R TTD T 18 " ideal model delta sigma weight residual 1.367 1.507 -0.140 2.00e-02 2.50e+03 4.87e+01 ... (remaining 66206 not shown) Histogram of bond angle deviations from ideal: 88.53 - 97.62: 4 97.62 - 106.72: 1563 106.72 - 115.81: 82697 115.81 - 124.91: 32331 124.91 - 134.00: 2249 Bond angle restraints: 118844 Sorted by residual: angle pdb=" CA GLN A 68 " pdb=" CB GLN A 68 " pdb=" CG GLN A 68 " ideal model delta sigma weight residual 114.10 124.87 -10.77 2.00e+00 2.50e-01 2.90e+01 angle pdb=" O4P TTD T 18 " pdb=" PB TTD T 18 " pdb=" O5P TTD T 18 " ideal model delta sigma weight residual 106.81 119.71 -12.90 3.00e+00 1.11e-01 1.85e+01 angle pdb=" CA PRO H 82 " pdb=" N PRO H 82 " pdb=" CD PRO H 82 " ideal model delta sigma weight residual 112.00 106.06 5.94 1.40e+00 5.10e-01 1.80e+01 angle pdb=" C1R TTD T 18 " pdb=" N1T TTD T 18 " pdb=" C2T TTD T 18 " ideal model delta sigma weight residual 120.03 108.72 11.31 3.00e+00 1.11e-01 1.42e+01 angle pdb=" OP1 TTD T 18 " pdb=" P TTD T 18 " pdb=" OP2 TTD T 18 " ideal model delta sigma weight residual 109.51 120.66 -11.15 3.00e+00 1.11e-01 1.38e+01 ... (remaining 118839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 29958 35.30 - 70.61: 968 70.61 - 105.91: 28 105.91 - 141.21: 4 141.21 - 176.51: 7 Dihedral angle restraints: 30965 sinusoidal: 16959 harmonic: 14006 Sorted by residual: dihedral pdb=" CA MET E 57 " pdb=" C MET E 57 " pdb=" N MET E 58 " pdb=" CA MET E 58 " ideal model delta harmonic sigma weight residual 180.00 152.29 27.71 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" C5R TTD T 18 " pdb=" O5R TTD T 18 " pdb=" PB TTD T 18 " pdb=" O3R TTD T 18 " ideal model delta sinusoidal sigma weight residual 110.90 -92.19 -156.91 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" C5R TTD T 18 " pdb=" O5R TTD T 18 " pdb=" PB TTD T 18 " pdb=" O5P TTD T 18 " ideal model delta sinusoidal sigma weight residual -0.75 153.59 -154.34 1 3.00e+01 1.11e-03 2.03e+01 ... (remaining 30962 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3840 0.033 - 0.067: 1109 0.067 - 0.100: 349 0.100 - 0.133: 211 0.133 - 0.167: 9 Chirality restraints: 5518 Sorted by residual: chirality pdb=" CB ILE A 30 " pdb=" CA ILE A 30 " pdb=" CG1 ILE A 30 " pdb=" CG2 ILE A 30 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 6.96e-01 chirality pdb=" C5 TTD T 18 " pdb=" C4 TTD T 18 " pdb=" C6 TTD T 18 " pdb=" C5T TTD T 18 " both_signs ideal model delta sigma weight residual False -2.75 -2.92 0.16 2.00e-01 2.50e+01 6.74e-01 chirality pdb=" CA ILE E 116 " pdb=" N ILE E 116 " pdb=" C ILE E 116 " pdb=" CB ILE E 116 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.16e-01 ... (remaining 5515 not shown) Planarity restraints: 9539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' TTD T 18 " 0.481 2.00e-02 2.50e+03 4.64e-01 4.30e+03 pdb=" O4' TTD T 18 " -0.601 2.00e-02 2.50e+03 pdb=" C2' TTD T 18 " 0.709 2.00e-02 2.50e+03 pdb=" C1' TTD T 18 " -0.342 2.00e-02 2.50e+03 pdb=" N1 TTD T 18 " 0.179 2.00e-02 2.50e+03 pdb=" C3R TTD T 18 " 0.379 2.00e-02 2.50e+03 pdb=" C4R TTD T 18 " -0.337 2.00e-02 2.50e+03 pdb=" O3R TTD T 18 " -0.467 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1R TTD T 18 " -0.622 2.00e-02 2.50e+03 2.73e-01 1.68e+03 pdb=" C2T TTD T 18 " 0.142 2.00e-02 2.50e+03 pdb=" C4T TTD T 18 " -0.067 2.00e-02 2.50e+03 pdb=" C5T TTD T 18 " 0.123 2.00e-02 2.50e+03 pdb=" C6T TTD T 18 " 0.226 2.00e-02 2.50e+03 pdb=" N1T TTD T 18 " 0.305 2.00e-02 2.50e+03 pdb=" N3T TTD T 18 " -0.038 2.00e-02 2.50e+03 pdb=" O2T TTD T 18 " 0.188 2.00e-02 2.50e+03 pdb=" O4T TTD T 18 " -0.255 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4' TTD T 18 " -0.303 2.00e-02 2.50e+03 2.71e-01 1.47e+03 pdb=" C3' TTD T 18 " 0.359 2.00e-02 2.50e+03 pdb=" O3' TTD T 18 " -0.058 2.00e-02 2.50e+03 pdb=" C1R TTD T 18 " -0.381 2.00e-02 2.50e+03 pdb=" C2R TTD T 18 " -0.089 2.00e-02 2.50e+03 pdb=" C5R TTD T 18 " 0.228 2.00e-02 2.50e+03 pdb=" N1T TTD T 18 " 0.375 2.00e-02 2.50e+03 pdb=" O4R TTD T 18 " -0.131 2.00e-02 2.50e+03 ... (remaining 9536 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 1393 2.08 - 2.71: 105411 2.71 - 3.34: 188999 3.34 - 3.97: 241138 3.97 - 4.60: 376995 Nonbonded interactions: 913936 Sorted by model distance: nonbonded pdb=" OE1 GLU C 215 " pdb=" H GLU C 215 " model vdw 1.454 1.850 nonbonded pdb=" OE1 GLU K 64 " pdb=" H GLU K 64 " model vdw 1.460 1.850 nonbonded pdb=" OE1 GLU J 32 " pdb=" H GLU J 32 " model vdw 1.469 1.850 nonbonded pdb=" O ARG D 72 " pdb="HH11 ARG D 72 " model vdw 1.477 1.850 nonbonded pdb=" OE1 GLU K 79 " pdb=" H GLU K 79 " model vdw 1.506 1.850 ... (remaining 913931 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.770 Extract box with map and model: 13.200 Check model and map are aligned: 0.760 Set scattering table: 0.490 Process input model: 202.670 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 223.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.172 35210 Z= 0.191 Angle : 0.575 12.904 48105 Z= 0.292 Chirality : 0.040 0.167 5518 Planarity : 0.009 0.464 5908 Dihedral : 15.415 168.505 13215 Min Nonbonded Distance : 1.638 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.31 % Favored : 96.64 % Rotamer: Outliers : 0.12 % Allowed : 2.58 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.14), residues: 3686 helix: 1.41 (0.15), residues: 1255 sheet: -0.56 (0.21), residues: 566 loop : 0.08 (0.15), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A1228 HIS 0.011 0.001 HIS A1124 PHE 0.029 0.001 PHE A 614 TYR 0.022 0.001 TYR H 102 ARG 0.010 0.000 ARG A1239 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 168 is missing expected H atoms. Skipping. Evaluate side-chains 218 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 214 time to evaluate : 4.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 236 HIS cc_start: 0.8360 (OUTLIER) cc_final: 0.7866 (p-80) REVERT: E 74 ASP cc_start: 0.9040 (p0) cc_final: 0.8534 (p0) outliers start: 4 outliers final: 3 residues processed: 216 average time/residue: 0.9222 time to fit residues: 326.9991 Evaluate side-chains 203 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 199 time to evaluate : 4.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain C residue 38 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 362 optimal weight: 3.9990 chunk 325 optimal weight: 20.0000 chunk 180 optimal weight: 3.9990 chunk 111 optimal weight: 20.0000 chunk 219 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 336 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 204 optimal weight: 2.9990 chunk 250 optimal weight: 6.9990 chunk 389 optimal weight: 50.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 ASN B 60 GLN B 975 GLN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.0802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 35210 Z= 0.441 Angle : 0.652 24.883 48105 Z= 0.331 Chirality : 0.041 0.316 5518 Planarity : 0.004 0.079 5908 Dihedral : 15.894 167.459 5767 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.07 % Favored : 94.87 % Rotamer: Outliers : 0.52 % Allowed : 3.01 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.14), residues: 3686 helix: 0.72 (0.14), residues: 1305 sheet: -0.65 (0.22), residues: 545 loop : -0.28 (0.15), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 79 HIS 0.008 0.001 HIS A 399 PHE 0.031 0.001 PHE A 614 TYR 0.017 0.001 TYR B 351 ARG 0.008 0.000 ARG A1239 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 168 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 200 time to evaluate : 4.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 75 MET cc_start: 0.9015 (mmm) cc_final: 0.8645 (tpt) outliers start: 17 outliers final: 14 residues processed: 209 average time/residue: 0.8246 time to fit residues: 278.7357 Evaluate side-chains 208 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 194 time to evaluate : 4.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1359 ASP Chi-restraints excluded: chain A residue 1389 PHE Chi-restraints excluded: chain A residue 1403 GLU Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 860 MET Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain K residue 71 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 216 optimal weight: 4.9990 chunk 120 optimal weight: 0.2980 chunk 324 optimal weight: 9.9990 chunk 265 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 390 optimal weight: 50.0000 chunk 421 optimal weight: 20.0000 chunk 347 optimal weight: 7.9990 chunk 387 optimal weight: 50.0000 chunk 133 optimal weight: 3.9990 chunk 313 optimal weight: 10.0000 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 GLN B 121 ASN H 35 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 35210 Z= 0.329 Angle : 0.590 23.167 48105 Z= 0.299 Chirality : 0.040 0.254 5518 Planarity : 0.004 0.055 5908 Dihedral : 15.960 171.345 5767 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.18 % Favored : 94.76 % Rotamer: Outliers : 0.55 % Allowed : 3.64 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.14), residues: 3686 helix: 0.79 (0.14), residues: 1299 sheet: -0.61 (0.23), residues: 503 loop : -0.33 (0.15), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 466 HIS 0.010 0.001 HIS A 399 PHE 0.034 0.001 PHE A 614 TYR 0.015 0.001 TYR B 351 ARG 0.007 0.000 ARG B 601 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 168 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 194 time to evaluate : 4.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 ASP cc_start: 0.9262 (m-30) cc_final: 0.9019 (t0) REVERT: B 1208 MET cc_start: 0.8868 (mmm) cc_final: 0.8645 (mtt) REVERT: C 75 MET cc_start: 0.8992 (mmm) cc_final: 0.8624 (tpt) outliers start: 18 outliers final: 14 residues processed: 206 average time/residue: 0.9305 time to fit residues: 312.8044 Evaluate side-chains 205 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 191 time to evaluate : 3.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1359 ASP Chi-restraints excluded: chain A residue 1389 PHE Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain K residue 71 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 385 optimal weight: 50.0000 chunk 293 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 186 optimal weight: 4.9990 chunk 262 optimal weight: 3.9990 chunk 391 optimal weight: 70.0000 chunk 414 optimal weight: 80.0000 chunk 204 optimal weight: 0.9980 chunk 371 optimal weight: 50.0000 chunk 111 optimal weight: 20.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN E 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 35210 Z= 0.339 Angle : 0.591 21.537 48105 Z= 0.298 Chirality : 0.040 0.307 5518 Planarity : 0.004 0.077 5908 Dihedral : 16.040 177.391 5765 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.53 % Favored : 94.38 % Rotamer: Outliers : 0.52 % Allowed : 4.56 % Favored : 94.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.14), residues: 3686 helix: 0.79 (0.15), residues: 1295 sheet: -0.75 (0.22), residues: 524 loop : -0.37 (0.15), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 466 HIS 0.009 0.001 HIS A 399 PHE 0.032 0.001 PHE A 614 TYR 0.016 0.001 TYR B 351 ARG 0.004 0.000 ARG A1239 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 168 is missing expected H atoms. Skipping. Evaluate side-chains 214 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 197 time to evaluate : 3.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 75 MET cc_start: 0.8987 (mmm) cc_final: 0.8619 (tpt) outliers start: 17 outliers final: 15 residues processed: 209 average time/residue: 0.8336 time to fit residues: 282.8578 Evaluate side-chains 206 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 191 time to evaluate : 4.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1359 ASP Chi-restraints excluded: chain A residue 1389 PHE Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 1101 ASP Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain K residue 71 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 345 optimal weight: 0.4980 chunk 235 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 308 optimal weight: 3.9990 chunk 171 optimal weight: 6.9990 chunk 353 optimal weight: 0.8980 chunk 286 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 211 optimal weight: 0.8980 chunk 372 optimal weight: 50.0000 chunk 104 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 35210 Z= 0.151 Angle : 0.539 20.056 48105 Z= 0.267 Chirality : 0.039 0.297 5518 Planarity : 0.003 0.046 5908 Dihedral : 15.967 167.430 5763 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.02 % Favored : 95.93 % Rotamer: Outliers : 0.39 % Allowed : 5.04 % Favored : 94.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.14), residues: 3686 helix: 1.14 (0.15), residues: 1299 sheet: -0.67 (0.22), residues: 515 loop : -0.18 (0.15), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 466 HIS 0.007 0.001 HIS A 399 PHE 0.032 0.001 PHE A 614 TYR 0.015 0.001 TYR B 351 ARG 0.005 0.000 ARG A 821 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 168 is missing expected H atoms. Skipping. Evaluate side-chains 215 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 202 time to evaluate : 4.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 341 MET cc_start: 0.9171 (mmm) cc_final: 0.8916 (mmm) REVERT: B 381 MET cc_start: 0.8525 (tmm) cc_final: 0.8114 (tmm) REVERT: C 75 MET cc_start: 0.8993 (mmm) cc_final: 0.8621 (tpt) outliers start: 13 outliers final: 11 residues processed: 211 average time/residue: 0.8756 time to fit residues: 302.3025 Evaluate side-chains 205 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 194 time to evaluate : 3.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1359 ASP Chi-restraints excluded: chain A residue 1389 PHE Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain K residue 71 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 139 optimal weight: 2.9990 chunk 373 optimal weight: 50.0000 chunk 81 optimal weight: 3.9990 chunk 243 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 415 optimal weight: 60.0000 chunk 344 optimal weight: 10.0000 chunk 192 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 217 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1124 HIS B 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 35210 Z= 0.217 Angle : 0.542 19.412 48105 Z= 0.270 Chirality : 0.039 0.313 5518 Planarity : 0.003 0.045 5908 Dihedral : 15.895 163.056 5761 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.69 % Favored : 95.25 % Rotamer: Outliers : 0.43 % Allowed : 5.44 % Favored : 94.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.14), residues: 3686 helix: 1.20 (0.15), residues: 1301 sheet: -0.69 (0.22), residues: 531 loop : -0.20 (0.15), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 656 HIS 0.007 0.001 HIS A 399 PHE 0.028 0.001 PHE A 614 TYR 0.015 0.001 TYR B 351 ARG 0.004 0.000 ARG A 821 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 168 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 197 time to evaluate : 4.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8214 (mmm) cc_final: 0.7951 (mmm) REVERT: A 341 MET cc_start: 0.9135 (mmm) cc_final: 0.8927 (mmm) REVERT: B 381 MET cc_start: 0.8617 (tmm) cc_final: 0.8194 (tmm) REVERT: C 75 MET cc_start: 0.9004 (mmm) cc_final: 0.8625 (tpt) outliers start: 14 outliers final: 14 residues processed: 206 average time/residue: 0.8341 time to fit residues: 279.6497 Evaluate side-chains 208 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 194 time to evaluate : 4.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1359 ASP Chi-restraints excluded: chain A residue 1389 PHE Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 1101 ASP Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain K residue 71 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 400 optimal weight: 60.0000 chunk 46 optimal weight: 2.9990 chunk 236 optimal weight: 0.0870 chunk 303 optimal weight: 2.9990 chunk 234 optimal weight: 0.9980 chunk 349 optimal weight: 5.9990 chunk 231 optimal weight: 2.9990 chunk 413 optimal weight: 70.0000 chunk 258 optimal weight: 0.0770 chunk 252 optimal weight: 6.9990 chunk 190 optimal weight: 2.9990 overall best weight: 1.4320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1124 HIS B 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 35210 Z= 0.204 Angle : 0.537 18.342 48105 Z= 0.268 Chirality : 0.039 0.317 5518 Planarity : 0.003 0.045 5908 Dihedral : 15.857 164.553 5761 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.67 % Favored : 95.28 % Rotamer: Outliers : 0.52 % Allowed : 5.59 % Favored : 93.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.14), residues: 3686 helix: 1.27 (0.15), residues: 1303 sheet: -0.74 (0.21), residues: 542 loop : -0.17 (0.15), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 656 HIS 0.013 0.001 HIS A1124 PHE 0.030 0.001 PHE A 252 TYR 0.015 0.001 TYR B 351 ARG 0.005 0.000 ARG A 821 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 168 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 195 time to evaluate : 4.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8175 (mmm) cc_final: 0.7941 (mmm) REVERT: B 381 MET cc_start: 0.8652 (tmm) cc_final: 0.8207 (tmm) REVERT: B 1208 MET cc_start: 0.8664 (mmm) cc_final: 0.8457 (mtt) REVERT: C 75 MET cc_start: 0.9010 (mmm) cc_final: 0.8629 (tpt) outliers start: 17 outliers final: 16 residues processed: 208 average time/residue: 0.8321 time to fit residues: 280.1991 Evaluate side-chains 208 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 192 time to evaluate : 3.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1359 ASP Chi-restraints excluded: chain A residue 1389 PHE Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 1101 ASP Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain K residue 71 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 255 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 246 optimal weight: 1.9990 chunk 124 optimal weight: 0.4980 chunk 81 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 262 optimal weight: 3.9990 chunk 281 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 325 optimal weight: 2.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1124 HIS B 60 GLN B 449 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 35210 Z= 0.273 Angle : 0.553 17.936 48105 Z= 0.278 Chirality : 0.039 0.322 5518 Planarity : 0.003 0.044 5908 Dihedral : 15.843 170.325 5761 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.15 % Favored : 94.79 % Rotamer: Outliers : 0.58 % Allowed : 5.77 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.14), residues: 3686 helix: 1.23 (0.15), residues: 1303 sheet: -0.73 (0.21), residues: 535 loop : -0.23 (0.15), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 466 HIS 0.022 0.001 HIS A1124 PHE 0.027 0.001 PHE A 614 TYR 0.016 0.001 TYR B 351 ARG 0.002 0.000 ARG A 821 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 168 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 191 time to evaluate : 3.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8178 (mmm) cc_final: 0.7942 (mmm) REVERT: B 381 MET cc_start: 0.8686 (tmm) cc_final: 0.8241 (tmm) REVERT: C 75 MET cc_start: 0.9009 (mmm) cc_final: 0.8645 (tpt) outliers start: 19 outliers final: 16 residues processed: 205 average time/residue: 0.8675 time to fit residues: 291.0576 Evaluate side-chains 205 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 189 time to evaluate : 3.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1359 ASP Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 1101 ASP Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain K residue 71 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 376 optimal weight: 40.0000 chunk 396 optimal weight: 50.0000 chunk 361 optimal weight: 1.9990 chunk 385 optimal weight: 50.0000 chunk 231 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 302 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 348 optimal weight: 2.9990 chunk 364 optimal weight: 2.9990 chunk 383 optimal weight: 60.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1124 HIS A1270 ASN D 40 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 35210 Z= 0.328 Angle : 0.571 17.747 48105 Z= 0.289 Chirality : 0.040 0.327 5518 Planarity : 0.004 0.042 5908 Dihedral : 15.846 178.639 5761 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.64 % Favored : 94.28 % Rotamer: Outliers : 0.52 % Allowed : 6.07 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.14), residues: 3686 helix: 1.16 (0.15), residues: 1302 sheet: -0.75 (0.21), residues: 542 loop : -0.29 (0.15), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 466 HIS 0.010 0.001 HIS A 399 PHE 0.027 0.001 PHE A 614 TYR 0.015 0.001 TYR B 351 ARG 0.003 0.000 ARG A 821 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 168 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 188 time to evaluate : 4.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 381 MET cc_start: 0.8707 (tmm) cc_final: 0.8261 (tmm) REVERT: C 75 MET cc_start: 0.9006 (mmm) cc_final: 0.8636 (tpt) outliers start: 17 outliers final: 14 residues processed: 200 average time/residue: 0.8416 time to fit residues: 273.8273 Evaluate side-chains 201 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 187 time to evaluate : 4.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1359 ASP Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 1101 ASP Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain K residue 71 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 253 optimal weight: 0.9990 chunk 407 optimal weight: 50.0000 chunk 248 optimal weight: 5.9990 chunk 193 optimal weight: 7.9990 chunk 283 optimal weight: 5.9990 chunk 427 optimal weight: 10.0000 chunk 393 optimal weight: 50.0000 chunk 340 optimal weight: 0.0060 chunk 35 optimal weight: 1.9990 chunk 262 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 35210 Z= 0.201 Angle : 0.541 17.414 48105 Z= 0.269 Chirality : 0.039 0.321 5518 Planarity : 0.003 0.044 5908 Dihedral : 15.784 169.106 5761 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.80 % Favored : 95.14 % Rotamer: Outliers : 0.46 % Allowed : 6.13 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.14), residues: 3686 helix: 1.31 (0.15), residues: 1302 sheet: -0.73 (0.22), residues: 532 loop : -0.22 (0.15), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 466 HIS 0.007 0.001 HIS A 399 PHE 0.029 0.001 PHE A 614 TYR 0.016 0.001 TYR B 351 ARG 0.004 0.000 ARG A 821 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 168 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 195 time to evaluate : 4.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8244 (mmm) cc_final: 0.7864 (mmm) REVERT: B 381 MET cc_start: 0.8690 (tmm) cc_final: 0.8240 (tmm) REVERT: C 75 MET cc_start: 0.8994 (mmm) cc_final: 0.8634 (tpt) outliers start: 15 outliers final: 15 residues processed: 207 average time/residue: 0.8611 time to fit residues: 289.4351 Evaluate side-chains 206 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 191 time to evaluate : 3.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1359 ASP Chi-restraints excluded: chain A residue 1389 PHE Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 1101 ASP Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain K residue 71 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 270 optimal weight: 20.0000 chunk 362 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 313 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 340 optimal weight: 0.9980 chunk 142 optimal weight: 0.6980 chunk 350 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.094402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.060819 restraints weight = 320188.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.063204 restraints weight = 128352.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.064574 restraints weight = 80074.780| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 35210 Z= 0.243 Angle : 0.548 17.403 48105 Z= 0.274 Chirality : 0.039 0.307 5518 Planarity : 0.003 0.059 5908 Dihedral : 15.707 160.296 5761 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.29 % Favored : 94.66 % Rotamer: Outliers : 0.46 % Allowed : 6.16 % Favored : 93.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.14), residues: 3686 helix: 1.32 (0.15), residues: 1303 sheet: -0.78 (0.21), residues: 541 loop : -0.25 (0.15), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 466 HIS 0.008 0.001 HIS A 399 PHE 0.028 0.001 PHE A 614 TYR 0.016 0.001 TYR B 351 ARG 0.007 0.000 ARG F 119 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8914.94 seconds wall clock time: 157 minutes 3.57 seconds (9423.57 seconds total)