Starting phenix.real_space_refine on Thu Feb 15 04:27:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvp_41647/02_2024/8tvp_41647_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvp_41647/02_2024/8tvp_41647.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvp_41647/02_2024/8tvp_41647_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvp_41647/02_2024/8tvp_41647_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvp_41647/02_2024/8tvp_41647_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvp_41647/02_2024/8tvp_41647.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvp_41647/02_2024/8tvp_41647.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvp_41647/02_2024/8tvp_41647_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvp_41647/02_2024/8tvp_41647_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.127 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 21124 2.51 5 N 5982 2.21 5 O 6693 1.98 5 H 29847 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 826": "OD1" <-> "OD2" Residue "A TYR 852": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 156": "OD1" <-> "OD2" Residue "E TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 63938 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: 5 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: 2686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 2686 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: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1861 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "J" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1074 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1673 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "L" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 752 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "M" Number of atoms: 2171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 2171 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 433} Link IDs: {'CIS': 1, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 867 Unresolved non-hydrogen angles: 1300 Unresolved non-hydrogen dihedrals: 434 Planarities with less than four sites: {'UNK:plan-1': 433} Unresolved non-hydrogen planarities: 433 Chain: "N" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 965 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Chain: "R" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 220 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 947 Unusual residues: {'TTD': 1} Classifications: {'DNA': 45, 'undetermined': 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: "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 2449 SG CYS A 167 79.322 97.554 27.615 1.00193.43 S ATOM 904 SG CYS A 67 106.978 75.574 61.392 1.00126.92 S ATOM 945 SG CYS A 70 109.746 77.857 59.663 1.00132.35 S ATOM 1040 SG CYS A 77 108.404 78.511 63.102 1.00112.65 S ATOM 37197 SG CYS B1163 107.945 92.021 54.919 1.00 96.52 S ATOM 37233 SG CYS B1166 104.360 90.928 53.697 1.00 92.99 S ATOM 37483 SG CYS B1182 107.314 88.625 53.439 1.00116.60 S ATOM 37522 SG CYS B1185 106.863 91.732 51.218 1.00115.70 S ATOM 39497 SG CYS C 86 107.698 55.884 126.645 1.00104.31 S ATOM 39527 SG CYS C 88 106.794 53.987 123.505 1.00110.66 S ATOM 39581 SG CYS C 92 106.358 52.431 126.949 1.00100.07 S ATOM 39625 SG CYS C 95 104.043 55.286 125.570 1.00 96.69 S ATOM 54291 SG CYS I 7 15.048 83.286 47.821 1.00277.53 S ATOM 54337 SG CYS I 10 17.216 80.859 46.280 1.00274.08 S ATOM 55393 SG CYS I 78 8.000 86.809 93.164 1.00278.65 S ATOM 55817 SG CYS I 103 12.124 85.705 94.713 1.00256.99 S ATOM 55857 SG CYS I 106 9.835 86.459 91.536 1.00263.77 S ATOM 56241 SG CYS J 7 74.279 65.845 125.765 1.00 59.67 S ATOM 56282 SG CYS J 10 75.251 67.772 129.178 1.00 65.82 S ATOM 56838 SG CYS J 45 72.317 68.543 127.780 1.00 59.05 S ATOM 56848 SG CYS J 46 72.654 64.954 129.033 1.00 59.93 S ATOM 58984 SG CYS L 31 79.332 32.191 94.755 1.00145.36 S ATOM 59279 SG CYS L 51 76.969 31.456 94.571 1.00145.94 S Time building chain proxies: 22.07, per 1000 atoms: 0.35 Number of scatterers: 63938 At special positions: 0 Unit cell: (162.4, 165.88, 167.04, 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 6693 8.00 N 5982 7.00 C 21124 6.00 H 29847 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: 42.87 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 77 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " 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 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " Number of angles added : 21 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: 7908 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 155 helices and 38 sheets defined 39.5% alpha, 13.0% beta 36 base pairs and 81 stacking pairs defined. Time for finding SS restraints: 30.43 Creating SS restraints... Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 93 through 103 removed outlier: 4.531A pdb=" N ALA A 97 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS A 103 " --> pdb=" O LYS A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 127 Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 216 through 222 removed outlier: 3.525A pdb=" N THR A 220 " --> pdb=" O VAL A 216 " (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 removed outlier: 3.543A pdb=" N ILE A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 304 removed outlier: 3.720A pdb=" N GLU A 291 " --> pdb=" O HIS A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 328 No H-bonds generated for 'chain 'A' and resid 326 through 328' Processing helix chain 'A' and resid 368 through 371 No H-bonds generated for 'chain 'A' and resid 368 through 371' Processing helix chain 'A' and resid 385 through 394 Processing helix chain 'A' and resid 420 through 422 No H-bonds generated for 'chain 'A' and resid 420 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 473 through 478 removed outlier: 3.689A pdb=" N SER A 476 " --> pdb=" O SER A 473 " (cutoff:3.500A) Proline residue: A 477 - end of helix No H-bonds generated for 'chain 'A' and resid 473 through 478' Processing helix chain 'A' and resid 495 through 504 removed outlier: 3.813A pdb=" N ALA A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 525 through 534 removed outlier: 4.139A pdb=" N GLY A 530 " --> pdb=" O THR A 527 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 531 " --> pdb=" O LEU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 552 removed outlier: 3.542A pdb=" N ASN A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 580 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 637 removed outlier: 3.766A pdb=" N ARG A 635 " --> pdb=" O HIS A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 659 removed outlier: 3.781A pdb=" N LYS A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 669 Processing helix chain 'A' and resid 673 through 698 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 794 through 797 No H-bonds generated for 'chain 'A' and resid 794 through 797' Processing helix chain 'A' and resid 810 through 831 removed outlier: 3.623A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 844 removed outlier: 3.643A pdb=" N ILE A 837 " --> pdb=" O GLU A 833 " (cutoff:3.500A) removed outlier: 3.731A 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 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 Processing helix chain 'A' and resid 960 through 970 Processing helix chain 'A' and resid 983 through 996 removed outlier: 3.723A 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 1205 Processing helix chain 'A' and resid 1209 through 1219 Processing helix chain 'A' and resid 1258 through 1268 removed outlier: 3.760A pdb=" N LEU A1268 " --> pdb=" O GLU A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1316 No H-bonds generated for 'chain 'A' and resid 1313 through 1316' Processing helix chain 'A' and resid 1324 through 1326 No H-bonds generated for 'chain 'A' and resid 1324 through 1326' Processing helix chain 'A' and resid 1332 through 1339 Processing helix chain 'A' and resid 1341 through 1359 removed outlier: 3.565A pdb=" N ALA A1346 " --> pdb=" O GLU A1342 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASP A1359 " --> pdb=" O VAL A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1374 Processing helix chain 'A' and resid 1396 through 1400 Processing helix chain 'A' and resid 1406 through 1414 removed outlier: 4.031A pdb=" N GLU A1411 " --> pdb=" O GLU A1407 " (cutoff:3.500A) 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 27 through 41 removed outlier: 3.500A pdb=" N TRP B 31 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 64 removed outlier: 3.650A pdb=" N SER B 50 " --> pdb=" O GLN B 46 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 119 removed outlier: 3.529A pdb=" N LEU B 119 " --> pdb=" O GLN B 115 " (cutoff:3.500A) 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: 4.799A 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 Processing helix chain 'B' and resid 368 through 390 removed outlier: 3.665A pdb=" N GLU B 371 " --> pdb=" O GLU B 368 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LYS B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET B 381 " --> pdb=" O LEU B 378 " (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 Processing helix chain 'B' and resid 443 through 463 removed outlier: 3.574A pdb=" N THR B 452 " --> pdb=" O ILE B 448 " (cutoff:3.500A) removed outlier: 3.516A 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 561 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 686 Processing helix chain 'B' and resid 695 through 700 removed outlier: 3.918A pdb=" N GLU B 699 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 4.455A 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 712 through 715 No H-bonds generated for 'chain 'B' and resid 712 through 715' Processing helix chain 'B' and resid 745 through 747 No H-bonds generated for 'chain 'B' and resid 745 through 747' Processing helix chain 'B' and resid 753 through 755 No H-bonds generated for 'chain 'B' and resid 753 through 755' Processing helix chain 'B' and resid 764 through 775 removed outlier: 3.656A pdb=" N THR B 768 " --> pdb=" O SER B 764 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 772 " --> pdb=" O THR B 768 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 812 removed outlier: 3.612A pdb=" N LEU B 812 " --> pdb=" O MET B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 847 Processing helix chain 'B' and resid 1014 through 1018 Proline residue: B1018 - end of helix Processing helix chain 'B' and resid 1023 through 1038 removed outlier: 3.704A pdb=" N LYS B1033 " --> pdb=" O CYS B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1052 through 1062 removed outlier: 3.581A pdb=" N LEU B1058 " --> pdb=" O GLY B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1132 through 1141 removed outlier: 3.611A pdb=" N MET B1138 " --> pdb=" O GLU B1134 " (cutoff:3.500A) Processing helix chain 'B' and resid 1144 through 1152 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: 3.584A 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 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' 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 208 removed outlier: 3.971A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 205 through 208' Processing helix chain 'C' and resid 240 through 265 Processing helix chain 'D' and resid 52 through 72 Processing helix chain 'D' and resid 119 through 133 removed outlier: 3.577A pdb=" N ASP D 127 " --> pdb=" O LEU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 149 Processing helix chain 'D' and resid 157 through 168 removed outlier: 3.845A pdb=" N ALA D 162 " --> pdb=" O GLU D 158 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL D 163 " --> pdb=" O THR D 159 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE D 164 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLN D 165 " --> pdb=" O GLY D 161 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 167 " --> pdb=" O VAL D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 180 removed outlier: 3.947A pdb=" N GLN D 179 " --> pdb=" O PHE D 175 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU D 180 " --> pdb=" O GLU D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 194 Processing helix chain 'D' and resid 204 through 220 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: 4.086A pdb=" N LYS G 23 " --> pdb=" O PRO G 20 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL G 34 " --> pdb=" O LEU G 31 " (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 27 Processing helix chain 'J' and resid 32 through 38 Processing helix chain 'J' and resid 44 through 52 removed outlier: 3.855A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (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: 3.782A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 118 removed outlier: 3.942A pdb=" N ALA K 115 " --> pdb=" O LEU K 111 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ASP K 118 " --> pdb=" O LEU K 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 299 through 313 Processing helix chain 'M' and resid 329 through 339 removed outlier: 3.705A 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 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 removed outlier: 3.853A pdb=" N UNK M 487 " --> pdb=" O UNK M 483 " (cutoff:3.500A) Processing helix chain 'M' and resid 505 through 515 removed outlier: 3.976A pdb=" N UNK M 510 " --> pdb=" O UNK M 506 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N UNK M 513 " --> pdb=" O UNK M 509 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N UNK M 514 " --> pdb=" O UNK M 510 " (cutoff:3.500A) Processing helix chain 'M' and resid 523 through 529 Processing helix chain 'M' and resid 531 through 536 Processing helix chain 'M' and resid 547 through 562 Processing helix chain 'M' and resid 591 through 601 Processing helix chain 'M' and resid 614 through 627 removed outlier: 4.381A 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 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 Processing helix chain 'M' and resid 730 through 735 removed outlier: 3.793A pdb=" N UNK M 734 " --> pdb=" O UNK M 730 " (cutoff:3.500A) removed outlier: 3.899A 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 757 through 764 removed outlier: 3.721A pdb=" N UNK M 762 " --> pdb=" O UNK M 759 " (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 Processing sheet with id= D, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.221A 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 365 through 367 removed outlier: 6.588A 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 878 through 882 Processing sheet with id= I, first strand: chain 'A' and resid 1237 through 1240 removed outlier: 3.837A pdb=" N CYS A1240 " --> pdb=" O LEU A1193 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1282 through 1292 Processing sheet with id= K, first strand: chain 'B' and resid 69 through 71 Processing sheet with id= L, first strand: chain 'B' and resid 95 through 97 removed outlier: 3.790A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 203 through 205 Processing sheet with id= N, first strand: chain 'B' and resid 215 through 218 Processing sheet with id= O, first strand: chain 'B' and resid 222 through 227 removed outlier: 3.681A pdb=" N ILE B 222 " --> pdb=" O ARG B 241 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG B 241 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL B 256 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS B 270 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 579 through 582 Processing sheet with id= Q, first strand: chain 'B' and resid 634 through 638 Processing sheet with id= R, first strand: chain 'B' and resid 793 through 796 removed outlier: 3.658A pdb=" N GLN B 951 " --> pdb=" O ARG B 967 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 1010 through 1012 Processing sheet with id= T, first strand: chain 'B' and resid 1159 through 1163 Processing sheet with id= U, first strand: chain 'B' and resid 839 through 842 removed outlier: 7.546A pdb=" N MET B 841 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR B 993 " --> pdb=" O MET B 841 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 176 through 179 removed outlier: 3.654A pdb=" N ASN C 231 " --> pdb=" O GLU C 177 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE C 20 " --> pdb=" O MET C 230 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 97 through 104 removed outlier: 3.772A pdb=" N SER C 48 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 111 through 114 removed outlier: 3.650A pdb=" N CYS C 145 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 78 through 82 removed outlier: 7.447A pdb=" N THR E 107 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N GLU E 81 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE E 109 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR E 131 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N PHE E 110 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLU E 133 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N TYR E 112 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N PHE E 135 " --> pdb=" O TYR E 112 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'E' and resid 153 through 155 Processing sheet with id= AA, first strand: chain 'F' and resid 133 through 137 Processing sheet with id= AB, first strand: chain 'G' and resid 2 through 13 removed outlier: 6.686A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER G 37 " --> pdb=" O ILE G 45 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'G' and resid 142 through 147 removed outlier: 3.776A pdb=" N GLU G 85 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 114 through 118 removed outlier: 5.245A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE H 42 " --> pdb=" O CYS H 24 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU H 27 " --> pdb=" O GLU H 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU H 14 " --> pdb=" O GLU H 27 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'H' and resid 58 through 60 Processing sheet with id= AF, first strand: chain 'I' and resid 16 through 19 Processing sheet with id= AG, first strand: chain 'I' and resid 100 through 103 removed outlier: 3.545A pdb=" N HIS I 108 " --> pdb=" O CYS I 103 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'K' and resid 19 through 23 Processing sheet with id= AI, first strand: chain 'M' and resid 318 through 320 removed outlier: 4.094A pdb=" N UNK M 318 " --> pdb=" O UNK M 493 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N UNK M 495 " --> pdb=" O UNK M 318 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N UNK M 496 " --> pdb=" O UNK M 468 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'M' and resid 349 through 353 removed outlier: 3.513A pdb=" N UNK M 446 " --> pdb=" O UNK M 351 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N UNK M 353 " --> pdb=" O UNK M 446 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'M' and resid 582 through 588 removed outlier: 5.540A pdb=" N UNK M 775 " --> pdb=" O UNK M 583 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N UNK M 585 " --> pdb=" O UNK M 775 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N UNK M 777 " --> pdb=" O UNK M 585 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N UNK M 587 " --> pdb=" O UNK M 777 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N UNK M 779 " --> pdb=" O UNK M 587 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK Processing sheet with id= AL, first strand: chain 'M' and resid 670 through 674 removed outlier: 7.122A pdb=" N UNK M 744 " --> pdb=" O UNK M 671 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N UNK M 673 " --> pdb=" O UNK M 744 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N UNK M 746 " --> pdb=" O UNK M 673 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL 1085 hydrogen bonds defined for protein. 2994 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 90 hydrogen bonds 172 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 81 stacking parallelities Total time for adding SS restraints: 23.02 Time building geometry restraints manager: 44.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.27: 35464 1.27 - 1.70: 28962 1.70 - 2.13: 287 2.13 - 2.57: 0 2.57 - 3.00: 1 Bond restraints: 64714 Sorted by residual: bond pdb=" C MET A 41 " pdb=" N GLN A 45 " ideal model delta sigma weight residual 1.332 2.998 -1.665 1.40e-02 5.10e+03 1.41e+04 bond pdb=" O3' DT N 11 " pdb=" P DC N 12 " ideal model delta sigma weight residual 1.607 1.549 0.058 1.50e-02 4.44e+03 1.52e+01 bond pdb=" C1' TTD T 18 " pdb=" N1 TTD T 18 " ideal model delta sigma weight residual 1.411 1.453 -0.042 2.00e-02 2.50e+03 4.31e+00 bond pdb=" O5R TTD T 18 " pdb=" PB TTD T 18 " ideal model delta sigma weight residual 1.726 1.685 0.041 2.00e-02 2.50e+03 4.30e+00 bond pdb=" C3' DC T 17 " pdb=" O3' DC T 17 " ideal model delta sigma weight residual 1.422 1.476 -0.054 3.00e-02 1.11e+03 3.23e+00 ... (remaining 64709 not shown) Histogram of bond angle deviations from ideal: 43.50 - 61.60: 1 61.60 - 79.69: 0 79.69 - 97.79: 4 97.79 - 115.88: 82072 115.88 - 133.98: 33561 Bond angle restraints: 115638 Sorted by residual: angle pdb=" O MET A 41 " pdb=" C MET A 41 " pdb=" N GLN A 45 " ideal model delta sigma weight residual 122.59 43.50 79.09 1.33e+00 5.65e-01 3.54e+03 angle pdb=" O3' DA N 30 " pdb=" C3' DA N 30 " pdb=" C2' DA N 30 " ideal model delta sigma weight residual 111.50 119.54 -8.04 1.50e+00 4.44e-01 2.88e+01 angle pdb=" OP1 DC N 12 " pdb=" P DC N 12 " pdb=" O5' DC N 12 " ideal model delta sigma weight residual 109.00 123.87 -14.87 3.00e+00 1.11e-01 2.46e+01 angle pdb=" CA MET A 41 " pdb=" C MET A 41 " pdb=" N GLN A 45 " ideal model delta sigma weight residual 116.84 108.38 8.46 1.71e+00 3.42e-01 2.45e+01 angle pdb=" O3' DG N 31 " pdb=" C3' DG N 31 " pdb=" C2' DG N 31 " ideal model delta sigma weight residual 111.50 105.59 5.91 1.50e+00 4.44e-01 1.55e+01 ... (remaining 115633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.14: 29091 29.14 - 58.28: 1373 58.28 - 87.43: 126 87.43 - 116.57: 6 116.57 - 145.71: 5 Dihedral angle restraints: 30601 sinusoidal: 16800 harmonic: 13801 Sorted by residual: dihedral pdb=" CA MET A 41 " pdb=" C MET A 41 " pdb=" N GLN A 45 " pdb=" CA GLN A 45 " ideal model delta harmonic sigma weight residual 180.00 74.36 105.64 0 5.00e+00 4.00e-02 4.46e+02 dihedral pdb=" C5R TTD T 18 " pdb=" O5R TTD T 18 " pdb=" PB TTD T 18 " pdb=" O4P TTD T 18 " ideal model delta sinusoidal sigma weight residual -120.88 24.83 -145.71 1 3.00e+01 1.11e-03 1.95e+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 -103.78 -145.32 1 3.00e+01 1.11e-03 1.94e+01 ... (remaining 30598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 4971 0.077 - 0.153: 460 0.153 - 0.230: 13 0.230 - 0.307: 4 0.307 - 0.384: 1 Chirality restraints: 5449 Sorted by residual: chirality pdb=" C3' DA N 30 " pdb=" C4' DA N 30 " pdb=" O3' DA N 30 " pdb=" C2' DA N 30 " both_signs ideal model delta sigma weight residual False -2.66 -2.28 -0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" C1' A R 1 " pdb=" O4' A R 1 " pdb=" C2' A R 1 " pdb=" N9 A R 1 " both_signs ideal model delta sigma weight residual False 2.46 2.18 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C3' U R 2 " pdb=" C4' U R 2 " pdb=" O3' U R 2 " pdb=" C2' U R 2 " both_signs ideal model delta sigma weight residual False -2.48 -2.74 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 5446 not shown) Planarity restraints: 9397 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' TTD T 18 " -0.497 2.00e-02 2.50e+03 5.95e-01 7.07e+03 pdb=" O4' TTD T 18 " 1.119 2.00e-02 2.50e+03 pdb=" C2' TTD T 18 " -0.868 2.00e-02 2.50e+03 pdb=" C1' TTD T 18 " 0.262 2.00e-02 2.50e+03 pdb=" N1 TTD T 18 " -0.192 2.00e-02 2.50e+03 pdb=" C3R TTD T 18 " -0.494 2.00e-02 2.50e+03 pdb=" C4R TTD T 18 " 0.366 2.00e-02 2.50e+03 pdb=" O3R TTD T 18 " 0.306 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4' TTD T 18 " 0.314 2.00e-02 2.50e+03 2.91e-01 1.69e+03 pdb=" C3' TTD T 18 " -0.376 2.00e-02 2.50e+03 pdb=" O3' TTD T 18 " 0.258 2.00e-02 2.50e+03 pdb=" C1R TTD T 18 " 0.397 2.00e-02 2.50e+03 pdb=" C2R TTD T 18 " -0.244 2.00e-02 2.50e+03 pdb=" C5R TTD T 18 " -0.282 2.00e-02 2.50e+03 pdb=" N1T TTD T 18 " -0.223 2.00e-02 2.50e+03 pdb=" O4R TTD T 18 " 0.156 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 41 " -0.136 2.00e-02 2.50e+03 2.44e-01 5.98e+02 pdb=" C MET A 41 " 0.368 2.00e-02 2.50e+03 pdb=" O MET A 41 " -0.287 2.00e-02 2.50e+03 pdb=" N GLN A 45 " 0.055 2.00e-02 2.50e+03 ... (remaining 9394 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.86: 490 1.86 - 2.55: 56092 2.55 - 3.23: 196845 3.23 - 3.92: 249159 3.92 - 4.60: 394466 Nonbonded interactions: 897052 Sorted by model distance: nonbonded pdb="HH12 ARG A 175 " pdb=" OP1 DG N 38 " model vdw 1.176 1.850 nonbonded pdb="HH22 ARG A 337 " pdb=" O4P TTD T 18 " model vdw 1.228 1.850 nonbonded pdb="HH12 ARG A 337 " pdb=" O5P TTD T 18 " model vdw 1.431 1.850 nonbonded pdb=" O LEU B 298 " pdb=" H CYS B 302 " model vdw 1.447 1.850 nonbonded pdb="HG13 VAL G 86 " pdb=" CD2 LEU G 168 " model vdw 1.488 2.920 ... (remaining 897047 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: 2.880 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: 12.890 Check model and map are aligned: 0.720 Set scattering table: 0.460 Process input model: 196.930 Find NCS groups from input model: 0.850 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:2.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 217.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 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 : 0.010 1.665 34867 Z= 0.710 Angle : 0.716 79.085 47628 Z= 0.424 Chirality : 0.043 0.384 5449 Planarity : 0.010 0.595 5841 Dihedral : 16.264 145.709 13148 Min Nonbonded Distance : 1.544 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.18 % Favored : 94.71 % Rotamer: Outliers : 0.06 % Allowed : 3.07 % Favored : 96.87 % 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: 0.58 (0.15), residues: 1273 sheet: -1.16 (0.21), residues: 576 loop : -0.33 (0.15), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1228 HIS 0.005 0.001 HIS A 399 PHE 0.010 0.001 PHE A 655 TYR 0.022 0.001 TYR H 102 ARG 0.003 0.000 ARG A 350 *********************** 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 **************************** Evaluate side-chains 182 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 180 time to evaluate : 3.853 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 1336 MET cc_start: 0.8999 (tmm) cc_final: 0.8367 (tmm) REVERT: B 552 MET cc_start: 0.9016 (mmm) cc_final: 0.8809 (mmp) REVERT: B 1021 MET cc_start: 0.7444 (mmm) cc_final: 0.7013 (mmm) REVERT: D 189 ASP cc_start: 0.9417 (m-30) cc_final: 0.8987 (p0) outliers start: 2 outliers final: 1 residues processed: 180 average time/residue: 0.8577 time to fit residues: 247.5621 Evaluate side-chains 167 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 3.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1389 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 356 optimal weight: 0.4980 chunk 319 optimal weight: 30.0000 chunk 177 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 330 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 chunk 246 optimal weight: 1.9990 chunk 383 optimal weight: 20.0000 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.0550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 34867 Z= 0.259 Angle : 0.594 18.860 47628 Z= 0.302 Chirality : 0.040 0.283 5449 Planarity : 0.004 0.047 5841 Dihedral : 17.151 146.933 5694 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.50 % Favored : 94.39 % Rotamer: Outliers : 0.15 % Allowed : 3.89 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.29 (0.14), residues: 3688 helix: 0.60 (0.14), residues: 1296 sheet: -1.06 (0.22), residues: 532 loop : -0.38 (0.15), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1228 HIS 0.005 0.001 HIS A 399 PHE 0.013 0.001 PHE A1053 TYR 0.025 0.001 TYR G 167 ARG 0.003 0.000 ARG B 857 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 172 time to evaluate : 3.764 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 1336 MET cc_start: 0.8967 (tmm) cc_final: 0.8378 (tmm) REVERT: B 313 MET cc_start: 0.9119 (tpp) cc_final: 0.8607 (tpp) REVERT: D 189 ASP cc_start: 0.9476 (m-30) cc_final: 0.9045 (p0) outliers start: 5 outliers final: 4 residues processed: 174 average time/residue: 0.8256 time to fit residues: 233.2731 Evaluate side-chains 170 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 166 time to evaluate : 3.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1389 PHE Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain K residue 111 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 212 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 318 optimal weight: 50.0000 chunk 260 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 383 optimal weight: 50.0000 chunk 414 optimal weight: 30.0000 chunk 341 optimal weight: 20.0000 chunk 380 optimal weight: 50.0000 chunk 130 optimal weight: 3.9990 chunk 307 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 34867 Z= 0.313 Angle : 0.579 23.196 47628 Z= 0.294 Chirality : 0.039 0.169 5449 Planarity : 0.004 0.045 5841 Dihedral : 16.976 162.392 5694 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.40 % Favored : 93.49 % Rotamer: Outliers : 0.46 % Allowed : 5.10 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.39 (0.14), residues: 3688 helix: 0.56 (0.14), residues: 1301 sheet: -1.20 (0.22), residues: 540 loop : -0.46 (0.15), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 466 HIS 0.006 0.001 HIS A 659 PHE 0.016 0.001 PHE C 219 TYR 0.020 0.001 TYR H 102 ARG 0.006 0.000 ARG B 857 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 170 time to evaluate : 3.816 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: 0.7939 (mmp) cc_final: 0.7712 (ptt) REVERT: A 74 MET cc_start: 0.8881 (ppp) cc_final: 0.8494 (ppp) REVERT: A 1336 MET cc_start: 0.8953 (tmm) cc_final: 0.8380 (tmm) REVERT: B 313 MET cc_start: 0.9108 (tpp) cc_final: 0.8710 (tpp) REVERT: D 189 ASP cc_start: 0.9474 (m-30) cc_final: 0.9036 (p0) outliers start: 15 outliers final: 8 residues processed: 181 average time/residue: 0.8152 time to fit residues: 242.5338 Evaluate side-chains 167 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 159 time to evaluate : 3.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1389 PHE Chi-restraints excluded: chain B residue 1190 ASP Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain K residue 111 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 379 optimal weight: 100.0000 chunk 288 optimal weight: 10.0000 chunk 199 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 183 optimal weight: 7.9990 chunk 257 optimal weight: 0.9980 chunk 385 optimal weight: 40.0000 chunk 407 optimal weight: 80.0000 chunk 201 optimal weight: 0.8980 chunk 365 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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** ** A 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 34867 Z= 0.329 Angle : 0.576 19.092 47628 Z= 0.293 Chirality : 0.039 0.215 5449 Planarity : 0.004 0.044 5841 Dihedral : 16.981 161.731 5694 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.26 % Favored : 93.63 % Rotamer: Outliers : 0.43 % Allowed : 6.19 % Favored : 93.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.43 (0.14), residues: 3688 helix: 0.54 (0.14), residues: 1303 sheet: -1.22 (0.21), residues: 541 loop : -0.49 (0.15), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 681 HIS 0.006 0.001 HIS A 659 PHE 0.013 0.001 PHE K 71 TYR 0.032 0.001 TYR G 167 ARG 0.005 0.000 ARG B 857 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 166 time to evaluate : 3.883 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 74 MET cc_start: 0.8943 (ppp) cc_final: 0.8612 (ppp) REVERT: A 1336 MET cc_start: 0.8969 (tmm) cc_final: 0.8381 (tmm) REVERT: B 313 MET cc_start: 0.9129 (tpp) cc_final: 0.8730 (tpp) REVERT: D 189 ASP cc_start: 0.9479 (m-30) cc_final: 0.9035 (p0) outliers start: 14 outliers final: 10 residues processed: 177 average time/residue: 0.8281 time to fit residues: 240.2927 Evaluate side-chains 166 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 156 time to evaluate : 3.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1056 SER Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 1190 ASP Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain K residue 111 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 339 optimal weight: 20.0000 chunk 231 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 chunk 303 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 chunk 348 optimal weight: 0.9980 chunk 281 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 366 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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** ** A 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 34867 Z= 0.244 Angle : 0.544 20.522 47628 Z= 0.273 Chirality : 0.038 0.186 5449 Planarity : 0.004 0.043 5841 Dihedral : 16.887 158.533 5692 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.94 % Favored : 94.01 % Rotamer: Outliers : 0.49 % Allowed : 6.65 % Favored : 92.86 % 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: 3688 helix: 0.76 (0.15), residues: 1306 sheet: -1.17 (0.22), residues: 541 loop : -0.43 (0.15), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 681 HIS 0.005 0.001 HIS A 399 PHE 0.013 0.001 PHE K 71 TYR 0.016 0.001 TYR H 102 ARG 0.004 0.000 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 168 time to evaluate : 3.850 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 74 MET cc_start: 0.8979 (ppp) cc_final: 0.8630 (ppp) REVERT: A 1336 MET cc_start: 0.8949 (tmm) cc_final: 0.8373 (tmm) REVERT: B 314 LEU cc_start: 0.9631 (mt) cc_final: 0.9411 (pp) REVERT: B 1208 MET cc_start: 0.9007 (mtt) cc_final: 0.8785 (mtt) REVERT: D 189 ASP cc_start: 0.9471 (m-30) cc_final: 0.9026 (p0) REVERT: J 49 MET cc_start: 0.7835 (mtp) cc_final: 0.7562 (mtp) outliers start: 16 outliers final: 12 residues processed: 182 average time/residue: 0.8382 time to fit residues: 249.7885 Evaluate side-chains 171 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 159 time to evaluate : 3.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1190 ASP Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain K residue 111 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 137 optimal weight: 0.4980 chunk 367 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 239 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 408 optimal weight: 110.0000 chunk 338 optimal weight: 0.9980 chunk 189 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 214 optimal weight: 3.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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** ** A 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 HIS ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 34867 Z= 0.287 Angle : 0.552 19.961 47628 Z= 0.278 Chirality : 0.038 0.182 5449 Planarity : 0.004 0.042 5841 Dihedral : 16.866 155.743 5692 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.10 % Favored : 93.84 % Rotamer: Outliers : 0.61 % Allowed : 7.05 % Favored : 92.35 % 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: -0.29 (0.14), residues: 3688 helix: 0.75 (0.15), residues: 1306 sheet: -1.19 (0.22), residues: 539 loop : -0.47 (0.15), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 681 HIS 0.005 0.001 HIS A 399 PHE 0.014 0.001 PHE K 71 TYR 0.013 0.001 TYR G 167 ARG 0.004 0.000 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 165 time to evaluate : 3.800 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 1336 MET cc_start: 0.8969 (tmm) cc_final: 0.8392 (tmm) REVERT: B 860 MET cc_start: 0.8272 (tmm) cc_final: 0.7988 (tmm) REVERT: C 76 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8268 (p0) REVERT: D 189 ASP cc_start: 0.9473 (m-30) cc_final: 0.9027 (p0) outliers start: 20 outliers final: 15 residues processed: 185 average time/residue: 0.8086 time to fit residues: 244.9128 Evaluate side-chains 174 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 158 time to evaluate : 3.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1056 SER Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1178 ASN Chi-restraints excluded: chain B residue 1190 ASP Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain K residue 111 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 393 optimal weight: 60.0000 chunk 46 optimal weight: 2.9990 chunk 232 optimal weight: 2.9990 chunk 298 optimal weight: 4.9990 chunk 231 optimal weight: 0.8980 chunk 343 optimal weight: 9.9990 chunk 227 optimal weight: 2.9990 chunk 406 optimal weight: 60.0000 chunk 254 optimal weight: 2.9990 chunk 247 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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** ** A 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 34867 Z= 0.288 Angle : 0.559 20.148 47628 Z= 0.280 Chirality : 0.038 0.174 5449 Planarity : 0.004 0.043 5841 Dihedral : 16.844 151.796 5692 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.10 % Favored : 93.84 % Rotamer: Outliers : 0.67 % Allowed : 7.23 % Favored : 92.10 % 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: -0.29 (0.14), residues: 3688 helix: 0.76 (0.15), residues: 1305 sheet: -1.19 (0.22), residues: 534 loop : -0.48 (0.15), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 681 HIS 0.005 0.001 HIS A 659 PHE 0.014 0.001 PHE K 71 TYR 0.015 0.001 TYR H 102 ARG 0.005 0.000 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 164 time to evaluate : 3.832 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: A 74 MET cc_start: 0.9018 (ppp) cc_final: 0.8683 (ppp) REVERT: A 1336 MET cc_start: 0.9014 (tmm) cc_final: 0.8451 (tmm) REVERT: B 526 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7279 (tm-30) REVERT: B 860 MET cc_start: 0.8272 (tmm) cc_final: 0.7986 (tmm) REVERT: C 76 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8257 (p0) REVERT: D 189 ASP cc_start: 0.9474 (m-30) cc_final: 0.9029 (p0) REVERT: F 89 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8529 (pm20) outliers start: 22 outliers final: 16 residues processed: 184 average time/residue: 0.8341 time to fit residues: 250.9240 Evaluate side-chains 176 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 158 time to evaluate : 3.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1056 SER Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain B residue 1178 ASN Chi-restraints excluded: chain B residue 1190 ASP Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain K residue 111 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 251 optimal weight: 3.9990 chunk 162 optimal weight: 20.0000 chunk 242 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 258 optimal weight: 1.9990 chunk 277 optimal weight: 8.9990 chunk 201 optimal weight: 3.9990 chunk 37 optimal weight: 0.0470 chunk 319 optimal weight: 20.0000 overall best weight: 1.5284 ------------------------------------------------------------------------------- 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** A 654 ASN ** A 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 ASN ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34867 Z= 0.193 Angle : 0.530 19.715 47628 Z= 0.262 Chirality : 0.038 0.179 5449 Planarity : 0.003 0.043 5841 Dihedral : 16.783 149.590 5692 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.72 % Favored : 94.22 % Rotamer: Outliers : 0.49 % Allowed : 7.68 % Favored : 91.83 % 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: -0.09 (0.14), residues: 3688 helix: 0.95 (0.15), residues: 1310 sheet: -1.11 (0.22), residues: 533 loop : -0.38 (0.15), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 201 HIS 0.004 0.001 HIS A 399 PHE 0.013 0.001 PHE K 71 TYR 0.012 0.001 TYR H 102 ARG 0.004 0.000 ARG D 155 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 176 time to evaluate : 3.907 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 47 ARG cc_start: 0.8194 (tmm160) cc_final: 0.7824 (ttp80) REVERT: A 1336 MET cc_start: 0.8986 (tmm) cc_final: 0.8439 (tmm) REVERT: B 526 GLU cc_start: 0.7599 (tm-30) cc_final: 0.7235 (tm-30) REVERT: D 189 ASP cc_start: 0.9465 (m-30) cc_final: 0.9021 (p0) REVERT: J 49 MET cc_start: 0.7792 (mtp) cc_final: 0.7524 (mtp) outliers start: 16 outliers final: 14 residues processed: 191 average time/residue: 0.8364 time to fit residues: 260.0826 Evaluate side-chains 181 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 167 time to evaluate : 3.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1056 SER Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 1178 ASN Chi-restraints excluded: chain B residue 1190 ASP Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain F residue 86 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 369 optimal weight: 3.9990 chunk 389 optimal weight: 50.0000 chunk 355 optimal weight: 2.9990 chunk 379 optimal weight: 110.0000 chunk 228 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 297 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 342 optimal weight: 4.9990 chunk 358 optimal weight: 3.9990 chunk 377 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 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1178 ASN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 34867 Z= 0.376 Angle : 0.589 20.230 47628 Z= 0.299 Chirality : 0.039 0.173 5449 Planarity : 0.004 0.043 5841 Dihedral : 16.804 144.666 5692 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.05 % Favored : 92.87 % Rotamer: Outliers : 0.73 % Allowed : 7.65 % Favored : 91.62 % 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: -0.45 (0.14), residues: 3688 helix: 0.63 (0.14), residues: 1316 sheet: -1.19 (0.22), residues: 539 loop : -0.61 (0.15), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 681 HIS 0.007 0.001 HIS A 659 PHE 0.018 0.001 PHE K 71 TYR 0.023 0.002 TYR H 102 ARG 0.007 0.000 ARG B 857 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 158 time to evaluate : 3.775 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 47 ARG cc_start: 0.8190 (tmm160) cc_final: 0.7770 (ttp80) REVERT: A 74 MET cc_start: 0.9030 (ppp) cc_final: 0.8646 (ppp) REVERT: A 971 PHE cc_start: 0.7449 (OUTLIER) cc_final: 0.6456 (p90) REVERT: A 1336 MET cc_start: 0.9052 (tmm) cc_final: 0.8493 (tmm) REVERT: B 526 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7310 (tm-30) REVERT: B 860 MET cc_start: 0.8267 (tmm) cc_final: 0.8004 (tmm) REVERT: C 76 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8290 (p0) REVERT: D 189 ASP cc_start: 0.9475 (m-30) cc_final: 0.9028 (p0) outliers start: 24 outliers final: 17 residues processed: 180 average time/residue: 0.8148 time to fit residues: 239.3146 Evaluate side-chains 175 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 156 time to evaluate : 3.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 971 PHE Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1056 SER Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1178 ASN Chi-restraints excluded: chain B residue 1190 ASP Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain K residue 111 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 248 optimal weight: 0.4980 chunk 400 optimal weight: 50.0000 chunk 244 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 278 optimal weight: 7.9990 chunk 420 optimal weight: 4.9990 chunk 386 optimal weight: 50.0000 chunk 334 optimal weight: 1.9990 chunk 34 optimal weight: 0.0970 chunk 258 optimal weight: 2.9990 chunk 205 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 GLN ** A 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34867 Z= 0.164 Angle : 0.533 19.686 47628 Z= 0.263 Chirality : 0.038 0.179 5449 Planarity : 0.003 0.043 5841 Dihedral : 16.748 146.009 5692 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.42 % Favored : 94.52 % Rotamer: Outliers : 0.43 % Allowed : 8.05 % Favored : 91.53 % 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: 3688 helix: 0.96 (0.15), residues: 1309 sheet: -1.08 (0.22), residues: 533 loop : -0.41 (0.15), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 201 HIS 0.004 0.001 HIS A 435 PHE 0.016 0.001 PHE E 42 TYR 0.021 0.001 TYR H 102 ARG 0.004 0.000 ARG D 155 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 175 time to evaluate : 3.904 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: A 45 GLN cc_start: 0.8449 (tp40) cc_final: 0.7749 (pp30) REVERT: A 47 ARG cc_start: 0.8169 (tmm160) cc_final: 0.7843 (ttp80) REVERT: A 1336 MET cc_start: 0.9008 (tmm) cc_final: 0.8450 (tmm) REVERT: B 381 MET cc_start: 0.9289 (ptp) cc_final: 0.8936 (pmm) REVERT: B 526 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7242 (tm-30) REVERT: B 792 MET cc_start: 0.6696 (mmp) cc_final: 0.6483 (mmp) REVERT: D 189 ASP cc_start: 0.9463 (m-30) cc_final: 0.9020 (p0) REVERT: J 49 MET cc_start: 0.7788 (mtp) cc_final: 0.7516 (mtp) outliers start: 14 outliers final: 13 residues processed: 189 average time/residue: 0.8196 time to fit residues: 252.6766 Evaluate side-chains 183 residues out of total 3293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 170 time to evaluate : 3.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1190 ASP Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain K residue 111 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 265 optimal weight: 1.9990 chunk 356 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 308 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 335 optimal weight: 0.5980 chunk 140 optimal weight: 6.9990 chunk 344 optimal weight: 0.0980 chunk 42 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 654 ASN ** A 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.090554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.061082 restraints weight = 382921.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.063165 restraints weight = 162829.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.064347 restraints weight = 105169.320| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 34867 Z= 0.133 Angle : 0.521 18.802 47628 Z= 0.254 Chirality : 0.038 0.178 5449 Planarity : 0.003 0.043 5841 Dihedral : 16.628 144.586 5692 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.69 % Favored : 95.25 % Rotamer: Outliers : 0.36 % Allowed : 8.17 % Favored : 91.47 % 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: 0.14 (0.14), residues: 3688 helix: 1.18 (0.15), residues: 1314 sheet: -0.98 (0.22), residues: 542 loop : -0.28 (0.15), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 201 HIS 0.005 0.001 HIS A1367 PHE 0.012 0.001 PHE E 42 TYR 0.018 0.001 TYR H 102 ARG 0.003 0.000 ARG D 155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7669.91 seconds wall clock time: 136 minutes 18.78 seconds (8178.78 seconds total)