Starting phenix.real_space_refine (version: dev) on Tue May 17 06:12:19 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g5l_3439/05_2022/5g5l_3439_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g5l_3439/05_2022/5g5l_3439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g5l_3439/05_2022/5g5l_3439.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g5l_3439/05_2022/5g5l_3439.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g5l_3439/05_2022/5g5l_3439_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g5l_3439/05_2022/5g5l_3439_neut.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.004 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 1290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1188": "OE1" <-> "OE2" Residue "D ASP 95": "OD1" <-> "OD2" Residue "H PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 37349 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 11686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1480, 11686 Classifications: {'peptide': 1480} Link IDs: {'PTRANS': 56, 'TRANS': 1418, 'PCIS': 5} Chain breaks: 7 Chain: "B" Number of atoms: 9327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1174, 9327 Classifications: {'peptide': 1174} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 58, 'TRANS': 1114, 'PCIS': 1} Chain breaks: 3 Chain: "C" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2423 Classifications: {'peptide': 305} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 285} Chain: "D" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 459 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain breaks: 1 Chain: "E" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1735 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 199, 'PCIS': 1} Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 823 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "G" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1520 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'CIS': 1, 'TRANS': 180} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1052 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain breaks: 1 Chain: "I" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain breaks: 2 Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 793 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "L" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 340 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "M" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 833 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "N" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1151 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 9, 'TRANS': 135} Chain breaks: 2 Chain: "O" Number of atoms: 3811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3811 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 449} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" 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: "B" 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 461 SG CYS A 62 73.565 67.732 56.295 1.00100.00 S ATOM 480 SG CYS A 65 70.454 68.719 55.630 1.00100.00 S ATOM 535 SG CYS A 72 72.337 69.734 58.423 1.00100.00 S ATOM 781 SG CYS A 102 74.663 25.214 85.575 1.00100.00 S ATOM 806 SG CYS A 105 71.287 24.061 84.197 1.00100.00 S ATOM 1589 SG CYS A 233 71.831 24.455 87.854 1.00100.00 S ATOM 1611 SG CYS A 236 73.621 21.734 85.953 1.00100.00 S ATOM 20306 SG CYS B1104 59.159 57.277 61.312 1.00100.00 S ATOM 20332 SG CYS B1107 61.714 56.177 63.772 1.00100.00 S ATOM 20479 SG CYS B1128 62.802 57.107 60.422 1.00100.00 S ATOM 20507 SG CYS B1131 60.612 54.001 60.755 1.00100.00 S ATOM 29088 SG CYS I 10 122.807 52.502 141.334 1.00100.00 S ATOM 29110 SG CYS I 13 123.129 53.945 137.856 1.00100.00 S ATOM 29230 SG CYS I 30 122.256 50.680 138.022 1.00100.00 S ATOM 29251 SG CYS I 33 125.713 51.663 139.148 1.00100.00 S ATOM 29615 SG CYS I 86 47.746 89.392 125.499 1.00100.00 S ATOM 29637 SG CYS I 89 45.724 89.284 128.958 1.00100.00 S ATOM 29755 SG CYS I 114 49.351 88.151 128.525 1.00100.00 S ATOM 29774 SG CYS I 117 47.130 86.224 127.148 1.00100.00 S ATOM 29899 SG CYS J 7 75.018 128.991 98.891 1.00100.00 S ATOM 29922 SG CYS J 10 73.623 130.485 99.850 1.00100.00 S ATOM 30202 SG CYS J 45 73.546 129.906 100.797 1.00100.00 S ATOM 30208 SG CYS J 46 74.925 132.127 100.212 1.00100.00 S ATOM 31250 SG CYS L 31 111.807 112.059 77.872 1.00100.00 S ATOM 31270 SG CYS L 34 114.302 114.668 77.724 1.00100.00 S ATOM 31374 SG CYS L 48 114.243 112.468 75.147 1.00100.00 S ATOM 31397 SG CYS L 51 115.613 112.195 79.208 1.00100.00 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="ZN ZN I1127 " occ=0.75 Time building chain proxies: 19.89, per 1000 atoms: 0.53 Number of scatterers: 37349 At special positions: 0 Unit cell: (159.3, 164.7, 182.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 7 29.99 S 191 16.00 O 7026 8.00 N 6428 7.00 C 23697 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.76 Conformation dependent library (CDL) restraints added in 5.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN A2663 " pdb="ZN ZN A2663 " - pdb=" NE2 HIS A 75 " pdb="ZN ZN A2663 " - pdb=" SG CYS A 62 " pdb="ZN ZN A2663 " - pdb=" SG CYS A 72 " pdb="ZN ZN A2663 " - pdb=" SG CYS A 65 " pdb=" ZN A2664 " pdb="ZN ZN A2664 " - pdb=" SG CYS A 105 " pdb="ZN ZN A2664 " - pdb=" SG CYS A 233 " pdb="ZN ZN A2664 " - pdb=" SG CYS A 236 " pdb="ZN ZN A2664 " - pdb=" SG CYS A 102 " pdb=" ZN B2204 " pdb="ZN ZN B2204 " - pdb=" SG CYS B1131 " pdb="ZN ZN B2204 " - pdb=" SG CYS B1128 " pdb="ZN ZN B2204 " - pdb=" SG CYS B1104 " pdb="ZN ZN B2204 " - pdb=" SG CYS B1107 " pdb=" ZN I1126 " pdb="ZN ZN I1126 " - pdb=" SG CYS I 13 " pdb="ZN ZN I1126 " - pdb=" SG CYS I 33 " pdb="ZN ZN I1126 " - pdb=" SG CYS I 30 " pdb="ZN ZN I1126 " - pdb=" SG CYS I 10 " pdb=" ZN I1127 " pdb="ZN ZN I1127 " - pdb=" SG CYS I 114 " pdb="ZN ZN I1127 " - pdb=" SG CYS I 86 " pdb="ZN ZN I1127 " - pdb=" SG CYS I 117 " pdb="ZN ZN I1127 " - pdb=" SG CYS I 89 " pdb=" ZN J1070 " pdb="ZN ZN J1070 " - pdb=" SG CYS J 7 " pdb="ZN ZN J1070 " - pdb=" SG CYS J 46 " pdb="ZN ZN J1070 " - pdb=" SG CYS J 45 " pdb="ZN ZN J1070 " - pdb=" SG CYS J 10 " pdb=" ZN L1070 " pdb="ZN ZN L1070 " - pdb=" SG CYS L 34 " pdb="ZN ZN L1070 " - pdb=" SG CYS L 51 " pdb="ZN ZN L1070 " - pdb=" SG CYS L 31 " pdb="ZN ZN L1070 " - pdb=" SG CYS L 48 " Number of angles added : 39 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8844 Finding SS restraints... Secondary structure from input PDB file: 193 helices and 54 sheets defined 42.8% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.76 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 Processing helix chain 'A' and resid 51 through 55 Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 91 through 101 Processing helix chain 'A' and resid 111 through 127 removed outlier: 3.906A pdb=" N TYR A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 removed outlier: 3.554A pdb=" N TYR A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 139 No H-bonds generated for 'chain 'A' and resid 137 through 139' Processing helix chain 'A' and resid 174 through 199 removed outlier: 4.002A pdb=" N ASN A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 229 Processing helix chain 'A' and resid 257 through 267 removed outlier: 3.584A pdb=" N LYS A 267 " --> pdb=" O ASN A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 331 Processing helix chain 'A' and resid 331 through 339 removed outlier: 3.739A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 Processing helix chain 'A' and resid 380 through 404 removed outlier: 3.533A pdb=" N LYS A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER A 404 " --> pdb=" O ASN A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 439 removed outlier: 3.757A pdb=" N VAL A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 438 " --> pdb=" O VAL A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 443 Processing helix chain 'A' and resid 455 through 462 Processing helix chain 'A' and resid 465 through 471 Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 515 through 526 Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 567 through 571 Processing helix chain 'A' and resid 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' Processing helix chain 'A' and resid 617 through 619 No H-bonds generated for 'chain 'A' and resid 617 through 619' Processing helix chain 'A' and resid 620 through 625 Processing helix chain 'A' and resid 640 through 650 Processing helix chain 'A' and resid 671 through 681 Processing helix chain 'A' and resid 689 through 701 removed outlier: 4.007A pdb=" N ARG A 701 " --> pdb=" O TYR A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 740 Processing helix chain 'A' and resid 756 through 760 Processing helix chain 'A' and resid 782 through 787 Processing helix chain 'A' and resid 792 through 825 Proline residue: A 803 - end of helix Processing helix chain 'A' and resid 829 through 834 Processing helix chain 'A' and resid 836 through 848 Processing helix chain 'A' and resid 849 through 851 No H-bonds generated for 'chain 'A' and resid 849 through 851' Processing helix chain 'A' and resid 852 through 862 Processing helix chain 'A' and resid 872 through 885 removed outlier: 3.735A pdb=" N ASP A 885 " --> pdb=" O GLU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 912 Processing helix chain 'A' and resid 923 through 931 Processing helix chain 'A' and resid 936 through 945 Processing helix chain 'A' and resid 975 through 979 Processing helix chain 'A' and resid 991 through 1010 removed outlier: 3.592A pdb=" N ALA A1010 " --> pdb=" O LEU A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1027 Processing helix chain 'A' and resid 1065 through 1071 Processing helix chain 'A' and resid 1072 through 1081 Processing helix chain 'A' and resid 1082 through 1089 removed outlier: 3.748A pdb=" N ILE A1086 " --> pdb=" O SER A1083 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N GLU A1087 " --> pdb=" O ALA A1084 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A1089 " --> pdb=" O ILE A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1108 Processing helix chain 'A' and resid 1112 through 1116 removed outlier: 3.734A pdb=" N GLN A1116 " --> pdb=" O HIS A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1127 removed outlier: 3.837A pdb=" N LYS A1126 " --> pdb=" O PRO A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1151 Processing helix chain 'A' and resid 1152 through 1156 Processing helix chain 'A' and resid 1162 through 1176 Processing helix chain 'A' and resid 1184 through 1195 Processing helix chain 'A' and resid 1196 through 1201 removed outlier: 3.661A pdb=" N THR A1201 " --> pdb=" O THR A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1227 Processing helix chain 'A' and resid 1247 through 1259 Processing helix chain 'A' and resid 1262 through 1266 removed outlier: 4.002A pdb=" N VAL A1266 " --> pdb=" O LEU A1262 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1262 through 1266' Processing helix chain 'A' and resid 1298 through 1307 Processing helix chain 'A' and resid 1309 through 1319 Processing helix chain 'A' and resid 1319 through 1336 removed outlier: 3.587A pdb=" N HIS A1323 " --> pdb=" O ASN A1319 " (cutoff:3.500A) Processing helix chain 'A' and resid 1441 through 1453 Processing helix chain 'A' and resid 1484 through 1494 Processing helix chain 'A' and resid 1525 through 1530 Processing helix chain 'A' and resid 1531 through 1533 No H-bonds generated for 'chain 'A' and resid 1531 through 1533' Processing helix chain 'A' and resid 1537 through 1541 Processing helix chain 'A' and resid 1545 through 1554 Processing helix chain 'A' and resid 1554 through 1573 removed outlier: 3.910A pdb=" N TYR A1573 " --> pdb=" O VAL A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1590 Processing helix chain 'A' and resid 1599 through 1604 Processing helix chain 'A' and resid 1608 through 1614 removed outlier: 3.718A pdb=" N LYS A1612 " --> pdb=" O SER A1608 " (cutoff:3.500A) Processing helix chain 'A' and resid 1617 through 1628 Processing helix chain 'A' and resid 1636 through 1644 Processing helix chain 'B' and resid 17 through 27 Processing helix chain 'B' and resid 35 through 51 removed outlier: 3.990A pdb=" N GLN B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Proline residue: B 44 - end of helix Processing helix chain 'B' and resid 59 through 69 removed outlier: 3.838A pdb=" N GLY B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 130 removed outlier: 3.677A pdb=" N SER B 126 " --> pdb=" O TYR B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 220 through 226 removed outlier: 3.756A pdb=" N ARG B 225 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY B 226 " --> pdb=" O ALA B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 281 removed outlier: 4.104A pdb=" N CYS B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 294 Processing helix chain 'B' and resid 299 through 314 removed outlier: 3.655A pdb=" N ARG B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 335 Processing helix chain 'B' and resid 345 through 358 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 366 through 386 Processing helix chain 'B' and resid 396 through 400 Processing helix chain 'B' and resid 404 through 435 Processing helix chain 'B' and resid 442 through 452 removed outlier: 3.767A pdb=" N ARG B 452 " --> pdb=" O ARG B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 468 removed outlier: 3.572A pdb=" N LYS B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 500 removed outlier: 4.015A pdb=" N PHE B 500 " --> pdb=" O PHE B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 511 removed outlier: 3.770A pdb=" N GLN B 511 " --> pdb=" O PHE B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 560 through 568 Processing helix chain 'B' and resid 574 through 576 No H-bonds generated for 'chain 'B' and resid 574 through 576' Processing helix chain 'B' and resid 597 through 615 Processing helix chain 'B' and resid 665 through 670 removed outlier: 4.015A pdb=" N VAL B 670 " --> pdb=" O PRO B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 681 removed outlier: 3.503A pdb=" N ILE B 681 " --> pdb=" O PRO B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 697 Processing helix chain 'B' and resid 698 through 704 Processing helix chain 'B' and resid 706 through 709 Processing helix chain 'B' and resid 711 through 723 removed outlier: 3.671A pdb=" N ASN B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS B 719 " --> pdb=" O ASN B 715 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN B 720 " --> pdb=" O MET B 716 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS B 723 " --> pdb=" O CYS B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 736 Processing helix chain 'B' and resid 754 through 760 removed outlier: 4.078A pdb=" N ASP B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 Processing helix chain 'B' and resid 791 through 796 Processing helix chain 'B' and resid 834 through 839 Processing helix chain 'B' and resid 950 through 954 Processing helix chain 'B' and resid 959 through 976 removed outlier: 4.044A pdb=" N PHE B 963 " --> pdb=" O THR B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1004 Processing helix chain 'B' and resid 1072 through 1083 removed outlier: 3.532A pdb=" N GLY B1083 " --> pdb=" O LEU B1079 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1093 Processing helix chain 'B' and resid 1135 through 1140 Processing helix chain 'B' and resid 1154 through 1156 No H-bonds generated for 'chain 'B' and resid 1154 through 1156' Processing helix chain 'B' and resid 1179 through 1192 removed outlier: 4.121A pdb=" N LYS B1183 " --> pdb=" O PRO B1179 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR B1184 " --> pdb=" O PHE B1180 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 40 Processing helix chain 'C' and resid 60 through 74 Processing helix chain 'C' and resid 93 through 104 Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'C' and resid 121 through 126 removed outlier: 3.801A pdb=" N PHE C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 174 through 179 Processing helix chain 'C' and resid 241 through 249 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 282 through 287 removed outlier: 4.257A pdb=" N ASP C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 330 Processing helix chain 'D' and resid 32 through 47 Processing helix chain 'D' and resid 80 through 97 Processing helix chain 'E' and resid 5 through 26 Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 54 through 59 removed outlier: 3.829A pdb=" N MET E 58 " --> pdb=" O GLN E 54 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER E 59 " --> pdb=" O ARG E 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 54 through 59' Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 103 Processing helix chain 'E' and resid 117 through 122 removed outlier: 3.604A pdb=" N LYS E 122 " --> pdb=" O PRO E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 140 No H-bonds generated for 'chain 'E' and resid 138 through 140' Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 168 Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 55 through 70 removed outlier: 3.650A pdb=" N GLN F 59 " --> pdb=" O PRO F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 79 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 50 through 54 Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'G' and resid 66 through 70 Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'I' and resid 19 through 23 Processing helix chain 'I' and resid 52 through 56 removed outlier: 4.460A pdb=" N PHE I 56 " --> pdb=" O ASP I 53 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 65 removed outlier: 4.172A pdb=" N SER I 65 " --> pdb=" O ARG I 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.704A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 69 through 81 removed outlier: 3.765A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 142 Processing helix chain 'M' and resid 69 through 72 removed outlier: 3.504A pdb=" N ALA M 72 " --> pdb=" O SER M 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 69 through 72' Processing helix chain 'M' and resid 103 through 107 removed outlier: 3.832A pdb=" N ASN M 107 " --> pdb=" O LYS M 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 103 through 107' Processing helix chain 'N' and resid 92 through 97 Processing helix chain 'N' and resid 149 through 154 Processing helix chain 'N' and resid 176 through 180 Processing helix chain 'O' and resid 48 through 65 removed outlier: 3.531A pdb=" N SER O 53 " --> pdb=" O ALA O 49 " (cutoff:3.500A) Processing helix chain 'O' and resid 68 through 80 removed outlier: 3.637A pdb=" N LEU O 80 " --> pdb=" O ASN O 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 103 removed outlier: 3.788A pdb=" N ASN O 103 " --> pdb=" O ILE O 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 104 through 107 Processing helix chain 'O' and resid 112 through 121 Processing helix chain 'O' and resid 124 through 128 Processing helix chain 'O' and resid 129 through 147 removed outlier: 3.729A pdb=" N SER O 146 " --> pdb=" O ILE O 142 " (cutoff:3.500A) Processing helix chain 'O' and resid 150 through 161 removed outlier: 3.579A pdb=" N ILE O 157 " --> pdb=" O ASP O 153 " (cutoff:3.500A) Processing helix chain 'O' and resid 162 through 164 No H-bonds generated for 'chain 'O' and resid 162 through 164' Processing helix chain 'O' and resid 169 through 183 Processing helix chain 'O' and resid 186 through 197 Processing helix chain 'O' and resid 204 through 220 removed outlier: 3.684A pdb=" N LEU O 215 " --> pdb=" O TYR O 211 " (cutoff:3.500A) Processing helix chain 'O' and resid 226 through 247 Processing helix chain 'O' and resid 325 through 347 removed outlier: 3.554A pdb=" N THR O 330 " --> pdb=" O LYS O 326 " (cutoff:3.500A) Processing helix chain 'O' and resid 348 through 354 Processing helix chain 'O' and resid 356 through 373 Processing helix chain 'O' and resid 381 through 390 removed outlier: 4.223A pdb=" N MET O 385 " --> pdb=" O ILE O 381 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN O 390 " --> pdb=" O PHE O 386 " (cutoff:3.500A) Processing helix chain 'O' and resid 392 through 408 removed outlier: 3.829A pdb=" N PHE O 408 " --> pdb=" O ILE O 404 " (cutoff:3.500A) Processing helix chain 'O' and resid 413 through 431 removed outlier: 3.667A pdb=" N ILE O 418 " --> pdb=" O ALA O 414 " (cutoff:3.500A) Processing helix chain 'O' and resid 435 through 456 removed outlier: 3.625A pdb=" N ILE O 439 " --> pdb=" O SER O 435 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE O 441 " --> pdb=" O THR O 437 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL O 442 " --> pdb=" O GLN O 438 " (cutoff:3.500A) Processing helix chain 'O' and resid 466 through 469 Processing helix chain 'O' and resid 470 through 488 Processing helix chain 'O' and resid 489 through 491 No H-bonds generated for 'chain 'O' and resid 489 through 491' Processing helix chain 'O' and resid 501 through 511 removed outlier: 3.876A pdb=" N GLN O 507 " --> pdb=" O ASP O 503 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG O 508 " --> pdb=" O LYS O 504 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET O 509 " --> pdb=" O PHE O 505 " (cutoff:3.500A) Processing helix chain 'O' and resid 515 through 520 removed outlier: 3.863A pdb=" N PHE O 519 " --> pdb=" O ASN O 515 " (cutoff:3.500A) Processing helix chain 'O' and resid 523 through 535 Processing helix chain 'O' and resid 540 through 551 Processing helix chain 'O' and resid 581 through 589 removed outlier: 3.773A pdb=" N PHE O 585 " --> pdb=" O THR O 581 " (cutoff:3.500A) Processing helix chain 'O' and resid 599 through 607 removed outlier: 3.520A pdb=" N ILE O 604 " --> pdb=" O LYS O 600 " (cutoff:3.500A) Processing helix chain 'O' and resid 608 through 610 No H-bonds generated for 'chain 'O' and resid 608 through 610' Processing sheet with id= AA, first strand: chain 'A' and resid 1631 through 1632 removed outlier: 5.329A pdb=" N ILE A 11 " --> pdb=" O GLU B1201 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLU B1201 " --> pdb=" O ILE A 11 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER A 13 " --> pdb=" O ASN B1199 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'A' and resid 77 through 86 removed outlier: 10.687A pdb=" N LEU A 81 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 10.957A pdb=" N VAL A 361 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 9.776A pdb=" N VAL A 83 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL A 359 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'A' and resid 242 through 245 Processing sheet with id= AD, first strand: chain 'A' and resid 371 through 373 Processing sheet with id= AE, first strand: chain 'A' and resid 480 through 486 Processing sheet with id= AF, first strand: chain 'A' and resid 507 through 510 removed outlier: 3.818A pdb=" N TYR A 507 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG A 579 " --> pdb=" O TYR A 507 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LYS A 576 " --> pdb=" O ILE A 536 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE A 536 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TYR A 578 " --> pdb=" O THR A 534 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'A' and resid 686 through 688 Processing sheet with id= AH, first strand: chain 'A' and resid 719 through 721 removed outlier: 5.172A pdb=" N ILE A 719 " --> pdb=" O TYR H 98 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N TYR H 98 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'A' and resid 749 through 752 removed outlier: 6.532A pdb=" N LEU A 770 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'A' and resid 948 through 949 Processing sheet with id= AK, first strand: chain 'A' and resid 1031 through 1032 removed outlier: 6.638A pdb=" N ILE A1038 " --> pdb=" O VAL A1046 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'A' and resid 1507 through 1508 Processing sheet with id= AM, first strand: chain 'A' and resid 1457 through 1462 removed outlier: 5.527A pdb=" N ILE A1457 " --> pdb=" O GLU A1475 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N GLU A1475 " --> pdb=" O ILE A1457 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A1459 " --> pdb=" O LYS A1473 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER A1289 " --> pdb=" O GLU A1274 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU A1274 " --> pdb=" O SER A1289 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL A1291 " --> pdb=" O VAL A1272 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL A1272 " --> pdb=" O VAL A1291 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N HIS A1293 " --> pdb=" O VAL A1270 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL A1270 " --> pdb=" O HIS A1293 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ARG A1295 " --> pdb=" O ASP A1268 " (cutoff:3.500A) Processing sheet with id= FA, first strand: chain 'F' and resid 143 through 147 Processing sheet with id= BA, first strand: chain 'B' and resid 70 through 74 removed outlier: 5.552A pdb=" N VAL B 97 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N SER B 144 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N VAL B 99 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LYS B 142 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN B 101 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N GLY B 135 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY B 160 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LEU B 137 " --> pdb=" O CYS B 158 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'B' and resid 108 through 109 Processing sheet with id= BC, first strand: chain 'B' and resid 194 through 196 removed outlier: 3.514A pdb=" N LEU B 202 " --> pdb=" O VAL B 486 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 486 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'B' and resid 214 through 218 removed outlier: 5.165A pdb=" N TYR B 232 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR B 247 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER B 263 " --> pdb=" O THR B 247 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'B' and resid 502 through 503 Processing sheet with id= BF, first strand: chain 'B' and resid 550 through 551 Processing sheet with id= BG, first strand: chain 'B' and resid 660 through 664 removed outlier: 3.558A pdb=" N LYS B 660 " --> pdb=" O TYR B 655 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'B' and resid 674 through 675 removed outlier: 3.558A pdb=" N LYS B 660 " --> pdb=" O TYR B 655 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'B' and resid 674 through 675 Processing sheet with id= BJ, first strand: chain 'B' and resid 571 through 572 removed outlier: 5.469A pdb=" N ILE B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE B 588 " --> pdb=" O ILE B 592 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'B' and resid 740 through 744 removed outlier: 7.575A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'B' and resid 740 through 744 removed outlier: 7.575A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'B' and resid 752 through 753 Processing sheet with id= BN, first strand: chain 'B' and resid 769 through 775 removed outlier: 4.418A pdb=" N TYR B1027 " --> pdb=" O VAL B 775 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1010 through 1011 current: chain 'B' and resid 924 through 931 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 916 through 919 current: chain 'B' and resid 947 through 949 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 947 through 949 current: chain 'B' and resid 769 through 775 Processing sheet with id= BO, first strand: chain 'B' and resid 823 through 825 removed outlier: 3.535A pdb=" N LYS B 868 " --> pdb=" O ASP B 863 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'B' and resid 938 through 939 Processing sheet with id= BQ, first strand: chain 'B' and resid 1099 through 1104 removed outlier: 3.962A pdb=" N THR B1099 " --> pdb=" O ILE B1178 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE B1178 " --> pdb=" O THR B1099 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'B' and resid 1113 through 1115 Processing sheet with id= BS, first strand: chain 'B' and resid 1133 through 1134 Processing sheet with id= CA, first strand: chain 'C' and resid 41 through 46 removed outlier: 5.716A pdb=" N VAL C 42 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE C 57 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE C 44 " --> pdb=" O ASP C 55 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP C 55 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N ARG C 293 " --> pdb=" O ASN C 234 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N ASN C 234 " --> pdb=" O ARG C 293 " (cutoff:3.500A) removed outlier: 9.731A pdb=" N ARG C 295 " --> pdb=" O GLN C 232 " (cutoff:3.500A) removed outlier: 10.284A pdb=" N GLN C 232 " --> pdb=" O ARG C 295 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N HIS C 297 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR C 224 " --> pdb=" O GLU C 303 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.239A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU C 201 " --> pdb=" O ASN C 87 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ASN C 87 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N SER C 203 " --> pdb=" O PHE C 85 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N PHE C 85 " --> pdb=" O SER C 203 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LYS C 205 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL C 83 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N HIS C 207 " --> pdb=" O GLU C 81 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE C 209 " --> pdb=" O ALA C 79 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'C' and resid 106 through 107 removed outlier: 4.453A pdb=" N VAL C 185 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'C' and resid 141 through 142 Processing sheet with id= CE, first strand: chain 'C' and resid 161 through 163 removed outlier: 6.778A pdb=" N VAL C 162 " --> pdb=" O LEU C 193 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'C' and resid 256 through 258 Processing sheet with id= DA, first strand: chain 'D' and resid 21 through 24 removed outlier: 4.013A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) Processing sheet with id= DB, first strand: chain 'D' and resid 29 through 30 Processing sheet with id= GA, first strand: chain 'G' and resid 73 through 74 removed outlier: 3.777A pdb=" N GLY G 79 " --> pdb=" O ASN G 74 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU G 82 " --> pdb=" O TRP G 125 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N TRP G 125 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N TYR G 84 " --> pdb=" O TYR G 123 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N TYR G 123 " --> pdb=" O TYR G 84 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLY G 86 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASN G 121 " --> pdb=" O GLY G 86 " (cutoff:3.500A) Processing sheet with id= GB, first strand: chain 'G' and resid 73 through 74 removed outlier: 3.777A pdb=" N GLY G 79 " --> pdb=" O ASN G 74 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU G 82 " --> pdb=" O TRP G 125 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N TRP G 125 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N TYR G 84 " --> pdb=" O TYR G 123 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N TYR G 123 " --> pdb=" O TYR G 84 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLY G 86 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASN G 121 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) Processing sheet with id= EA, first strand: chain 'E' and resid 60 through 62 Processing sheet with id= EB, first strand: chain 'E' and resid 87 through 88 Processing sheet with id= EC, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.881A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id= GC, first strand: chain 'G' and resid 132 through 140 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 228 through 237 current: chain 'G' and resid 153 through 158 Processing sheet with id= GD, first strand: chain 'G' and resid 167 through 169 Processing sheet with id= IA, first strand: chain 'I' and resid 3 through 4 removed outlier: 3.663A pdb=" N LEU I 7 " --> pdb=" O VAL I 4 " (cutoff:3.500A) Processing sheet with id= IB, first strand: chain 'I' and resid 27 through 29 Processing sheet with id= IC, first strand: chain 'I' and resid 82 through 83 Processing sheet with id= KA, first strand: chain 'K' and resid 47 through 49 removed outlier: 6.554A pdb=" N ASN K 102 " --> pdb=" O TYR K 91 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TYR K 91 " --> pdb=" O ASN K 102 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ARG K 104 " --> pdb=" O CYS K 89 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N CYS K 89 " --> pdb=" O ARG K 104 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLN K 106 " --> pdb=" O GLU K 87 " (cutoff:3.500A) Processing sheet with id= MA, first strand: chain 'M' and resid 11 through 16 removed outlier: 7.338A pdb=" N LEU M 90 " --> pdb=" O GLU M 13 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL M 15 " --> pdb=" O LEU M 90 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS M 92 " --> pdb=" O VAL M 15 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER M 87 " --> pdb=" O ASN M 82 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS N 135 " --> pdb=" O VAL N 53 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N GLU N 141 " --> pdb=" O PRO N 59 " (cutoff:3.500A) Processing sheet with id= MB, first strand: chain 'M' and resid 22 through 25 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 107 through 112 current: chain 'M' and resid 48 through 56 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 48 through 56 current: chain 'M' and resid 37 through 45 1642 hydrogen bonds defined for protein. 4545 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 18.04 Time building geometry restraints manager: 16.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 12247 1.35 - 1.50: 10418 1.50 - 1.65: 15118 1.65 - 1.80: 178 1.80 - 1.95: 122 Bond restraints: 38083 Sorted by residual: bond pdb=" C PHE O 198 " pdb=" N PRO O 199 " ideal model delta sigma weight residual 1.331 1.202 0.129 1.31e-02 5.83e+03 9.64e+01 bond pdb=" C LEU A1622 " pdb=" N THR A1623 " ideal model delta sigma weight residual 1.335 1.253 0.082 1.31e-02 5.83e+03 3.89e+01 bond pdb=" CA THR O 212 " pdb=" CB THR O 212 " ideal model delta sigma weight residual 1.532 1.618 -0.086 1.57e-02 4.06e+03 3.03e+01 bond pdb=" C LEU O 128 " pdb=" N PRO O 129 " ideal model delta sigma weight residual 1.329 1.389 -0.059 1.18e-02 7.18e+03 2.53e+01 bond pdb=" CA LEU D 99 " pdb=" C LEU D 99 " ideal model delta sigma weight residual 1.524 1.585 -0.061 1.26e-02 6.30e+03 2.37e+01 ... (remaining 38078 not shown) Histogram of bond angle deviations from ideal: 90.91 - 100.56: 49 100.56 - 110.21: 8329 110.21 - 119.86: 24843 119.86 - 129.51: 17989 129.51 - 139.16: 241 Bond angle restraints: 51451 Sorted by residual: angle pdb=" N GLU O 460 " pdb=" CA GLU O 460 " pdb=" C GLU O 460 " ideal model delta sigma weight residual 112.89 90.91 21.98 1.24e+00 6.50e-01 3.14e+02 angle pdb=" N PHE O 598 " pdb=" CA PHE O 598 " pdb=" C PHE O 598 " ideal model delta sigma weight residual 111.14 129.62 -18.48 1.08e+00 8.57e-01 2.93e+02 angle pdb=" N LEU A 413 " pdb=" CA LEU A 413 " pdb=" C LEU A 413 " ideal model delta sigma weight residual 112.54 99.33 13.21 1.22e+00 6.72e-01 1.17e+02 angle pdb=" CA LEU A1622 " pdb=" C LEU A1622 " pdb=" N THR A1623 " ideal model delta sigma weight residual 117.39 106.69 10.70 1.24e+00 6.50e-01 7.45e+01 angle pdb=" C SER G 35 " pdb=" N ASN G 36 " pdb=" CA ASN G 36 " ideal model delta sigma weight residual 122.77 111.29 11.48 1.33e+00 5.65e-01 7.44e+01 ... (remaining 51446 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.17: 20563 18.17 - 36.35: 1840 36.35 - 54.52: 608 54.52 - 72.69: 152 72.69 - 90.86: 51 Dihedral angle restraints: 23214 sinusoidal: 9543 harmonic: 13671 Sorted by residual: dihedral pdb=" CA THR O 375 " pdb=" C THR O 375 " pdb=" N TYR O 376 " pdb=" CA TYR O 376 " ideal model delta harmonic sigma weight residual -180.00 -126.97 -53.03 0 5.00e+00 4.00e-02 1.13e+02 dihedral pdb=" CA LEU O 599 " pdb=" C LEU O 599 " pdb=" N LYS O 600 " pdb=" CA LYS O 600 " ideal model delta harmonic sigma weight residual 180.00 -129.58 -50.42 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" CA PHE O 598 " pdb=" C PHE O 598 " pdb=" N LEU O 599 " pdb=" CA LEU O 599 " ideal model delta harmonic sigma weight residual -180.00 -130.86 -49.14 0 5.00e+00 4.00e-02 9.66e+01 ... (remaining 23211 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.162: 5344 0.162 - 0.323: 367 0.323 - 0.485: 33 0.485 - 0.646: 1 0.646 - 0.808: 2 Chirality restraints: 5747 Sorted by residual: chirality pdb=" CA THR C 224 " pdb=" N THR C 224 " pdb=" C THR C 224 " pdb=" CB THR C 224 " both_signs ideal model delta sigma weight residual False 2.53 1.72 0.81 2.00e-01 2.50e+01 1.63e+01 chirality pdb=" CG LEU O 180 " pdb=" CB LEU O 180 " pdb=" CD1 LEU O 180 " pdb=" CD2 LEU O 180 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" CA PHE O 598 " pdb=" N PHE O 598 " pdb=" C PHE O 598 " pdb=" CB PHE O 598 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.16e+00 ... (remaining 5744 not shown) Planarity restraints: 6629 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 553 " 0.023 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C THR B 553 " -0.079 2.00e-02 2.50e+03 pdb=" O THR B 553 " 0.030 2.00e-02 2.50e+03 pdb=" N GLN B 554 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU O 345 " 0.020 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C GLU O 345 " -0.073 2.00e-02 2.50e+03 pdb=" O GLU O 345 " 0.028 2.00e-02 2.50e+03 pdb=" N GLN O 346 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU O 458 " 0.019 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C GLU O 458 " -0.072 2.00e-02 2.50e+03 pdb=" O GLU O 458 " 0.029 2.00e-02 2.50e+03 pdb=" N GLU O 459 " 0.024 2.00e-02 2.50e+03 ... (remaining 6626 not shown) Histogram of nonbonded interaction distances: 0.68 - 1.52: 17 1.52 - 2.37: 215 2.37 - 3.21: 36171 3.21 - 4.06: 96224 4.06 - 4.90: 175748 Warning: very small nonbonded interaction distances. Nonbonded interactions: 308375 Sorted by model distance: nonbonded pdb=" NZ LYS G 158 " pdb=" OE2 GLU O 108 " model vdw 0.675 2.520 nonbonded pdb=" CE LYS G 158 " pdb=" OE2 GLU O 108 " model vdw 0.833 3.440 nonbonded pdb=" NZ LYS G 158 " pdb=" CD GLU O 108 " model vdw 0.836 3.350 nonbonded pdb=" OD2 ASP O 191 " pdb=" NE2 GLN O 228 " model vdw 0.893 2.520 nonbonded pdb=" OD2 ASP A1655 " pdb=" OH TYR F 137 " model vdw 1.076 2.440 ... (remaining 308370 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 7 6.06 5 S 191 5.16 5 C 23697 2.51 5 N 6428 2.21 5 O 7026 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 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: 0.760 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: 0.030 Extract box with map and model: 7.030 Check model and map are aligned: 0.550 Convert atoms to be neutral: 0.320 Process input model: 105.070 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 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 0.140 38083 Z= 0.631 Angle : 1.377 21.982 51451 Z= 0.917 Chirality : 0.087 0.808 5747 Planarity : 0.005 0.066 6629 Dihedral : 16.599 90.865 14370 Min Nonbonded Distance : 0.675 Molprobity Statistics. All-atom Clashscore : 31.29 Ramachandran Plot: Outliers : 1.78 % Allowed : 6.00 % Favored : 92.23 % Rotamer Outliers : 7.76 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.38 (0.11), residues: 4618 helix: -1.88 (0.10), residues: 1646 sheet: -0.61 (0.20), residues: 623 loop : -1.56 (0.12), residues: 2349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1537 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 324 poor density : 1213 time to evaluate : 5.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 324 outliers final: 45 residues processed: 1451 average time/residue: 0.5452 time to fit residues: 1275.1005 Evaluate side-chains 690 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 645 time to evaluate : 4.487 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 2 residues processed: 45 average time/residue: 0.4283 time to fit residues: 38.4309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 390 optimal weight: 10.0000 chunk 350 optimal weight: 6.9990 chunk 194 optimal weight: 8.9990 chunk 119 optimal weight: 6.9990 chunk 236 optimal weight: 6.9990 chunk 187 optimal weight: 3.9990 chunk 362 optimal weight: 9.9990 chunk 140 optimal weight: 2.9990 chunk 220 optimal weight: 9.9990 chunk 270 optimal weight: 1.9990 chunk 420 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN A 60 ASN A 76 GLN A 378 HIS A 432 ASN A 489 ASN A 639 GLN A 691 GLN A 863 ASN A 926 GLN A1072 ASN A1453 HIS A1567 ASN A1581 HIS A1629 ASN B 209 GLN B 254 ASN B 328 GLN B 504 HIS ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 ASN ** B 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 829 ASN B 912 GLN B1008 HIS ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 HIS H 33 GLN ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 HIS K 70 HIS L 53 HIS ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 HIS N 41 ASN N 52 GLN ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 131 HIS O 173 HIS O 390 GLN O 521 ASN O 547 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 38083 Z= 0.298 Angle : 0.764 14.442 51451 Z= 0.404 Chirality : 0.048 0.246 5747 Planarity : 0.006 0.051 6629 Dihedral : 5.633 35.112 5076 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.44 % Favored : 96.38 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 (0.12), residues: 4618 helix: 0.23 (0.12), residues: 1701 sheet: -0.44 (0.20), residues: 623 loop : -0.56 (0.13), residues: 2294 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 793 time to evaluate : 4.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 0 residues processed: 798 average time/residue: 0.4933 time to fit residues: 648.8309 Evaluate side-chains 506 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 506 time to evaluate : 4.812 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.0355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 233 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 chunk 349 optimal weight: 40.0000 chunk 286 optimal weight: 0.1980 chunk 115 optimal weight: 10.0000 chunk 421 optimal weight: 30.0000 chunk 455 optimal weight: 4.9990 chunk 375 optimal weight: 10.0000 chunk 417 optimal weight: 20.0000 chunk 143 optimal weight: 1.9990 chunk 337 optimal weight: 10.0000 overall best weight: 4.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 ASN ** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 887 ASN B 45 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN B 427 GLN ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 ASN B1038 HIS ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 HIS ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 HIS ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 GLN O 131 HIS ** O 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.5494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 38083 Z= 0.302 Angle : 0.714 14.382 51451 Z= 0.374 Chirality : 0.045 0.188 5747 Planarity : 0.005 0.060 6629 Dihedral : 5.316 27.536 5076 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.83 % Favored : 96.04 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.02 % 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 (0.12), residues: 4618 helix: 0.79 (0.12), residues: 1705 sheet: -0.34 (0.19), residues: 635 loop : -0.27 (0.13), residues: 2278 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 632 time to evaluate : 4.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 635 average time/residue: 0.4812 time to fit residues: 506.5558 Evaluate side-chains 407 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 405 time to evaluate : 4.778 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3169 time to fit residues: 7.5145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 416 optimal weight: 20.0000 chunk 316 optimal weight: 9.9990 chunk 218 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 201 optimal weight: 9.9990 chunk 282 optimal weight: 7.9990 chunk 422 optimal weight: 20.0000 chunk 447 optimal weight: 9.9990 chunk 220 optimal weight: 10.0000 chunk 400 optimal weight: 30.0000 chunk 120 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 HIS A1532 GLN A1564 ASN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 ASN B 724 GLN ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1114 GLN B1157 GLN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 GLN ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 ASN O 94 ASN ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 362 ASN ** O 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.6688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.088 38083 Z= 0.431 Angle : 0.844 15.428 51451 Z= 0.442 Chirality : 0.047 0.212 5747 Planarity : 0.006 0.099 6629 Dihedral : 5.719 30.685 5076 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 26.24 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.24 % Favored : 95.60 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.32 (0.12), residues: 4618 helix: 0.40 (0.12), residues: 1708 sheet: -0.48 (0.19), residues: 632 loop : -0.51 (0.13), residues: 2278 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 510 time to evaluate : 5.097 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 outliers start: 5 outliers final: 2 residues processed: 515 average time/residue: 0.5041 time to fit residues: 435.1681 Evaluate side-chains 349 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 347 time to evaluate : 4.836 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3469 time to fit residues: 7.8814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 372 optimal weight: 10.0000 chunk 254 optimal weight: 1.9990 chunk 6 optimal weight: 20.0000 chunk 333 optimal weight: 9.9990 chunk 184 optimal weight: 4.9990 chunk 381 optimal weight: 1.9990 chunk 309 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 228 optimal weight: 10.0000 chunk 401 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1008 HIS ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 HIS ** K 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 ASN N 52 GLN N 170 HIS ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 131 HIS ** O 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 451 ASN O 533 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.6791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 38083 Z= 0.203 Angle : 0.637 11.678 51451 Z= 0.330 Chirality : 0.044 0.249 5747 Planarity : 0.004 0.059 6629 Dihedral : 5.144 25.744 5076 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.42 % Favored : 96.45 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.02 % 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: 0.22 (0.12), residues: 4618 helix: 1.03 (0.12), residues: 1710 sheet: -0.42 (0.19), residues: 674 loop : -0.27 (0.13), residues: 2234 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 551 time to evaluate : 5.057 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 outliers start: 1 outliers final: 0 residues processed: 552 average time/residue: 0.4863 time to fit residues: 451.8849 Evaluate side-chains 376 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 376 time to evaluate : 4.798 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.3564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 150 optimal weight: 10.0000 chunk 403 optimal weight: 30.0000 chunk 88 optimal weight: 0.0270 chunk 262 optimal weight: 20.0000 chunk 110 optimal weight: 6.9990 chunk 447 optimal weight: 20.0000 chunk 371 optimal weight: 20.0000 chunk 207 optimal weight: 7.9990 chunk 37 optimal weight: 30.0000 chunk 148 optimal weight: 10.0000 chunk 235 optimal weight: 9.9990 overall best weight: 7.0048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 HIS ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1180 ASN B 171 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1089 GLN B1094 ASN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN F 61 HIS ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 ASN N 52 GLN O 70 GLN ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 GLN O 131 HIS ** O 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 392 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.7368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.084 38083 Z= 0.367 Angle : 0.743 11.767 51451 Z= 0.389 Chirality : 0.045 0.322 5747 Planarity : 0.005 0.058 6629 Dihedral : 5.413 28.059 5076 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 24.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.48 % Favored : 95.43 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.02 % 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: -0.12 (0.12), residues: 4618 helix: 0.71 (0.12), residues: 1711 sheet: -0.45 (0.19), residues: 647 loop : -0.49 (0.13), residues: 2260 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 471 time to evaluate : 4.745 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 outliers start: 1 outliers final: 0 residues processed: 472 average time/residue: 0.4940 time to fit residues: 391.5935 Evaluate side-chains 344 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 344 time to evaluate : 4.900 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.4927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 431 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 255 optimal weight: 6.9990 chunk 327 optimal weight: 5.9990 chunk 253 optimal weight: 10.0000 chunk 377 optimal weight: 3.9990 chunk 250 optimal weight: 20.0000 chunk 446 optimal weight: 6.9990 chunk 279 optimal weight: 0.1980 chunk 272 optimal weight: 2.9990 chunk 206 optimal weight: 0.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 GLN A 435 ASN A 590 ASN ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 HIS ** K 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 ASN N 52 GLN N 170 HIS O 94 ASN ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 131 HIS ** O 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 387 HIS ** O 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.7416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 38083 Z= 0.186 Angle : 0.626 11.224 51451 Z= 0.323 Chirality : 0.044 0.222 5747 Planarity : 0.004 0.076 6629 Dihedral : 5.017 29.997 5076 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.40 % Favored : 96.51 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.02 % 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: 0.22 (0.12), residues: 4618 helix: 1.06 (0.12), residues: 1722 sheet: -0.33 (0.20), residues: 637 loop : -0.34 (0.13), residues: 2259 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 521 time to evaluate : 5.447 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 outliers start: 0 outliers final: 0 residues processed: 521 average time/residue: 0.5186 time to fit residues: 459.3237 Evaluate side-chains 354 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 354 time to evaluate : 5.289 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.7661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 276 optimal weight: 8.9990 chunk 178 optimal weight: 6.9990 chunk 266 optimal weight: 8.9990 chunk 134 optimal weight: 8.9990 chunk 87 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 283 optimal weight: 3.9990 chunk 304 optimal weight: 6.9990 chunk 220 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 chunk 350 optimal weight: 10.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1089 GLN C 172 GLN C 237 GLN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 HIS ** K 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 170 HIS ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.7662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 38083 Z= 0.245 Angle : 0.650 10.916 51451 Z= 0.338 Chirality : 0.044 0.405 5747 Planarity : 0.004 0.059 6629 Dihedral : 5.050 29.453 5076 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.01 % Favored : 95.93 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.02 % 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 (0.12), residues: 4618 helix: 1.01 (0.12), residues: 1723 sheet: -0.38 (0.20), residues: 652 loop : -0.40 (0.13), residues: 2243 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 483 time to evaluate : 5.232 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 outliers start: 1 outliers final: 0 residues processed: 484 average time/residue: 0.5005 time to fit residues: 410.3298 Evaluate side-chains 339 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 5.073 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.7570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 405 optimal weight: 3.9990 chunk 427 optimal weight: 6.9990 chunk 390 optimal weight: 0.0370 chunk 415 optimal weight: 7.9990 chunk 250 optimal weight: 8.9990 chunk 181 optimal weight: 20.0000 chunk 326 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 375 optimal weight: 0.3980 chunk 393 optimal weight: 30.0000 chunk 414 optimal weight: 8.9990 overall best weight: 3.8864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 GLN N 170 HIS ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 131 HIS ** O 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.7876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 38083 Z= 0.235 Angle : 0.638 9.807 51451 Z= 0.333 Chirality : 0.044 0.267 5747 Planarity : 0.004 0.055 6629 Dihedral : 5.017 30.247 5076 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.22 % Favored : 95.71 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.02 % 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: 0.15 (0.12), residues: 4618 helix: 1.04 (0.12), residues: 1720 sheet: -0.41 (0.20), residues: 642 loop : -0.40 (0.13), residues: 2256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 481 time to evaluate : 4.802 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 outliers start: 0 outliers final: 0 residues processed: 481 average time/residue: 0.5069 time to fit residues: 410.7212 Evaluate side-chains 340 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 340 time to evaluate : 5.007 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.0739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 273 optimal weight: 0.0020 chunk 439 optimal weight: 0.1980 chunk 268 optimal weight: 4.9990 chunk 208 optimal weight: 7.9990 chunk 305 optimal weight: 4.9990 chunk 461 optimal weight: 0.5980 chunk 424 optimal weight: 0.9990 chunk 367 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 283 optimal weight: 1.9990 chunk 225 optimal weight: 10.0000 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 HIS ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 GLN ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1082 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 170 HIS ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 131 HIS ** O 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 589 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.7917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 38083 Z= 0.167 Angle : 0.636 10.044 51451 Z= 0.326 Chirality : 0.045 0.255 5747 Planarity : 0.004 0.063 6629 Dihedral : 4.787 28.806 5076 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.59 % Favored : 96.34 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.02 % 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 (0.12), residues: 4618 helix: 1.17 (0.13), residues: 1705 sheet: -0.29 (0.20), residues: 657 loop : -0.31 (0.14), residues: 2256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 507 time to evaluate : 4.887 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 outliers start: 0 outliers final: 0 residues processed: 507 average time/residue: 0.4825 time to fit residues: 422.2907 Evaluate side-chains 358 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 358 time to evaluate : 4.950 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.5513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 291 optimal weight: 8.9990 chunk 391 optimal weight: 8.9990 chunk 112 optimal weight: 0.0010 chunk 338 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 102 optimal weight: 0.9980 chunk 367 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 chunk 377 optimal weight: 0.0370 chunk 46 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 overall best weight: 2.6068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1082 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 ASN C 237 GLN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 170 HIS ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 131 HIS ** O 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.048833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.036031 restraints weight = 262895.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.037345 restraints weight = 167016.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.038307 restraints weight = 120682.113| |-----------------------------------------------------------------------------| r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.8083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 38083 Z= 0.198 Angle : 0.624 9.454 51451 Z= 0.322 Chirality : 0.044 0.249 5747 Planarity : 0.004 0.059 6629 Dihedral : 4.772 27.802 5076 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.16 % Favored : 95.78 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.12), residues: 4618 helix: 1.24 (0.13), residues: 1698 sheet: -0.32 (0.19), residues: 662 loop : -0.33 (0.13), residues: 2258 =============================================================================== Job complete usr+sys time: 8846.37 seconds wall clock time: 161 minutes 39.78 seconds (9699.78 seconds total)