Starting phenix.real_space_refine on Sat Mar 23 14:42:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g5l_3439/03_2024/5g5l_3439_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g5l_3439/03_2024/5g5l_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_3439/03_2024/5g5l_3439.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g5l_3439/03_2024/5g5l_3439.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g5l_3439/03_2024/5g5l_3439_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g5l_3439/03_2024/5g5l_3439_neut.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 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. 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-5265/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: {'PCIS': 5, 'PTRANS': 56, 'TRANS': 1418} 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: {'PCIS': 1, 'PTRANS': 58, 'TRANS': 1114} 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: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 199} 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: {'CIS': 1, 'PTRANS': 11, '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: 18.83, per 1000 atoms: 0.50 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: 13.55 Conformation dependent library (CDL) restraints added in 6.3 seconds Dynamic metal 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: 4.63 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: 17.30 Time building geometry restraints manager: 14.72 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 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: 0.740 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 5.530 Check model and map are aligned: 0.600 Set scattering table: 0.370 Process input model: 103.120 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 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= 0.918 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 : 31.05 Ramachandran Plot: Outliers : 1.78 % Allowed : 6.00 % Favored : 92.23 % Rotamer: Outliers : 7.76 % Allowed : 9.46 % Favored : 82.77 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 143 HIS 0.010 0.002 HIS A 43 PHE 0.029 0.003 PHE B1180 TYR 0.040 0.004 TYR A 995 ARG 0.012 0.001 ARG A 422 *********************** 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 : 4.171 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 REVERT: A 15 ASP cc_start: 0.7198 (m-30) cc_final: 0.6887 (m-30) REVERT: A 124 LEU cc_start: 0.9586 (mt) cc_final: 0.9321 (mt) REVERT: A 215 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7699 (mm-30) REVERT: A 227 LEU cc_start: 0.8587 (mt) cc_final: 0.8302 (mt) REVERT: A 315 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8438 (mm) REVERT: A 328 PHE cc_start: 0.8188 (m-80) cc_final: 0.7980 (m-80) REVERT: A 354 SER cc_start: 0.9253 (m) cc_final: 0.9016 (p) REVERT: A 439 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.6949 (m-30) REVERT: A 466 LEU cc_start: 0.8778 (tp) cc_final: 0.8526 (tp) REVERT: A 483 VAL cc_start: 0.9528 (t) cc_final: 0.9230 (p) REVERT: A 582 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7816 (tptp) REVERT: A 617 HIS cc_start: 0.9294 (t-90) cc_final: 0.9023 (t-90) REVERT: A 625 ASN cc_start: 0.8415 (t0) cc_final: 0.8206 (t0) REVERT: A 633 MET cc_start: 0.8338 (mtp) cc_final: 0.4330 (mtp) REVERT: A 642 ASN cc_start: 0.8922 (m-40) cc_final: 0.8100 (m-40) REVERT: A 646 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8029 (mt-10) REVERT: A 675 SER cc_start: 0.9680 (m) cc_final: 0.9350 (p) REVERT: A 708 THR cc_start: 0.8196 (OUTLIER) cc_final: 0.7530 (t) REVERT: A 813 LEU cc_start: 0.9765 (mt) cc_final: 0.9553 (mt) REVERT: A 817 PHE cc_start: 0.9142 (m-80) cc_final: 0.8881 (m-80) REVERT: A 826 PHE cc_start: 0.7739 (t80) cc_final: 0.7504 (t80) REVERT: A 833 LEU cc_start: 0.9239 (mt) cc_final: 0.8687 (mt) REVERT: A 994 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7657 (mt-10) REVERT: A 995 TYR cc_start: 0.9070 (t80) cc_final: 0.8606 (t80) REVERT: A 1056 ASP cc_start: 0.8196 (t0) cc_final: 0.7318 (t0) REVERT: A 1059 LYS cc_start: 0.8231 (mttt) cc_final: 0.7545 (ttpp) REVERT: A 1136 VAL cc_start: 0.9381 (OUTLIER) cc_final: 0.9002 (m) REVERT: A 1170 MET cc_start: 0.9128 (mmm) cc_final: 0.8858 (mmm) REVERT: A 1226 VAL cc_start: 0.9539 (OUTLIER) cc_final: 0.9226 (p) REVERT: A 1291 VAL cc_start: 0.8322 (t) cc_final: 0.7730 (t) REVERT: A 1310 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7727 (ptmm) REVERT: A 1441 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8507 (tmtt) REVERT: A 1483 LEU cc_start: 0.9034 (mt) cc_final: 0.8318 (tp) REVERT: A 1508 VAL cc_start: 0.7478 (OUTLIER) cc_final: 0.7270 (p) REVERT: A 1518 VAL cc_start: 0.8729 (OUTLIER) cc_final: 0.8412 (m) REVERT: A 1575 ILE cc_start: 0.8897 (mt) cc_final: 0.8273 (mt) REVERT: A 1588 MET cc_start: 0.8252 (tpt) cc_final: 0.7807 (tpp) REVERT: A 1589 MET cc_start: 0.8321 (mtm) cc_final: 0.8001 (mtm) REVERT: A 1634 LEU cc_start: 0.9296 (mt) cc_final: 0.9076 (mt) REVERT: A 1635 ASP cc_start: 0.6869 (OUTLIER) cc_final: 0.6305 (p0) REVERT: B 172 LEU cc_start: 0.9058 (mt) cc_final: 0.8792 (mt) REVERT: B 258 VAL cc_start: 0.8624 (t) cc_final: 0.8328 (t) REVERT: B 296 ASP cc_start: 0.8283 (m-30) cc_final: 0.7963 (t0) REVERT: B 330 LEU cc_start: 0.9054 (mt) cc_final: 0.8321 (tt) REVERT: B 334 PHE cc_start: 0.8067 (m-80) cc_final: 0.7609 (m-80) REVERT: B 374 LEU cc_start: 0.9615 (tp) cc_final: 0.9410 (mt) REVERT: B 397 THR cc_start: 0.9265 (m) cc_final: 0.8744 (p) REVERT: B 457 ILE cc_start: 0.9518 (mt) cc_final: 0.8707 (tt) REVERT: B 465 LEU cc_start: 0.9671 (mt) cc_final: 0.9369 (mt) REVERT: B 493 PHE cc_start: 0.8243 (t80) cc_final: 0.8015 (t80) REVERT: B 495 ARG cc_start: 0.8899 (ttm-80) cc_final: 0.8315 (tpm170) REVERT: B 499 HIS cc_start: 0.8222 (m-70) cc_final: 0.6664 (m-70) REVERT: B 502 MET cc_start: 0.8254 (tmt) cc_final: 0.7423 (tpt) REVERT: B 528 LEU cc_start: 0.9357 (mt) cc_final: 0.9060 (tt) REVERT: B 542 LEU cc_start: 0.8815 (mt) cc_final: 0.8464 (mp) REVERT: B 561 ILE cc_start: 0.9730 (mm) cc_final: 0.9523 (mm) REVERT: B 622 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7995 (pt) REVERT: B 695 ASN cc_start: 0.9565 (m-40) cc_final: 0.8106 (m110) REVERT: B 700 LEU cc_start: 0.9516 (mp) cc_final: 0.9100 (tp) REVERT: B 706 PHE cc_start: 0.8781 (m-80) cc_final: 0.8530 (m-10) REVERT: B 744 LEU cc_start: 0.8291 (tp) cc_final: 0.8082 (tp) REVERT: B 770 ASN cc_start: 0.8361 (m-40) cc_final: 0.8039 (p0) REVERT: B 782 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.6994 (t0) REVERT: B 783 MET cc_start: 0.7625 (mtp) cc_final: 0.7146 (ttm) REVERT: B 845 LEU cc_start: 0.8830 (mt) cc_final: 0.8423 (mt) REVERT: B 898 LEU cc_start: 0.7607 (tp) cc_final: 0.6779 (tp) REVERT: B 983 PRO cc_start: 0.9246 (Cg_exo) cc_final: 0.8999 (Cg_endo) REVERT: B 1064 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7411 (tttt) REVERT: B 1074 MET cc_start: 0.8586 (mtm) cc_final: 0.7865 (mmt) REVERT: B 1084 THR cc_start: 0.8906 (p) cc_final: 0.8651 (t) REVERT: B 1087 LEU cc_start: 0.9722 (mt) cc_final: 0.9189 (mt) REVERT: B 1163 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7783 (mp10) REVERT: C 68 ARG cc_start: 0.7553 (ttt-90) cc_final: 0.7102 (ttt180) REVERT: C 82 TYR cc_start: 0.6985 (m-80) cc_final: 0.6498 (m-80) REVERT: C 94 ASP cc_start: 0.8257 (m-30) cc_final: 0.7829 (p0) REVERT: C 136 LEU cc_start: 0.9262 (tp) cc_final: 0.8988 (mp) REVERT: C 184 VAL cc_start: 0.7568 (t) cc_final: 0.7349 (t) REVERT: C 191 ILE cc_start: 0.9193 (mt) cc_final: 0.8135 (mm) REVERT: C 222 VAL cc_start: 0.9441 (OUTLIER) cc_final: 0.9189 (p) REVERT: C 282 TYR cc_start: 0.7260 (m-80) cc_final: 0.6921 (m-10) REVERT: C 298 PHE cc_start: 0.6982 (m-80) cc_final: 0.6623 (m-80) REVERT: C 302 VAL cc_start: 0.8603 (t) cc_final: 0.8302 (p) REVERT: C 308 MET cc_start: 0.6305 (mtm) cc_final: 0.6098 (mpp) REVERT: D 21 VAL cc_start: 0.8453 (p) cc_final: 0.7897 (t) REVERT: E 21 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8258 (mt-10) REVERT: E 58 MET cc_start: 0.8733 (mtp) cc_final: 0.8138 (mtp) REVERT: E 78 LEU cc_start: 0.9350 (tp) cc_final: 0.8921 (tp) REVERT: E 188 LEU cc_start: 0.9301 (mt) cc_final: 0.9100 (mt) REVERT: E 214 CYS cc_start: 0.6542 (t) cc_final: 0.6308 (t) REVERT: F 74 ILE cc_start: 0.9575 (mt) cc_final: 0.8764 (mm) REVERT: F 89 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8004 (mm-30) REVERT: F 92 ARG cc_start: 0.9349 (ttt180) cc_final: 0.8604 (ttp80) REVERT: F 120 ILE cc_start: 0.8868 (mt) cc_final: 0.8529 (mt) REVERT: F 129 LYS cc_start: 0.9021 (mmtm) cc_final: 0.8682 (mttt) REVERT: G 93 ASP cc_start: 0.7943 (t0) cc_final: 0.7445 (t0) REVERT: G 243 VAL cc_start: 0.7638 (OUTLIER) cc_final: 0.7398 (p) REVERT: H 10 PHE cc_start: 0.8779 (m-80) cc_final: 0.8403 (m-80) REVERT: H 39 THR cc_start: 0.9096 (OUTLIER) cc_final: 0.8277 (p) REVERT: H 59 ILE cc_start: 0.9231 (mt) cc_final: 0.8786 (tp) REVERT: H 112 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8509 (pt) REVERT: H 142 LEU cc_start: 0.9023 (tp) cc_final: 0.8612 (tp) REVERT: H 143 LEU cc_start: 0.9045 (mp) cc_final: 0.8175 (mp) REVERT: I 15 ASP cc_start: 0.6638 (OUTLIER) cc_final: 0.6437 (m-30) REVERT: I 16 LEU cc_start: 0.8032 (tp) cc_final: 0.7419 (tp) REVERT: I 56 PHE cc_start: 0.8727 (m-80) cc_final: 0.8329 (m-10) REVERT: I 66 VAL cc_start: 0.8100 (m) cc_final: 0.7807 (p) REVERT: I 69 THR cc_start: 0.7268 (p) cc_final: 0.6372 (p) REVERT: I 94 MET cc_start: 0.7574 (mtp) cc_final: 0.7331 (ttp) REVERT: I 110 VAL cc_start: 0.6666 (t) cc_final: 0.6341 (m) REVERT: I 123 THR cc_start: 0.6724 (m) cc_final: 0.5836 (m) REVERT: I 124 ASN cc_start: 0.5386 (t0) cc_final: 0.4618 (t0) REVERT: J 21 TYR cc_start: 0.9131 (t80) cc_final: 0.8842 (t80) REVERT: J 24 LEU cc_start: 0.9471 (mt) cc_final: 0.9265 (mt) REVERT: J 56 LEU cc_start: 0.9290 (tp) cc_final: 0.8757 (tp) REVERT: J 57 ILE cc_start: 0.9405 (tt) cc_final: 0.8796 (tp) REVERT: J 59 LYS cc_start: 0.9231 (mtpt) cc_final: 0.8997 (ttmt) REVERT: K 57 ASP cc_start: 0.8916 (p0) cc_final: 0.8300 (p0) REVERT: K 85 ASP cc_start: 0.8037 (t70) cc_final: 0.6875 (t0) REVERT: K 105 ILE cc_start: 0.9333 (mt) cc_final: 0.8472 (mm) REVERT: K 128 CYS cc_start: 0.9009 (m) cc_final: 0.8620 (m) REVERT: L 41 SER cc_start: 0.7722 (OUTLIER) cc_final: 0.7266 (p) REVERT: L 67 PHE cc_start: 0.7510 (m-80) cc_final: 0.7022 (m-80) REVERT: M 60 LEU cc_start: 0.9213 (mt) cc_final: 0.8616 (mp) REVERT: M 90 LEU cc_start: 0.9020 (mt) cc_final: 0.8776 (mt) REVERT: M 91 TYR cc_start: 0.7504 (m-80) cc_final: 0.6942 (m-80) REVERT: M 98 SER cc_start: 0.8374 (OUTLIER) cc_final: 0.8037 (p) REVERT: M 100 VAL cc_start: 0.7653 (t) cc_final: 0.7220 (m) REVERT: N 58 PHE cc_start: 0.8712 (m-80) cc_final: 0.8380 (m-10) REVERT: N 111 VAL cc_start: 0.6477 (m) cc_final: 0.6146 (m) REVERT: N 136 VAL cc_start: 0.8625 (t) cc_final: 0.7574 (t) REVERT: O 194 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9207 (tp) REVERT: O 242 VAL cc_start: 0.9121 (t) cc_final: 0.8569 (t) REVERT: O 248 LEU cc_start: 0.4114 (OUTLIER) cc_final: 0.3856 (mm) REVERT: O 424 LEU cc_start: 0.9616 (tp) cc_final: 0.9379 (mt) REVERT: O 454 VAL cc_start: 0.7285 (OUTLIER) cc_final: 0.6881 (p) REVERT: O 509 MET cc_start: 0.6414 (mmm) cc_final: 0.5924 (mmm) outliers start: 324 outliers final: 45 residues processed: 1451 average time/residue: 0.5114 time to fit residues: 1173.4283 Evaluate side-chains 749 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 679 time to evaluate : 4.347 ------------------------------------------------------------------------------- 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: 8.9990 chunk 350 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 119 optimal weight: 8.9990 chunk 236 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 362 optimal weight: 7.9990 chunk 140 optimal weight: 0.9990 chunk 220 optimal weight: 9.9990 chunk 270 optimal weight: 6.9990 chunk 420 optimal weight: 0.6980 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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 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 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 829 ASN B 912 GLN B1008 HIS ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1082 HIS ** 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 59 GLN ** 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: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 38083 Z= 0.294 Angle : 0.753 14.034 51451 Z= 0.399 Chirality : 0.047 0.235 5747 Planarity : 0.006 0.069 6629 Dihedral : 5.621 34.648 5076 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.49 % Favored : 96.34 % Rotamer: Outliers : 0.14 % Allowed : 3.45 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.25 (0.12), residues: 1699 sheet: -0.49 (0.19), residues: 629 loop : -0.56 (0.13), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 836 HIS 0.017 0.002 HIS C 161 PHE 0.030 0.002 PHE F 58 TYR 0.028 0.002 TYR O 138 ARG 0.013 0.001 ARG A 709 *********************** 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 817 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 811 time to evaluate : 4.395 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: A 15 ASP cc_start: 0.7432 (m-30) cc_final: 0.7050 (m-30) REVERT: A 90 PHE cc_start: 0.8429 (m-80) cc_final: 0.7918 (m-10) REVERT: A 125 LEU cc_start: 0.9398 (mt) cc_final: 0.8997 (tt) REVERT: A 324 LEU cc_start: 0.9414 (mm) cc_final: 0.9064 (mm) REVERT: A 355 PHE cc_start: 0.7603 (m-80) cc_final: 0.7356 (m-80) REVERT: A 589 MET cc_start: 0.8686 (tpt) cc_final: 0.8138 (tpp) REVERT: A 620 ASN cc_start: 0.9345 (m110) cc_final: 0.9121 (m110) REVERT: A 625 ASN cc_start: 0.8479 (t0) cc_final: 0.7897 (t0) REVERT: A 633 MET cc_start: 0.8612 (mtp) cc_final: 0.5300 (mtt) REVERT: A 637 PHE cc_start: 0.8764 (t80) cc_final: 0.8283 (t80) REVERT: A 642 ASN cc_start: 0.8955 (m-40) cc_final: 0.8354 (m-40) REVERT: A 671 GLN cc_start: 0.9242 (mt0) cc_final: 0.8440 (mm110) REVERT: A 675 SER cc_start: 0.9850 (m) cc_final: 0.9647 (p) REVERT: A 917 MET cc_start: 0.8800 (ttp) cc_final: 0.8542 (ttp) REVERT: A 928 MET cc_start: 0.9194 (mtm) cc_final: 0.8898 (mtt) REVERT: A 995 TYR cc_start: 0.8986 (t80) cc_final: 0.8378 (t80) REVERT: A 1038 ILE cc_start: 0.9574 (mm) cc_final: 0.9217 (mm) REVERT: A 1049 MET cc_start: 0.7752 (ttm) cc_final: 0.7267 (ttm) REVERT: A 1056 ASP cc_start: 0.7091 (t0) cc_final: 0.6560 (t0) REVERT: A 1059 LYS cc_start: 0.8033 (mtmt) cc_final: 0.7814 (mtmt) REVERT: A 1140 PHE cc_start: 0.8778 (t80) cc_final: 0.8521 (t80) REVERT: A 1224 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8203 (tp30) REVERT: A 1238 MET cc_start: 0.8175 (mtp) cc_final: 0.7900 (mtt) REVERT: A 1263 LEU cc_start: 0.8951 (tp) cc_final: 0.8669 (tp) REVERT: A 1562 ILE cc_start: 0.9502 (mt) cc_final: 0.9025 (mt) REVERT: A 1588 MET cc_start: 0.8230 (tpt) cc_final: 0.7705 (tpt) REVERT: A 1589 MET cc_start: 0.8279 (mtm) cc_final: 0.7800 (mtm) REVERT: A 1623 THR cc_start: 0.9389 (m) cc_final: 0.9044 (m) REVERT: A 1657 LEU cc_start: 0.9223 (mm) cc_final: 0.9015 (mm) REVERT: B 175 MET cc_start: 0.8737 (mmp) cc_final: 0.7981 (mmm) REVERT: B 330 LEU cc_start: 0.9282 (mt) cc_final: 0.8505 (tt) REVERT: B 334 PHE cc_start: 0.8203 (m-80) cc_final: 0.7836 (m-80) REVERT: B 338 PHE cc_start: 0.7755 (m-80) cc_final: 0.7526 (m-10) REVERT: B 377 MET cc_start: 0.9135 (mtm) cc_final: 0.8668 (ptp) REVERT: B 427 GLN cc_start: 0.8387 (tp-100) cc_final: 0.7859 (tp-100) REVERT: B 457 ILE cc_start: 0.9591 (mt) cc_final: 0.8834 (mp) REVERT: B 465 LEU cc_start: 0.9661 (mt) cc_final: 0.9426 (mt) REVERT: B 493 PHE cc_start: 0.8204 (t80) cc_final: 0.7724 (t80) REVERT: B 539 CYS cc_start: 0.8477 (p) cc_final: 0.8250 (p) REVERT: B 542 LEU cc_start: 0.9082 (mt) cc_final: 0.8772 (mm) REVERT: B 551 ILE cc_start: 0.8991 (mm) cc_final: 0.8671 (mm) REVERT: B 700 LEU cc_start: 0.9399 (mp) cc_final: 0.8957 (tt) REVERT: B 715 ASN cc_start: 0.9489 (m-40) cc_final: 0.9159 (m110) REVERT: B 746 THR cc_start: 0.8769 (m) cc_final: 0.8465 (p) REVERT: B 749 THR cc_start: 0.9273 (m) cc_final: 0.8547 (t) REVERT: B 762 MET cc_start: 0.7995 (tpt) cc_final: 0.7719 (tpp) REVERT: B 770 ASN cc_start: 0.8455 (m-40) cc_final: 0.8009 (p0) REVERT: B 898 LEU cc_start: 0.7702 (tp) cc_final: 0.6864 (tp) REVERT: B 943 ILE cc_start: 0.9498 (mt) cc_final: 0.9152 (tp) REVERT: B 1013 MET cc_start: 0.6758 (ttm) cc_final: 0.6480 (ttm) REVERT: B 1087 LEU cc_start: 0.9698 (mt) cc_final: 0.9497 (mt) REVERT: C 56 LEU cc_start: 0.8623 (mt) cc_final: 0.8125 (mt) REVERT: C 94 ASP cc_start: 0.8307 (m-30) cc_final: 0.7936 (p0) REVERT: C 157 TYR cc_start: 0.7996 (m-10) cc_final: 0.7744 (m-10) REVERT: C 191 ILE cc_start: 0.9337 (mt) cc_final: 0.8456 (mt) REVERT: C 192 LEU cc_start: 0.8644 (tp) cc_final: 0.8279 (mt) REVERT: C 193 LEU cc_start: 0.9463 (mt) cc_final: 0.9196 (mt) REVERT: D 21 VAL cc_start: 0.8689 (p) cc_final: 0.7885 (t) REVERT: D 46 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8117 (mm-30) REVERT: E 23 VAL cc_start: 0.9671 (t) cc_final: 0.9446 (t) REVERT: E 75 MET cc_start: 0.8163 (ttt) cc_final: 0.7548 (tpp) REVERT: E 78 LEU cc_start: 0.9235 (tp) cc_final: 0.8643 (tp) REVERT: E 100 ILE cc_start: 0.9031 (mm) cc_final: 0.8541 (mm) REVERT: E 107 THR cc_start: 0.8202 (m) cc_final: 0.7142 (m) REVERT: E 109 ILE cc_start: 0.9386 (mm) cc_final: 0.8981 (mm) REVERT: E 145 THR cc_start: 0.9196 (p) cc_final: 0.8989 (p) REVERT: E 170 LEU cc_start: 0.9367 (mt) cc_final: 0.9051 (tp) REVERT: E 214 CYS cc_start: 0.6664 (t) cc_final: 0.6350 (t) REVERT: F 154 ASP cc_start: 0.8088 (m-30) cc_final: 0.7017 (t70) REVERT: H 10 PHE cc_start: 0.8961 (m-80) cc_final: 0.8245 (m-80) REVERT: H 38 LEU cc_start: 0.9154 (tp) cc_final: 0.8890 (tp) REVERT: H 42 ILE cc_start: 0.9482 (mm) cc_final: 0.9200 (mm) REVERT: H 95 TYR cc_start: 0.8188 (t80) cc_final: 0.7842 (t80) REVERT: H 96 VAL cc_start: 0.9308 (t) cc_final: 0.8551 (t) REVERT: H 143 LEU cc_start: 0.9122 (mp) cc_final: 0.8326 (mm) REVERT: I 56 PHE cc_start: 0.8920 (m-80) cc_final: 0.8601 (m-80) REVERT: I 61 ARG cc_start: 0.8773 (tpp80) cc_final: 0.8519 (tpp80) REVERT: I 119 TYR cc_start: 0.8202 (t80) cc_final: 0.7783 (t80) REVERT: J 1 MET cc_start: 0.8782 (tpp) cc_final: 0.8509 (tpp) REVERT: J 55 ASP cc_start: 0.7499 (t0) cc_final: 0.7219 (t0) REVERT: J 56 LEU cc_start: 0.9419 (tp) cc_final: 0.9203 (tp) REVERT: J 57 ILE cc_start: 0.9500 (tt) cc_final: 0.9093 (tp) REVERT: J 66 LEU cc_start: 0.9106 (mp) cc_final: 0.8748 (tt) REVERT: K 57 ASP cc_start: 0.9305 (p0) cc_final: 0.8286 (p0) REVERT: K 81 MET cc_start: 0.8238 (mmp) cc_final: 0.8035 (tpp) REVERT: K 85 ASP cc_start: 0.7500 (t70) cc_final: 0.7251 (t0) REVERT: K 124 LEU cc_start: 0.9392 (tp) cc_final: 0.8934 (tp) REVERT: K 125 MET cc_start: 0.8687 (mtm) cc_final: 0.8280 (mtt) REVERT: K 128 CYS cc_start: 0.9248 (m) cc_final: 0.8775 (m) REVERT: M 60 LEU cc_start: 0.9016 (mt) cc_final: 0.8355 (mp) REVERT: M 100 VAL cc_start: 0.7689 (t) cc_final: 0.7080 (m) REVERT: N 58 PHE cc_start: 0.8773 (m-80) cc_final: 0.8552 (m-10) REVERT: O 131 HIS cc_start: 0.8383 (p90) cc_final: 0.8176 (p-80) REVERT: O 156 MET cc_start: 0.8952 (ptt) cc_final: 0.8578 (ptt) REVERT: O 385 MET cc_start: 0.8709 (tpt) cc_final: 0.8503 (tpp) REVERT: O 424 LEU cc_start: 0.9582 (tp) cc_final: 0.9276 (mt) REVERT: O 509 MET cc_start: 0.6755 (mmm) cc_final: 0.6453 (mmm) outliers start: 6 outliers final: 0 residues processed: 814 average time/residue: 0.4889 time to fit residues: 652.2961 Evaluate side-chains 548 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 548 time to evaluate : 3.837 ------------------------------------------------------------------------------- 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: 10.0000 chunk 130 optimal weight: 7.9990 chunk 349 optimal weight: 20.0000 chunk 286 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 421 optimal weight: 20.0000 chunk 455 optimal weight: 20.0000 chunk 375 optimal weight: 9.9990 chunk 417 optimal weight: 20.0000 chunk 143 optimal weight: 6.9990 chunk 337 optimal weight: 4.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 590 ASN ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 887 ASN A1047 GLN A1108 HIS A1532 GLN B 45 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN ** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1038 HIS ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 ASN G 119 HIS I 124 ASN ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 HIS ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 GLN ** 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.5650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 38083 Z= 0.377 Angle : 0.779 14.314 51451 Z= 0.410 Chirality : 0.046 0.256 5747 Planarity : 0.006 0.067 6629 Dihedral : 5.468 28.364 5076 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 20.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.88 % Favored : 95.99 % Rotamer: Outliers : 0.10 % Allowed : 4.46 % Favored : 95.45 % 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: -0.10 (0.12), residues: 4618 helix: 0.57 (0.12), residues: 1718 sheet: -0.42 (0.19), residues: 662 loop : -0.34 (0.13), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 984 HIS 0.010 0.002 HIS B 45 PHE 0.035 0.003 PHE F 58 TYR 0.028 0.003 TYR B 409 ARG 0.012 0.001 ARG B1035 *********************** 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 615 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 611 time to evaluate : 4.354 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: A 90 PHE cc_start: 0.8833 (m-80) cc_final: 0.8598 (m-80) REVERT: A 324 LEU cc_start: 0.9508 (mm) cc_final: 0.9232 (mm) REVERT: A 355 PHE cc_start: 0.7943 (m-80) cc_final: 0.7384 (m-80) REVERT: A 505 LEU cc_start: 0.9046 (mt) cc_final: 0.8724 (mp) REVERT: A 589 MET cc_start: 0.8642 (tpt) cc_final: 0.8356 (tpp) REVERT: A 620 ASN cc_start: 0.9342 (m110) cc_final: 0.8908 (m110) REVERT: A 625 ASN cc_start: 0.8920 (t0) cc_final: 0.8345 (t0) REVERT: A 633 MET cc_start: 0.8709 (mtp) cc_final: 0.4851 (mtt) REVERT: A 637 PHE cc_start: 0.8981 (t80) cc_final: 0.8436 (t80) REVERT: A 743 ASP cc_start: 0.8579 (p0) cc_final: 0.7984 (p0) REVERT: A 766 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8084 (tp30) REVERT: A 780 ILE cc_start: 0.9212 (pt) cc_final: 0.8705 (pt) REVERT: A 925 MET cc_start: 0.8623 (mmp) cc_final: 0.8407 (mmm) REVERT: A 928 MET cc_start: 0.8921 (mtm) cc_final: 0.8651 (ttm) REVERT: A 1038 ILE cc_start: 0.9667 (mm) cc_final: 0.9444 (mm) REVERT: A 1049 MET cc_start: 0.8263 (ttm) cc_final: 0.7530 (ttm) REVERT: A 1059 LYS cc_start: 0.8473 (mtmt) cc_final: 0.8142 (mtpt) REVERT: A 1238 MET cc_start: 0.8124 (mtp) cc_final: 0.7419 (mtt) REVERT: A 1325 LEU cc_start: 0.9269 (tp) cc_final: 0.9065 (tp) REVERT: A 1483 LEU cc_start: 0.8539 (tp) cc_final: 0.8251 (tt) REVERT: A 1583 ASP cc_start: 0.9091 (p0) cc_final: 0.8769 (p0) REVERT: A 1588 MET cc_start: 0.8153 (tpt) cc_final: 0.7905 (tpt) REVERT: A 1634 LEU cc_start: 0.9399 (mt) cc_final: 0.9034 (mt) REVERT: B 175 MET cc_start: 0.8946 (mmp) cc_final: 0.8245 (mmm) REVERT: B 248 ASN cc_start: 0.8616 (m-40) cc_final: 0.8349 (m110) REVERT: B 388 GLU cc_start: 0.7038 (tt0) cc_final: 0.6792 (tt0) REVERT: B 408 LEU cc_start: 0.9634 (tp) cc_final: 0.9381 (tt) REVERT: B 457 ILE cc_start: 0.9724 (mt) cc_final: 0.9230 (pt) REVERT: B 493 PHE cc_start: 0.8012 (t80) cc_final: 0.7611 (t80) REVERT: B 640 LEU cc_start: 0.9275 (tp) cc_final: 0.9024 (tp) REVERT: B 700 LEU cc_start: 0.9494 (mp) cc_final: 0.9178 (tt) REVERT: B 726 MET cc_start: 0.7716 (mmp) cc_final: 0.7419 (tpp) REVERT: B 744 LEU cc_start: 0.8638 (tp) cc_final: 0.8151 (tp) REVERT: B 746 THR cc_start: 0.8897 (m) cc_final: 0.8569 (p) REVERT: B 749 THR cc_start: 0.9199 (m) cc_final: 0.8909 (t) REVERT: B 770 ASN cc_start: 0.8646 (m-40) cc_final: 0.7829 (p0) REVERT: B 886 ASN cc_start: 0.7922 (m-40) cc_final: 0.7593 (m110) REVERT: B 1000 LEU cc_start: 0.9398 (mt) cc_final: 0.9181 (mt) REVERT: B 1033 TYR cc_start: 0.8145 (t80) cc_final: 0.7912 (t80) REVERT: B 1074 MET cc_start: 0.9026 (mtm) cc_final: 0.8595 (mmt) REVERT: B 1087 LEU cc_start: 0.9662 (mt) cc_final: 0.9363 (mt) REVERT: B 1196 LEU cc_start: 0.8574 (tp) cc_final: 0.8140 (tp) REVERT: C 94 ASP cc_start: 0.8157 (m-30) cc_final: 0.7607 (p0) REVERT: C 192 LEU cc_start: 0.9030 (tp) cc_final: 0.8613 (tp) REVERT: D 46 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8223 (mm-30) REVERT: E 22 MET cc_start: 0.8703 (tmm) cc_final: 0.8406 (tmm) REVERT: E 58 MET cc_start: 0.8989 (mtp) cc_final: 0.8405 (mtt) REVERT: E 75 MET cc_start: 0.7784 (ttt) cc_final: 0.7339 (tpp) REVERT: E 78 LEU cc_start: 0.9215 (tp) cc_final: 0.8861 (tp) REVERT: E 100 ILE cc_start: 0.9253 (mm) cc_final: 0.8901 (mm) REVERT: E 170 LEU cc_start: 0.9425 (mt) cc_final: 0.8915 (tp) REVERT: E 175 LEU cc_start: 0.9024 (tp) cc_final: 0.8791 (tp) REVERT: E 182 ASP cc_start: 0.9098 (t0) cc_final: 0.8746 (t70) REVERT: E 214 CYS cc_start: 0.6588 (t) cc_final: 0.6080 (t) REVERT: F 94 LEU cc_start: 0.9663 (mt) cc_final: 0.9461 (mt) REVERT: F 154 ASP cc_start: 0.7908 (m-30) cc_final: 0.7259 (t70) REVERT: G 32 ASN cc_start: 0.8424 (OUTLIER) cc_final: 0.8145 (t0) REVERT: H 38 LEU cc_start: 0.9232 (tp) cc_final: 0.9021 (tp) REVERT: H 143 LEU cc_start: 0.9146 (mp) cc_final: 0.8431 (mm) REVERT: I 56 PHE cc_start: 0.9068 (m-80) cc_final: 0.8704 (m-10) REVERT: I 123 THR cc_start: 0.8166 (m) cc_final: 0.7825 (p) REVERT: J 55 ASP cc_start: 0.7873 (t0) cc_final: 0.7640 (t0) REVERT: J 56 LEU cc_start: 0.9573 (tp) cc_final: 0.9077 (tp) REVERT: J 66 LEU cc_start: 0.9072 (mp) cc_final: 0.8731 (tt) REVERT: K 49 LEU cc_start: 0.9153 (tt) cc_final: 0.8938 (tt) REVERT: K 57 ASP cc_start: 0.9037 (p0) cc_final: 0.8228 (p0) REVERT: K 81 MET cc_start: 0.8654 (mmp) cc_final: 0.8409 (tpp) REVERT: K 85 ASP cc_start: 0.8186 (t0) cc_final: 0.5867 (t0) REVERT: K 125 MET cc_start: 0.8713 (mtm) cc_final: 0.8183 (mtt) REVERT: K 126 ASP cc_start: 0.9218 (m-30) cc_final: 0.8979 (m-30) REVERT: K 142 MET cc_start: 0.5551 (mmt) cc_final: 0.4853 (mtt) REVERT: L 67 PHE cc_start: 0.7822 (m-80) cc_final: 0.6553 (m-80) REVERT: M 60 LEU cc_start: 0.9271 (mt) cc_final: 0.8632 (mp) REVERT: N 55 LEU cc_start: 0.8339 (pp) cc_final: 0.7578 (pp) REVERT: N 58 PHE cc_start: 0.8889 (m-80) cc_final: 0.8687 (m-10) REVERT: O 131 HIS cc_start: 0.8360 (p90) cc_final: 0.8135 (p-80) REVERT: O 156 MET cc_start: 0.9122 (ptt) cc_final: 0.8766 (ptt) REVERT: O 191 ASP cc_start: 0.8180 (t0) cc_final: 0.7792 (t70) REVERT: O 424 LEU cc_start: 0.9509 (tp) cc_final: 0.9277 (mt) REVERT: O 509 MET cc_start: 0.7153 (mmm) cc_final: 0.6727 (mmm) outliers start: 4 outliers final: 2 residues processed: 615 average time/residue: 0.4780 time to fit residues: 484.7666 Evaluate side-chains 426 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 423 time to evaluate : 4.525 ------------------------------------------------------------------------------- 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: 10.0000 chunk 316 optimal weight: 6.9990 chunk 218 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 201 optimal weight: 20.0000 chunk 282 optimal weight: 8.9990 chunk 422 optimal weight: 10.0000 chunk 447 optimal weight: 20.0000 chunk 220 optimal weight: 8.9990 chunk 400 optimal weight: 30.0000 chunk 120 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN B 543 ASN ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 724 GLN ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1114 GLN C 237 GLN ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 HIS G 140 GLN ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 124 ASN ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 GLN ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 362 ASN O 533 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.6260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 38083 Z= 0.319 Angle : 0.691 12.928 51451 Z= 0.365 Chirality : 0.044 0.225 5747 Planarity : 0.005 0.060 6629 Dihedral : 5.294 28.296 5076 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.72 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % 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: 0.13 (0.12), residues: 4618 helix: 0.89 (0.12), residues: 1708 sheet: -0.39 (0.19), residues: 647 loop : -0.29 (0.13), residues: 2263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 143 HIS 0.008 0.002 HIS G 20 PHE 0.027 0.002 PHE K 135 TYR 0.034 0.002 TYR I 119 ARG 0.012 0.001 ARG B 305 *********************** 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 547 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 547 time to evaluate : 4.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 LEU cc_start: 0.9464 (mm) cc_final: 0.9147 (mm) REVERT: A 472 MET cc_start: 0.8785 (mmm) cc_final: 0.8334 (mmm) REVERT: A 601 MET cc_start: 0.8303 (mmt) cc_final: 0.7801 (mmm) REVERT: A 620 ASN cc_start: 0.9171 (m110) cc_final: 0.8920 (m110) REVERT: A 625 ASN cc_start: 0.9125 (t0) cc_final: 0.8527 (t0) REVERT: A 633 MET cc_start: 0.8691 (mtp) cc_final: 0.4862 (mtt) REVERT: A 646 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8097 (mt-10) REVERT: A 657 TYR cc_start: 0.8594 (t80) cc_final: 0.8317 (t80) REVERT: A 743 ASP cc_start: 0.8655 (p0) cc_final: 0.8107 (p0) REVERT: A 928 MET cc_start: 0.9095 (mtm) cc_final: 0.8706 (mtt) REVERT: A 1038 ILE cc_start: 0.9683 (mm) cc_final: 0.9466 (mm) REVERT: A 1049 MET cc_start: 0.7966 (ttm) cc_final: 0.7433 (ttm) REVERT: A 1059 LYS cc_start: 0.8333 (mtmt) cc_final: 0.8058 (mtmt) REVERT: A 1200 MET cc_start: 0.8168 (mmp) cc_final: 0.7832 (mmp) REVERT: A 1225 ILE cc_start: 0.9447 (mt) cc_final: 0.9132 (mm) REVERT: A 1238 MET cc_start: 0.7970 (mtp) cc_final: 0.7363 (mtt) REVERT: A 1483 LEU cc_start: 0.8775 (tp) cc_final: 0.8538 (tt) REVERT: A 1490 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8467 (pt0) REVERT: A 1562 ILE cc_start: 0.9546 (mt) cc_final: 0.9281 (mt) REVERT: A 1583 ASP cc_start: 0.9048 (p0) cc_final: 0.8746 (p0) REVERT: A 1588 MET cc_start: 0.8252 (tpt) cc_final: 0.7918 (tpp) REVERT: A 1595 TYR cc_start: 0.9147 (t80) cc_final: 0.8612 (t80) REVERT: A 1634 LEU cc_start: 0.9335 (mt) cc_final: 0.9016 (mt) REVERT: B 215 MET cc_start: 0.8273 (mmm) cc_final: 0.7914 (mmp) REVERT: B 248 ASN cc_start: 0.8791 (m-40) cc_final: 0.8525 (m-40) REVERT: B 308 LEU cc_start: 0.9347 (mt) cc_final: 0.9105 (tt) REVERT: B 388 GLU cc_start: 0.7088 (tt0) cc_final: 0.6796 (tt0) REVERT: B 457 ILE cc_start: 0.9652 (mt) cc_final: 0.8837 (tt) REVERT: B 493 PHE cc_start: 0.8061 (t80) cc_final: 0.7611 (t80) REVERT: B 502 MET cc_start: 0.7658 (tpt) cc_final: 0.7338 (tpt) REVERT: B 528 LEU cc_start: 0.9481 (tp) cc_final: 0.9052 (tp) REVERT: B 640 LEU cc_start: 0.9271 (tp) cc_final: 0.9023 (tp) REVERT: B 726 MET cc_start: 0.8070 (mmp) cc_final: 0.7379 (tpp) REVERT: B 744 LEU cc_start: 0.8809 (tp) cc_final: 0.8456 (tp) REVERT: B 749 THR cc_start: 0.9401 (m) cc_final: 0.9074 (t) REVERT: B 762 MET cc_start: 0.8487 (tpt) cc_final: 0.8212 (tpt) REVERT: B 770 ASN cc_start: 0.8376 (m-40) cc_final: 0.7838 (p0) REVERT: B 853 GLU cc_start: 0.8852 (pm20) cc_final: 0.8443 (pp20) REVERT: B 878 GLU cc_start: 0.8276 (mp0) cc_final: 0.7982 (mp0) REVERT: B 967 LEU cc_start: 0.9505 (mt) cc_final: 0.9269 (mt) REVERT: B 1000 LEU cc_start: 0.9322 (mt) cc_final: 0.9093 (mt) REVERT: B 1074 MET cc_start: 0.8932 (mtm) cc_final: 0.8417 (mmt) REVERT: B 1087 LEU cc_start: 0.9757 (mt) cc_final: 0.9133 (mt) REVERT: B 1196 LEU cc_start: 0.8674 (tp) cc_final: 0.8339 (tt) REVERT: C 157 TYR cc_start: 0.8377 (m-10) cc_final: 0.8142 (m-10) REVERT: C 192 LEU cc_start: 0.8860 (tp) cc_final: 0.8539 (tp) REVERT: D 46 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8117 (mm-30) REVERT: E 22 MET cc_start: 0.8723 (tmm) cc_final: 0.8414 (tmm) REVERT: E 23 VAL cc_start: 0.9713 (t) cc_final: 0.9483 (t) REVERT: E 75 MET cc_start: 0.7687 (ttt) cc_final: 0.7093 (tpp) REVERT: E 170 LEU cc_start: 0.9440 (mt) cc_final: 0.8840 (tp) REVERT: F 92 ARG cc_start: 0.9573 (ttt180) cc_final: 0.8762 (ttp-170) REVERT: F 94 LEU cc_start: 0.9767 (mt) cc_final: 0.9431 (mt) REVERT: F 154 ASP cc_start: 0.7954 (m-30) cc_final: 0.7349 (t70) REVERT: H 95 TYR cc_start: 0.8326 (t80) cc_final: 0.7937 (t80) REVERT: I 56 PHE cc_start: 0.9125 (m-80) cc_final: 0.8841 (m-10) REVERT: J 55 ASP cc_start: 0.8081 (t0) cc_final: 0.7726 (t0) REVERT: J 56 LEU cc_start: 0.9445 (tp) cc_final: 0.9218 (tp) REVERT: J 59 LYS cc_start: 0.9103 (ttmt) cc_final: 0.8860 (mtpt) REVERT: J 66 LEU cc_start: 0.9058 (mp) cc_final: 0.8727 (tt) REVERT: K 57 ASP cc_start: 0.9031 (p0) cc_final: 0.8237 (p0) REVERT: K 85 ASP cc_start: 0.8390 (t0) cc_final: 0.7257 (t0) REVERT: K 115 ASP cc_start: 0.8540 (m-30) cc_final: 0.8290 (m-30) REVERT: K 125 MET cc_start: 0.8764 (mtm) cc_final: 0.8241 (mtt) REVERT: K 126 ASP cc_start: 0.8990 (m-30) cc_final: 0.8769 (m-30) REVERT: K 135 PHE cc_start: 0.9324 (t80) cc_final: 0.8839 (t80) REVERT: M 60 LEU cc_start: 0.9229 (mt) cc_final: 0.8598 (mp) REVERT: O 131 HIS cc_start: 0.8303 (p90) cc_final: 0.8073 (p-80) REVERT: O 156 MET cc_start: 0.9114 (ptt) cc_final: 0.8744 (ptt) REVERT: O 385 MET cc_start: 0.8695 (tpt) cc_final: 0.8475 (tpp) REVERT: O 509 MET cc_start: 0.7163 (mmm) cc_final: 0.6755 (mmm) outliers start: 0 outliers final: 0 residues processed: 547 average time/residue: 0.4818 time to fit residues: 436.4045 Evaluate side-chains 397 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 397 time to evaluate : 4.438 ------------------------------------------------------------------------------- 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: 7.9990 chunk 254 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 333 optimal weight: 20.0000 chunk 184 optimal weight: 2.9990 chunk 381 optimal weight: 9.9990 chunk 309 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 228 optimal weight: 0.0870 chunk 401 optimal weight: 6.9990 chunk 112 optimal weight: 0.1980 overall best weight: 2.0564 ------------------------------------------------------------------------------- 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 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1180 ASN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 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 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 170 HIS ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 583 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.6468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 38083 Z= 0.192 Angle : 0.607 11.290 51451 Z= 0.315 Chirality : 0.044 0.254 5747 Planarity : 0.004 0.060 6629 Dihedral : 4.940 25.507 5076 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.44 % Favored : 96.43 % Rotamer: Outliers : 0.02 % Allowed : 2.35 % Favored : 97.63 % 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: 0.48 (0.12), residues: 4618 helix: 1.26 (0.13), residues: 1723 sheet: -0.28 (0.19), residues: 665 loop : -0.13 (0.14), residues: 2230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 931 HIS 0.007 0.001 HIS N 170 PHE 0.028 0.002 PHE B1086 TYR 0.021 0.002 TYR A 478 ARG 0.008 0.001 ARG A1506 *********************** 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 577 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 576 time to evaluate : 4.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 LEU cc_start: 0.9410 (mm) cc_final: 0.9067 (mm) REVERT: A 509 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8388 (mm-30) REVERT: A 570 THR cc_start: 0.8698 (p) cc_final: 0.8472 (t) REVERT: A 583 ASN cc_start: 0.8357 (m-40) cc_final: 0.8004 (m-40) REVERT: A 601 MET cc_start: 0.8077 (mmt) cc_final: 0.7555 (mmm) REVERT: A 617 HIS cc_start: 0.9421 (t-90) cc_final: 0.8840 (t-90) REVERT: A 625 ASN cc_start: 0.9074 (t0) cc_final: 0.8510 (t0) REVERT: A 657 TYR cc_start: 0.8524 (t80) cc_final: 0.8299 (t80) REVERT: A 780 ILE cc_start: 0.9135 (pt) cc_final: 0.8925 (pt) REVERT: A 925 MET cc_start: 0.8548 (mmp) cc_final: 0.8343 (mmp) REVERT: A 1038 ILE cc_start: 0.9574 (mm) cc_final: 0.9311 (mm) REVERT: A 1049 MET cc_start: 0.7731 (ttm) cc_final: 0.7180 (ttm) REVERT: A 1056 ASP cc_start: 0.6984 (t0) cc_final: 0.6761 (t0) REVERT: A 1059 LYS cc_start: 0.8561 (mtmt) cc_final: 0.8075 (mtpt) REVERT: A 1200 MET cc_start: 0.8020 (mmp) cc_final: 0.7757 (mmp) REVERT: A 1238 MET cc_start: 0.8024 (mtp) cc_final: 0.6015 (mtt) REVERT: A 1483 LEU cc_start: 0.8635 (tp) cc_final: 0.8399 (tt) REVERT: A 1490 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8449 (pt0) REVERT: A 1543 SER cc_start: 0.6817 (p) cc_final: 0.6538 (p) REVERT: A 1562 ILE cc_start: 0.9552 (mt) cc_final: 0.9306 (mt) REVERT: A 1583 ASP cc_start: 0.9013 (p0) cc_final: 0.8609 (p0) REVERT: A 1588 MET cc_start: 0.8161 (tpt) cc_final: 0.7801 (tpt) REVERT: A 1595 TYR cc_start: 0.9178 (t80) cc_final: 0.8468 (t80) REVERT: A 1634 LEU cc_start: 0.9322 (mt) cc_final: 0.8902 (mt) REVERT: B 248 ASN cc_start: 0.8923 (m-40) cc_final: 0.8655 (m-40) REVERT: B 308 LEU cc_start: 0.9340 (mt) cc_final: 0.9034 (tt) REVERT: B 374 LEU cc_start: 0.9376 (tp) cc_final: 0.9006 (tt) REVERT: B 457 ILE cc_start: 0.9625 (mt) cc_final: 0.8981 (mp) REVERT: B 493 PHE cc_start: 0.7931 (t80) cc_final: 0.7499 (t80) REVERT: B 502 MET cc_start: 0.7403 (tpt) cc_final: 0.6623 (tpt) REVERT: B 528 LEU cc_start: 0.9437 (tp) cc_final: 0.9057 (tp) REVERT: B 640 LEU cc_start: 0.9301 (tp) cc_final: 0.8953 (tp) REVERT: B 703 LEU cc_start: 0.9225 (mt) cc_final: 0.8992 (mt) REVERT: B 726 MET cc_start: 0.7647 (mmp) cc_final: 0.7063 (tpp) REVERT: B 744 LEU cc_start: 0.8769 (tp) cc_final: 0.8391 (tp) REVERT: B 746 THR cc_start: 0.8851 (m) cc_final: 0.8491 (p) REVERT: B 853 GLU cc_start: 0.8806 (pm20) cc_final: 0.8456 (pp20) REVERT: B 878 GLU cc_start: 0.8309 (mp0) cc_final: 0.8031 (mp0) REVERT: B 886 ASN cc_start: 0.7813 (m-40) cc_final: 0.7510 (m-40) REVERT: B 967 LEU cc_start: 0.9422 (mt) cc_final: 0.9137 (mt) REVERT: B 1000 LEU cc_start: 0.9223 (mt) cc_final: 0.9009 (mt) REVERT: B 1074 MET cc_start: 0.8795 (mtm) cc_final: 0.8397 (mmm) REVERT: B 1087 LEU cc_start: 0.9673 (mt) cc_final: 0.9465 (mt) REVERT: B 1196 LEU cc_start: 0.8561 (tp) cc_final: 0.8288 (tt) REVERT: C 82 TYR cc_start: 0.6950 (m-10) cc_final: 0.6732 (m-10) REVERT: C 94 ASP cc_start: 0.8239 (p0) cc_final: 0.7638 (p0) REVERT: C 192 LEU cc_start: 0.8543 (tp) cc_final: 0.8327 (tp) REVERT: C 208 CYS cc_start: 0.8526 (m) cc_final: 0.8271 (m) REVERT: D 46 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8140 (mm-30) REVERT: E 22 MET cc_start: 0.8605 (tmm) cc_final: 0.8384 (tmm) REVERT: E 23 VAL cc_start: 0.9751 (t) cc_final: 0.9511 (t) REVERT: E 75 MET cc_start: 0.7545 (ttt) cc_final: 0.7046 (tpp) REVERT: E 170 LEU cc_start: 0.9379 (mt) cc_final: 0.8816 (tp) REVERT: E 175 LEU cc_start: 0.9099 (tp) cc_final: 0.8889 (tp) REVERT: E 182 ASP cc_start: 0.9258 (t0) cc_final: 0.8990 (t70) REVERT: F 92 ARG cc_start: 0.9549 (ttt180) cc_final: 0.8728 (ttp-170) REVERT: F 108 PHE cc_start: 0.8903 (m-80) cc_final: 0.8352 (m-10) REVERT: F 154 ASP cc_start: 0.7765 (m-30) cc_final: 0.7343 (t70) REVERT: H 22 LYS cc_start: 0.8775 (mptt) cc_final: 0.8221 (mmtm) REVERT: H 95 TYR cc_start: 0.8231 (t80) cc_final: 0.7813 (t80) REVERT: I 56 PHE cc_start: 0.9109 (m-80) cc_final: 0.8805 (m-10) REVERT: I 94 MET cc_start: 0.8532 (mmm) cc_final: 0.8322 (mmm) REVERT: J 57 ILE cc_start: 0.9455 (tt) cc_final: 0.9229 (tt) REVERT: J 66 LEU cc_start: 0.8998 (mp) cc_final: 0.8709 (tt) REVERT: K 85 ASP cc_start: 0.8505 (t0) cc_final: 0.6356 (t0) REVERT: K 125 MET cc_start: 0.8735 (mtm) cc_final: 0.8317 (mtt) REVERT: K 126 ASP cc_start: 0.8960 (m-30) cc_final: 0.8694 (m-30) REVERT: K 135 PHE cc_start: 0.9318 (t80) cc_final: 0.8804 (t80) REVERT: K 142 MET cc_start: 0.5862 (mtt) cc_final: 0.5365 (mtm) REVERT: M 60 LEU cc_start: 0.9248 (mt) cc_final: 0.8786 (mp) REVERT: N 55 LEU cc_start: 0.8303 (pp) cc_final: 0.7863 (pp) REVERT: O 156 MET cc_start: 0.9152 (ptt) cc_final: 0.8798 (ptt) REVERT: O 187 MET cc_start: 0.8586 (ptm) cc_final: 0.8265 (ptm) REVERT: O 191 ASP cc_start: 0.8569 (t0) cc_final: 0.8076 (t0) REVERT: O 509 MET cc_start: 0.7184 (mmm) cc_final: 0.6691 (mmm) outliers start: 1 outliers final: 0 residues processed: 577 average time/residue: 0.4576 time to fit residues: 442.8471 Evaluate side-chains 405 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 405 time to evaluate : 4.683 ------------------------------------------------------------------------------- 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: 9.9990 chunk 403 optimal weight: 30.0000 chunk 88 optimal weight: 10.0000 chunk 262 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 447 optimal weight: 20.0000 chunk 371 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 148 optimal weight: 8.9990 chunk 235 optimal weight: 0.9980 overall best weight: 5.9988 ------------------------------------------------------------------------------- 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 926 GLN A1601 GLN B 171 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1089 GLN B1094 ASN B1157 GLN C 237 GLN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 HIS ** 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 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 ASN ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 GLN O 121 ASN O 131 HIS ** O 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 392 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.7025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 38083 Z= 0.330 Angle : 0.701 13.114 51451 Z= 0.368 Chirality : 0.044 0.198 5747 Planarity : 0.005 0.052 6629 Dihedral : 5.216 25.024 5076 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 21.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.24 % Favored : 95.67 % Rotamer: Outliers : 0.02 % Allowed : 2.23 % Favored : 97.75 % 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: 1.01 (0.12), residues: 1714 sheet: -0.37 (0.19), residues: 673 loop : -0.27 (0.13), residues: 2231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 760 HIS 0.010 0.002 HIS G 119 PHE 0.030 0.002 PHE D 96 TYR 0.023 0.002 TYR F 84 ARG 0.008 0.001 ARG F 90 *********************** 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 513 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 512 time to evaluate : 4.244 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: A 570 THR cc_start: 0.8964 (p) cc_final: 0.8731 (t) REVERT: A 601 MET cc_start: 0.8182 (mmt) cc_final: 0.7492 (mmm) REVERT: A 625 ASN cc_start: 0.9174 (t0) cc_final: 0.8551 (t0) REVERT: A 657 TYR cc_start: 0.8593 (t80) cc_final: 0.8250 (t80) REVERT: A 928 MET cc_start: 0.9058 (mtm) cc_final: 0.8754 (mtt) REVERT: A 1049 MET cc_start: 0.7882 (ttm) cc_final: 0.7420 (ttm) REVERT: A 1050 TYR cc_start: 0.8553 (t80) cc_final: 0.8344 (t80) REVERT: A 1059 LYS cc_start: 0.8810 (mtmt) cc_final: 0.8305 (mtpt) REVERT: A 1200 MET cc_start: 0.8383 (mmp) cc_final: 0.8096 (mmp) REVERT: A 1483 LEU cc_start: 0.8804 (tp) cc_final: 0.8581 (tt) REVERT: A 1583 ASP cc_start: 0.8958 (p0) cc_final: 0.8702 (p0) REVERT: A 1588 MET cc_start: 0.8312 (tpt) cc_final: 0.7949 (tpt) REVERT: A 1634 LEU cc_start: 0.9380 (mt) cc_final: 0.9032 (mt) REVERT: A 1642 VAL cc_start: 0.9567 (t) cc_final: 0.9346 (t) REVERT: B 248 ASN cc_start: 0.8827 (m-40) cc_final: 0.8529 (m-40) REVERT: B 308 LEU cc_start: 0.9420 (mt) cc_final: 0.9154 (tt) REVERT: B 413 LEU cc_start: 0.9673 (tp) cc_final: 0.9469 (tp) REVERT: B 457 ILE cc_start: 0.9681 (mt) cc_final: 0.9127 (mp) REVERT: B 493 PHE cc_start: 0.7882 (t80) cc_final: 0.7567 (t80) REVERT: B 502 MET cc_start: 0.7450 (tpt) cc_final: 0.7112 (tpt) REVERT: B 528 LEU cc_start: 0.9534 (tp) cc_final: 0.9219 (tp) REVERT: B 640 LEU cc_start: 0.9308 (tp) cc_final: 0.9007 (tp) REVERT: B 726 MET cc_start: 0.8030 (mmp) cc_final: 0.7524 (tpp) REVERT: B 744 LEU cc_start: 0.8949 (tp) cc_final: 0.8513 (tp) REVERT: B 751 ILE cc_start: 0.9363 (mm) cc_final: 0.9157 (mm) REVERT: B 783 MET cc_start: 0.8781 (mmp) cc_final: 0.8403 (mmm) REVERT: B 853 GLU cc_start: 0.8878 (pm20) cc_final: 0.8485 (pp20) REVERT: B 878 GLU cc_start: 0.8202 (mp0) cc_final: 0.7968 (mp0) REVERT: B 886 ASN cc_start: 0.7897 (m-40) cc_final: 0.7614 (m-40) REVERT: B 967 LEU cc_start: 0.9510 (mt) cc_final: 0.9302 (mt) REVERT: B 1074 MET cc_start: 0.8890 (mtm) cc_final: 0.8425 (mmm) REVERT: B 1087 LEU cc_start: 0.9659 (mt) cc_final: 0.9341 (mt) REVERT: B 1196 LEU cc_start: 0.8578 (tp) cc_final: 0.8319 (tp) REVERT: C 82 TYR cc_start: 0.7131 (m-10) cc_final: 0.6888 (m-10) REVERT: C 94 ASP cc_start: 0.8303 (p0) cc_final: 0.7820 (p0) REVERT: C 157 TYR cc_start: 0.8449 (m-10) cc_final: 0.8195 (m-10) REVERT: C 192 LEU cc_start: 0.8800 (tp) cc_final: 0.8596 (tp) REVERT: C 208 CYS cc_start: 0.8501 (m) cc_final: 0.8189 (m) REVERT: E 22 MET cc_start: 0.8737 (tmm) cc_final: 0.8367 (tmm) REVERT: E 23 VAL cc_start: 0.9701 (t) cc_final: 0.9490 (t) REVERT: E 75 MET cc_start: 0.7784 (ttt) cc_final: 0.7101 (tpp) REVERT: E 182 ASP cc_start: 0.9476 (t0) cc_final: 0.9226 (t70) REVERT: F 92 ARG cc_start: 0.9558 (ttt180) cc_final: 0.8853 (ttp-170) REVERT: F 154 ASP cc_start: 0.7735 (m-30) cc_final: 0.7312 (t70) REVERT: H 38 LEU cc_start: 0.9255 (tp) cc_final: 0.9036 (tp) REVERT: H 95 TYR cc_start: 0.8509 (t80) cc_final: 0.8230 (t80) REVERT: H 142 LEU cc_start: 0.9299 (tp) cc_final: 0.9096 (tp) REVERT: H 143 LEU cc_start: 0.9142 (mp) cc_final: 0.8821 (mp) REVERT: J 66 LEU cc_start: 0.9067 (mp) cc_final: 0.8736 (tt) REVERT: K 57 ASP cc_start: 0.9029 (p0) cc_final: 0.8267 (p0) REVERT: K 125 MET cc_start: 0.8803 (mtm) cc_final: 0.8377 (mtt) REVERT: L 67 PHE cc_start: 0.7522 (m-80) cc_final: 0.7026 (m-80) REVERT: M 60 LEU cc_start: 0.9290 (mt) cc_final: 0.8841 (mp) REVERT: N 55 LEU cc_start: 0.8433 (pp) cc_final: 0.7682 (pp) REVERT: O 156 MET cc_start: 0.9161 (ptt) cc_final: 0.8791 (ptt) REVERT: O 187 MET cc_start: 0.8710 (ptm) cc_final: 0.8474 (ptm) REVERT: O 191 ASP cc_start: 0.8692 (t0) cc_final: 0.8243 (t0) REVERT: O 509 MET cc_start: 0.7169 (mmm) cc_final: 0.6751 (mmm) outliers start: 1 outliers final: 0 residues processed: 513 average time/residue: 0.4663 time to fit residues: 399.0079 Evaluate side-chains 372 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 4.518 ------------------------------------------------------------------------------- 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: 9.9990 chunk 50 optimal weight: 0.9980 chunk 255 optimal weight: 10.0000 chunk 327 optimal weight: 3.9990 chunk 253 optimal weight: 5.9990 chunk 377 optimal weight: 0.8980 chunk 250 optimal weight: 9.9990 chunk 446 optimal weight: 10.0000 chunk 279 optimal weight: 0.4980 chunk 272 optimal weight: 7.9990 chunk 206 optimal weight: 3.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- 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 590 ASN A 636 HIS ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 GLN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 GLN ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 HIS ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 ASN N 52 GLN N 170 HIS O 70 GLN ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 121 ASN O 131 HIS ** O 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.7144 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= 0.187 Angle : 0.610 10.005 51451 Z= 0.316 Chirality : 0.044 0.194 5747 Planarity : 0.004 0.048 6629 Dihedral : 4.864 27.201 5076 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.51 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % 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: 0.40 (0.12), residues: 4618 helix: 1.23 (0.12), residues: 1723 sheet: -0.33 (0.19), residues: 672 loop : -0.21 (0.14), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 832 HIS 0.011 0.001 HIS G 119 PHE 0.025 0.002 PHE B 25 TYR 0.038 0.002 TYR L 29 ARG 0.007 0.000 ARG B 305 *********************** 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 531 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 531 time to evaluate : 4.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 PHE cc_start: 0.8961 (m-80) cc_final: 0.8581 (m-80) REVERT: A 509 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8491 (mm-30) REVERT: A 570 THR cc_start: 0.8775 (p) cc_final: 0.8508 (t) REVERT: A 600 MET cc_start: 0.9437 (mmm) cc_final: 0.8790 (tpt) REVERT: A 601 MET cc_start: 0.7879 (mmt) cc_final: 0.7124 (mmm) REVERT: A 617 HIS cc_start: 0.9408 (t-90) cc_final: 0.8873 (t-90) REVERT: A 625 ASN cc_start: 0.9108 (t0) cc_final: 0.8697 (t0) REVERT: A 636 HIS cc_start: 0.8202 (m-70) cc_final: 0.7746 (m-70) REVERT: A 657 TYR cc_start: 0.8566 (t80) cc_final: 0.8280 (t80) REVERT: A 926 GLN cc_start: 0.9453 (pt0) cc_final: 0.9244 (pp30) REVERT: A 928 MET cc_start: 0.9003 (mtm) cc_final: 0.8621 (ttm) REVERT: A 1049 MET cc_start: 0.7688 (ttm) cc_final: 0.7319 (ttm) REVERT: A 1050 TYR cc_start: 0.8466 (t80) cc_final: 0.8247 (t80) REVERT: A 1059 LYS cc_start: 0.8700 (mtmt) cc_final: 0.8209 (mtpt) REVERT: A 1562 ILE cc_start: 0.9563 (mt) cc_final: 0.9320 (mm) REVERT: A 1583 ASP cc_start: 0.8929 (p0) cc_final: 0.8663 (p0) REVERT: A 1634 LEU cc_start: 0.9310 (mt) cc_final: 0.8904 (mt) REVERT: B 248 ASN cc_start: 0.9029 (m-40) cc_final: 0.8737 (m-40) REVERT: B 308 LEU cc_start: 0.9419 (mt) cc_final: 0.9126 (tt) REVERT: B 413 LEU cc_start: 0.9643 (tp) cc_final: 0.9431 (tp) REVERT: B 457 ILE cc_start: 0.9620 (mt) cc_final: 0.8994 (mp) REVERT: B 493 PHE cc_start: 0.7765 (t80) cc_final: 0.7545 (t80) REVERT: B 520 LEU cc_start: 0.8976 (tt) cc_final: 0.8465 (tp) REVERT: B 528 LEU cc_start: 0.9570 (tp) cc_final: 0.9239 (tp) REVERT: B 640 LEU cc_start: 0.9242 (tp) cc_final: 0.8917 (tp) REVERT: B 703 LEU cc_start: 0.9260 (mt) cc_final: 0.9004 (mt) REVERT: B 726 MET cc_start: 0.7915 (mmp) cc_final: 0.7262 (tpp) REVERT: B 744 LEU cc_start: 0.8904 (tp) cc_final: 0.8472 (tp) REVERT: B 853 GLU cc_start: 0.8798 (pm20) cc_final: 0.8478 (pp20) REVERT: B 878 GLU cc_start: 0.8192 (mp0) cc_final: 0.7980 (mp0) REVERT: B 886 ASN cc_start: 0.7734 (m-40) cc_final: 0.7453 (m-40) REVERT: B 962 MET cc_start: 0.9245 (mmm) cc_final: 0.9026 (mmm) REVERT: B 967 LEU cc_start: 0.9426 (mt) cc_final: 0.9195 (mt) REVERT: B 1074 MET cc_start: 0.8731 (mtm) cc_final: 0.8438 (mmm) REVERT: B 1087 LEU cc_start: 0.9658 (mt) cc_final: 0.9441 (mt) REVERT: B 1196 LEU cc_start: 0.8547 (tp) cc_final: 0.8319 (tp) REVERT: C 82 TYR cc_start: 0.7080 (m-10) cc_final: 0.6857 (m-10) REVERT: C 94 ASP cc_start: 0.8385 (p0) cc_final: 0.7827 (p0) REVERT: C 157 TYR cc_start: 0.8200 (m-10) cc_final: 0.7845 (m-10) REVERT: C 192 LEU cc_start: 0.8691 (tp) cc_final: 0.8459 (tp) REVERT: D 46 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8170 (mm-30) REVERT: E 22 MET cc_start: 0.8617 (tmm) cc_final: 0.8355 (tmm) REVERT: E 23 VAL cc_start: 0.9742 (t) cc_final: 0.9504 (t) REVERT: E 75 MET cc_start: 0.7541 (ttt) cc_final: 0.7047 (tpp) REVERT: E 182 ASP cc_start: 0.9463 (t0) cc_final: 0.9234 (t70) REVERT: F 84 TYR cc_start: 0.8263 (m-80) cc_final: 0.7819 (m-10) REVERT: F 92 ARG cc_start: 0.9524 (ttt180) cc_final: 0.9225 (ttt180) REVERT: G 54 LEU cc_start: 0.9303 (mt) cc_final: 0.9098 (tp) REVERT: H 95 TYR cc_start: 0.8334 (t80) cc_final: 0.8104 (t80) REVERT: H 142 LEU cc_start: 0.9138 (tp) cc_final: 0.8906 (tp) REVERT: H 143 LEU cc_start: 0.9206 (mp) cc_final: 0.8714 (mp) REVERT: J 49 MET cc_start: 0.9334 (mmp) cc_final: 0.9115 (mmm) REVERT: K 125 MET cc_start: 0.8722 (mtm) cc_final: 0.8308 (mtt) REVERT: K 135 PHE cc_start: 0.9228 (t80) cc_final: 0.8778 (t80) REVERT: L 67 PHE cc_start: 0.7477 (m-80) cc_final: 0.7022 (m-80) REVERT: O 156 MET cc_start: 0.9184 (ptt) cc_final: 0.8784 (ptt) REVERT: O 191 ASP cc_start: 0.8631 (t0) cc_final: 0.8238 (t70) REVERT: O 509 MET cc_start: 0.7172 (mmm) cc_final: 0.6753 (mmm) outliers start: 0 outliers final: 0 residues processed: 531 average time/residue: 0.4552 time to fit residues: 403.8601 Evaluate side-chains 385 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 4.446 ------------------------------------------------------------------------------- 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: 9.9990 chunk 266 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 283 optimal weight: 0.8980 chunk 304 optimal weight: 6.9990 chunk 220 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 350 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 GLN A 435 ASN A1026 GLN A1180 ASN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 GLN ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1034 GLN B1089 GLN C 237 GLN ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 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 ** 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.7422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 38083 Z= 0.237 Angle : 0.628 9.260 51451 Z= 0.327 Chirality : 0.044 0.274 5747 Planarity : 0.005 0.088 6629 Dihedral : 4.921 27.735 5076 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.98 % Favored : 95.95 % Rotamer: Outliers : 0.02 % Allowed : 1.08 % Favored : 98.90 % 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: 0.30 (0.12), residues: 4618 helix: 1.11 (0.12), residues: 1735 sheet: -0.32 (0.20), residues: 665 loop : -0.27 (0.14), residues: 2218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 760 HIS 0.008 0.001 HIS A 378 PHE 0.043 0.002 PHE F 58 TYR 0.029 0.002 TYR L 29 ARG 0.015 0.001 ARG C 281 *********************** 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 503 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 502 time to evaluate : 4.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 PHE cc_start: 0.8940 (m-80) cc_final: 0.8596 (m-80) REVERT: A 227 LEU cc_start: 0.8836 (pp) cc_final: 0.8518 (pp) REVERT: A 570 THR cc_start: 0.8817 (p) cc_final: 0.8569 (t) REVERT: A 589 MET cc_start: 0.8402 (tpt) cc_final: 0.8128 (tpp) REVERT: A 601 MET cc_start: 0.8209 (mmt) cc_final: 0.7328 (mmm) REVERT: A 617 HIS cc_start: 0.9448 (t-90) cc_final: 0.8905 (t-90) REVERT: A 625 ASN cc_start: 0.9049 (t0) cc_final: 0.8567 (t0) REVERT: A 657 TYR cc_start: 0.8610 (t80) cc_final: 0.8303 (t80) REVERT: A 736 LEU cc_start: 0.9425 (mm) cc_final: 0.9050 (tt) REVERT: A 925 MET cc_start: 0.8762 (mmp) cc_final: 0.8517 (mmp) REVERT: A 926 GLN cc_start: 0.9481 (pt0) cc_final: 0.9268 (pp30) REVERT: A 928 MET cc_start: 0.9102 (mtm) cc_final: 0.8701 (ttm) REVERT: A 944 MET cc_start: 0.9092 (mmp) cc_final: 0.8825 (mmm) REVERT: A 1049 MET cc_start: 0.7767 (ttm) cc_final: 0.7480 (ttm) REVERT: A 1050 TYR cc_start: 0.8452 (t80) cc_final: 0.8136 (t80) REVERT: A 1059 LYS cc_start: 0.8809 (mtmt) cc_final: 0.8312 (mtpt) REVERT: A 1200 MET cc_start: 0.8146 (mmp) cc_final: 0.7840 (mmp) REVERT: A 1603 MET cc_start: 0.7862 (ppp) cc_final: 0.7470 (ppp) REVERT: A 1634 LEU cc_start: 0.9377 (mt) cc_final: 0.8986 (mt) REVERT: B 248 ASN cc_start: 0.8971 (m-40) cc_final: 0.8700 (m-40) REVERT: B 308 LEU cc_start: 0.9428 (mt) cc_final: 0.9123 (tt) REVERT: B 457 ILE cc_start: 0.9649 (mt) cc_final: 0.9093 (mp) REVERT: B 493 PHE cc_start: 0.7727 (t80) cc_final: 0.7476 (t80) REVERT: B 502 MET cc_start: 0.7596 (tpt) cc_final: 0.7202 (tpt) REVERT: B 520 LEU cc_start: 0.9005 (tt) cc_final: 0.8474 (tp) REVERT: B 528 LEU cc_start: 0.9502 (tp) cc_final: 0.9294 (tp) REVERT: B 593 ILE cc_start: 0.9493 (mp) cc_final: 0.9102 (tp) REVERT: B 640 LEU cc_start: 0.9272 (tp) cc_final: 0.8965 (tp) REVERT: B 726 MET cc_start: 0.8111 (mmp) cc_final: 0.7512 (tpp) REVERT: B 744 LEU cc_start: 0.8975 (tp) cc_final: 0.8578 (tp) REVERT: B 853 GLU cc_start: 0.8830 (pm20) cc_final: 0.8481 (pp20) REVERT: B 886 ASN cc_start: 0.7790 (m-40) cc_final: 0.7451 (m-40) REVERT: B 962 MET cc_start: 0.9173 (mmm) cc_final: 0.8904 (mmm) REVERT: B 1074 MET cc_start: 0.8747 (mtm) cc_final: 0.8326 (mmm) REVERT: B 1087 LEU cc_start: 0.9640 (mt) cc_final: 0.9436 (mt) REVERT: B 1196 LEU cc_start: 0.8601 (tp) cc_final: 0.8326 (tp) REVERT: C 82 TYR cc_start: 0.7159 (m-10) cc_final: 0.6951 (m-10) REVERT: C 94 ASP cc_start: 0.8390 (p0) cc_final: 0.7813 (p0) REVERT: C 192 LEU cc_start: 0.8810 (tp) cc_final: 0.8565 (tp) REVERT: E 22 MET cc_start: 0.8608 (tmm) cc_final: 0.8247 (tmm) REVERT: E 23 VAL cc_start: 0.9749 (t) cc_final: 0.9521 (t) REVERT: E 75 MET cc_start: 0.7729 (ttt) cc_final: 0.7170 (tpp) REVERT: E 182 ASP cc_start: 0.9395 (t0) cc_final: 0.9170 (t70) REVERT: F 92 ARG cc_start: 0.9457 (ttt180) cc_final: 0.9179 (ttt180) REVERT: H 38 LEU cc_start: 0.9177 (tp) cc_final: 0.8923 (tp) REVERT: H 95 TYR cc_start: 0.8453 (t80) cc_final: 0.8155 (t80) REVERT: H 142 LEU cc_start: 0.9200 (tp) cc_final: 0.8657 (tp) REVERT: H 143 LEU cc_start: 0.9211 (mp) cc_final: 0.8757 (mp) REVERT: I 119 TYR cc_start: 0.7910 (t80) cc_final: 0.7119 (t80) REVERT: K 85 ASP cc_start: 0.9030 (t0) cc_final: 0.8417 (t0) REVERT: K 135 PHE cc_start: 0.9209 (t80) cc_final: 0.8810 (t80) REVERT: L 67 PHE cc_start: 0.7660 (m-80) cc_final: 0.7161 (m-80) REVERT: N 55 LEU cc_start: 0.8873 (tt) cc_final: 0.8503 (tt) REVERT: O 131 HIS cc_start: 0.8164 (p90) cc_final: 0.7859 (p-80) REVERT: O 156 MET cc_start: 0.9205 (ptt) cc_final: 0.8848 (ptt) REVERT: O 509 MET cc_start: 0.7230 (mmm) cc_final: 0.6827 (mmm) REVERT: O 525 MET cc_start: 0.5108 (mtt) cc_final: 0.4857 (mtt) outliers start: 1 outliers final: 0 residues processed: 503 average time/residue: 0.4648 time to fit residues: 393.8057 Evaluate side-chains 370 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 370 time to evaluate : 4.627 ------------------------------------------------------------------------------- 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: 5.9990 chunk 427 optimal weight: 5.9990 chunk 390 optimal weight: 5.9990 chunk 415 optimal weight: 10.0000 chunk 250 optimal weight: 9.9990 chunk 181 optimal weight: 20.0000 chunk 326 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 375 optimal weight: 0.7980 chunk 393 optimal weight: 30.0000 chunk 414 optimal weight: 0.6980 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1026 GLN A1113 HIS A1180 ASN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 94 ASN ** O 105 ASN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.7646 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= 0.233 Angle : 0.620 8.767 51451 Z= 0.324 Chirality : 0.044 0.305 5747 Planarity : 0.004 0.063 6629 Dihedral : 4.916 29.357 5076 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.03 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: 0.32 (0.12), residues: 4618 helix: 1.14 (0.12), residues: 1730 sheet: -0.34 (0.19), residues: 673 loop : -0.26 (0.14), residues: 2215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 760 HIS 0.008 0.001 HIS A 378 PHE 0.038 0.002 PHE D 43 TYR 0.025 0.002 TYR L 29 ARG 0.007 0.000 ARG C 281 *********************** 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 488 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 488 time to evaluate : 4.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 PHE cc_start: 0.8970 (m-80) cc_final: 0.8576 (m-80) REVERT: A 355 PHE cc_start: 0.7943 (m-80) cc_final: 0.7622 (m-80) REVERT: A 570 THR cc_start: 0.8808 (p) cc_final: 0.8555 (t) REVERT: A 589 MET cc_start: 0.8364 (tpt) cc_final: 0.8085 (tpp) REVERT: A 600 MET cc_start: 0.9335 (mmm) cc_final: 0.8741 (tpt) REVERT: A 601 MET cc_start: 0.8333 (mmt) cc_final: 0.7232 (mmm) REVERT: A 617 HIS cc_start: 0.9456 (t-90) cc_final: 0.8902 (t-90) REVERT: A 625 ASN cc_start: 0.9034 (t0) cc_final: 0.8578 (t0) REVERT: A 636 HIS cc_start: 0.8194 (m-70) cc_final: 0.7787 (m-70) REVERT: A 657 TYR cc_start: 0.8513 (t80) cc_final: 0.8120 (t80) REVERT: A 925 MET cc_start: 0.8786 (mmp) cc_final: 0.8579 (mmp) REVERT: A 928 MET cc_start: 0.9117 (mtm) cc_final: 0.8761 (ttp) REVERT: A 944 MET cc_start: 0.9116 (mmp) cc_final: 0.8744 (mmm) REVERT: A 1049 MET cc_start: 0.7793 (ttm) cc_final: 0.7477 (ttm) REVERT: A 1059 LYS cc_start: 0.8885 (mtmt) cc_final: 0.8382 (mtpt) REVERT: A 1483 LEU cc_start: 0.9312 (mp) cc_final: 0.9058 (mp) REVERT: A 1603 MET cc_start: 0.7645 (ppp) cc_final: 0.7405 (ppp) REVERT: A 1634 LEU cc_start: 0.9367 (mt) cc_final: 0.8948 (mt) REVERT: B 248 ASN cc_start: 0.9013 (m-40) cc_final: 0.8724 (m-40) REVERT: B 308 LEU cc_start: 0.9448 (mt) cc_final: 0.9144 (tt) REVERT: B 373 MET cc_start: 0.8030 (mmp) cc_final: 0.7780 (mmp) REVERT: B 493 PHE cc_start: 0.7664 (t80) cc_final: 0.7306 (t80) REVERT: B 528 LEU cc_start: 0.9575 (tp) cc_final: 0.9260 (tp) REVERT: B 593 ILE cc_start: 0.9462 (mp) cc_final: 0.9036 (tp) REVERT: B 640 LEU cc_start: 0.9290 (tp) cc_final: 0.9021 (tp) REVERT: B 726 MET cc_start: 0.7890 (mmp) cc_final: 0.7312 (tpp) REVERT: B 744 LEU cc_start: 0.9042 (tp) cc_final: 0.8782 (tp) REVERT: B 853 GLU cc_start: 0.8818 (pm20) cc_final: 0.8508 (pp20) REVERT: B 886 ASN cc_start: 0.7789 (m-40) cc_final: 0.7450 (m-40) REVERT: B 962 MET cc_start: 0.9139 (mmm) cc_final: 0.8923 (mmm) REVERT: B 1074 MET cc_start: 0.8814 (mtm) cc_final: 0.8364 (mmm) REVERT: B 1196 LEU cc_start: 0.8563 (tp) cc_final: 0.8272 (tp) REVERT: C 82 TYR cc_start: 0.7074 (m-10) cc_final: 0.6824 (m-10) REVERT: C 94 ASP cc_start: 0.8590 (p0) cc_final: 0.8060 (p0) REVERT: E 22 MET cc_start: 0.8620 (tmm) cc_final: 0.8264 (tmm) REVERT: E 23 VAL cc_start: 0.9749 (t) cc_final: 0.9518 (t) REVERT: E 75 MET cc_start: 0.7747 (ttt) cc_final: 0.7180 (tpp) REVERT: E 115 ASN cc_start: 0.9227 (t0) cc_final: 0.9015 (t0) REVERT: E 121 MET cc_start: 0.8559 (pmm) cc_final: 0.8163 (pmm) REVERT: E 182 ASP cc_start: 0.9422 (t0) cc_final: 0.9147 (t70) REVERT: F 92 ARG cc_start: 0.9476 (ttt180) cc_final: 0.9077 (ttt-90) REVERT: H 95 TYR cc_start: 0.8477 (t80) cc_final: 0.8142 (t80) REVERT: H 142 LEU cc_start: 0.9166 (tp) cc_final: 0.8692 (tp) REVERT: H 143 LEU cc_start: 0.9219 (mp) cc_final: 0.8832 (mt) REVERT: J 49 MET cc_start: 0.9255 (mmp) cc_final: 0.9053 (mmm) REVERT: K 85 ASP cc_start: 0.9173 (t0) cc_final: 0.8428 (t0) REVERT: K 126 ASP cc_start: 0.9076 (m-30) cc_final: 0.8843 (m-30) REVERT: K 135 PHE cc_start: 0.9275 (t80) cc_final: 0.8887 (t80) REVERT: L 67 PHE cc_start: 0.7690 (m-80) cc_final: 0.7202 (m-80) REVERT: M 90 LEU cc_start: 0.8966 (mt) cc_final: 0.8738 (mt) REVERT: N 37 ASN cc_start: 0.7436 (p0) cc_final: 0.7135 (p0) REVERT: N 55 LEU cc_start: 0.8811 (tt) cc_final: 0.8387 (tt) REVERT: O 131 HIS cc_start: 0.8211 (p90) cc_final: 0.7986 (p-80) REVERT: O 156 MET cc_start: 0.9220 (ptt) cc_final: 0.8880 (ptt) REVERT: O 509 MET cc_start: 0.7233 (mmm) cc_final: 0.6831 (mmm) REVERT: O 525 MET cc_start: 0.5113 (mtt) cc_final: 0.4375 (mtt) outliers start: 0 outliers final: 0 residues processed: 488 average time/residue: 0.4790 time to fit residues: 392.8682 Evaluate side-chains 363 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 4.577 ------------------------------------------------------------------------------- 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: 0.9980 chunk 439 optimal weight: 0.0770 chunk 268 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 chunk 305 optimal weight: 0.2980 chunk 461 optimal weight: 6.9990 chunk 424 optimal weight: 10.0000 chunk 367 optimal weight: 4.9990 chunk 38 optimal weight: 20.0000 chunk 283 optimal weight: 0.0270 chunk 225 optimal weight: 9.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- 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** ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1180 ASN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 ASN ** B 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 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** ** O 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.7675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 38083 Z= 0.159 Angle : 0.626 11.528 51451 Z= 0.318 Chirality : 0.045 0.223 5747 Planarity : 0.004 0.056 6629 Dihedral : 4.683 28.164 5076 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.25 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: 0.48 (0.13), residues: 4618 helix: 1.27 (0.13), residues: 1729 sheet: -0.27 (0.19), residues: 705 loop : -0.16 (0.14), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 760 HIS 0.008 0.001 HIS A 378 PHE 0.030 0.001 PHE F 58 TYR 0.023 0.001 TYR L 29 ARG 0.017 0.000 ARG F 135 ********************** 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 526 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 526 time to evaluate : 4.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 PHE cc_start: 0.8897 (m-80) cc_final: 0.8530 (m-80) REVERT: A 94 LEU cc_start: 0.9088 (tp) cc_final: 0.8873 (tp) REVERT: A 125 LEU cc_start: 0.9312 (mt) cc_final: 0.9085 (tt) REVERT: A 227 LEU cc_start: 0.8853 (pp) cc_final: 0.8549 (pp) REVERT: A 466 LEU cc_start: 0.9167 (tp) cc_final: 0.8295 (mt) REVERT: A 600 MET cc_start: 0.9211 (mmm) cc_final: 0.8723 (tpt) REVERT: A 601 MET cc_start: 0.8312 (mmt) cc_final: 0.7151 (mmm) REVERT: A 617 HIS cc_start: 0.9287 (t-90) cc_final: 0.8870 (t-90) REVERT: A 625 ASN cc_start: 0.8965 (t0) cc_final: 0.8461 (t0) REVERT: A 636 HIS cc_start: 0.8177 (m-70) cc_final: 0.7868 (m-70) REVERT: A 657 TYR cc_start: 0.8491 (t80) cc_final: 0.8216 (t80) REVERT: A 743 ASP cc_start: 0.8571 (p0) cc_final: 0.8264 (p0) REVERT: A 928 MET cc_start: 0.9141 (mtm) cc_final: 0.8663 (ttm) REVERT: A 944 MET cc_start: 0.9066 (mmp) cc_final: 0.8818 (mmm) REVERT: A 1049 MET cc_start: 0.7718 (ttm) cc_final: 0.7374 (ttm) REVERT: A 1056 ASP cc_start: 0.7300 (t0) cc_final: 0.7001 (t0) REVERT: A 1059 LYS cc_start: 0.8761 (mtmt) cc_final: 0.8270 (mtpt) REVERT: A 1200 MET cc_start: 0.7535 (mmp) cc_final: 0.6409 (tpp) REVERT: A 1201 THR cc_start: 0.8711 (p) cc_final: 0.8276 (t) REVERT: A 1238 MET cc_start: 0.8747 (mtt) cc_final: 0.8380 (mpp) REVERT: A 1596 LEU cc_start: 0.8775 (mt) cc_final: 0.8296 (tp) REVERT: A 1603 MET cc_start: 0.7773 (ppp) cc_final: 0.7361 (ppp) REVERT: A 1634 LEU cc_start: 0.9326 (mt) cc_final: 0.8907 (mt) REVERT: B 248 ASN cc_start: 0.9049 (m-40) cc_final: 0.8723 (m110) REVERT: B 308 LEU cc_start: 0.9398 (mt) cc_final: 0.9085 (tt) REVERT: B 493 PHE cc_start: 0.7586 (t80) cc_final: 0.7352 (t80) REVERT: B 502 MET cc_start: 0.7479 (tpt) cc_final: 0.7100 (tpt) REVERT: B 528 LEU cc_start: 0.9573 (tp) cc_final: 0.9264 (tp) REVERT: B 593 ILE cc_start: 0.9415 (mp) cc_final: 0.8964 (tp) REVERT: B 640 LEU cc_start: 0.9181 (tp) cc_final: 0.8849 (tp) REVERT: B 703 LEU cc_start: 0.9272 (mt) cc_final: 0.8915 (mt) REVERT: B 726 MET cc_start: 0.7534 (mmp) cc_final: 0.6936 (tpp) REVERT: B 744 LEU cc_start: 0.8946 (tp) cc_final: 0.8623 (tp) REVERT: B 783 MET cc_start: 0.8223 (mmp) cc_final: 0.7954 (mmp) REVERT: B 853 GLU cc_start: 0.8763 (pm20) cc_final: 0.8480 (pp20) REVERT: B 886 ASN cc_start: 0.7471 (m-40) cc_final: 0.7231 (m-40) REVERT: B 1074 MET cc_start: 0.8672 (mtm) cc_final: 0.8264 (mmm) REVERT: B 1196 LEU cc_start: 0.8583 (tp) cc_final: 0.8087 (tp) REVERT: C 94 ASP cc_start: 0.8583 (p0) cc_final: 0.8138 (p0) REVERT: C 157 TYR cc_start: 0.8195 (m-10) cc_final: 0.7896 (m-10) REVERT: C 192 LEU cc_start: 0.8524 (tp) cc_final: 0.8302 (tp) REVERT: E 75 MET cc_start: 0.7554 (ttt) cc_final: 0.7240 (tpp) REVERT: E 115 ASN cc_start: 0.9219 (t0) cc_final: 0.8910 (t0) REVERT: E 182 ASP cc_start: 0.9390 (t0) cc_final: 0.9156 (t70) REVERT: H 38 LEU cc_start: 0.9024 (tp) cc_final: 0.8748 (tp) REVERT: H 95 TYR cc_start: 0.8376 (t80) cc_final: 0.8124 (t80) REVERT: H 142 LEU cc_start: 0.9013 (tp) cc_final: 0.8432 (tp) REVERT: H 143 LEU cc_start: 0.9184 (mp) cc_final: 0.8777 (mt) REVERT: I 119 TYR cc_start: 0.7670 (t80) cc_final: 0.7127 (t80) REVERT: I 122 ARG cc_start: 0.4022 (tpt170) cc_final: 0.3675 (tpt170) REVERT: J 61 LEU cc_start: 0.9418 (mt) cc_final: 0.9113 (mt) REVERT: K 125 MET cc_start: 0.8998 (mmm) cc_final: 0.8695 (mmm) REVERT: K 135 PHE cc_start: 0.9241 (t80) cc_final: 0.8880 (t80) REVERT: L 67 PHE cc_start: 0.7649 (m-80) cc_final: 0.7373 (m-80) REVERT: N 55 LEU cc_start: 0.8830 (tt) cc_final: 0.8214 (tt) REVERT: O 131 HIS cc_start: 0.8173 (p90) cc_final: 0.7900 (p-80) REVERT: O 156 MET cc_start: 0.9183 (ptt) cc_final: 0.8964 (ptt) REVERT: O 182 MET cc_start: 0.8847 (mpp) cc_final: 0.8570 (mpp) REVERT: O 191 ASP cc_start: 0.8442 (t0) cc_final: 0.8051 (t70) REVERT: O 509 MET cc_start: 0.7138 (mmm) cc_final: 0.6721 (mmm) REVERT: O 525 MET cc_start: 0.4969 (mtt) cc_final: 0.4281 (mtt) outliers start: 0 outliers final: 0 residues processed: 526 average time/residue: 0.4529 time to fit residues: 399.7220 Evaluate side-chains 388 residues out of total 4180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 388 time to evaluate : 3.826 ------------------------------------------------------------------------------- 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: 6.9990 chunk 391 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 338 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 chunk 367 optimal weight: 6.9990 chunk 153 optimal weight: 20.0000 chunk 377 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 67 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** A1180 ASN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1082 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.048130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.035316 restraints weight = 265928.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.036605 restraints weight = 170242.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.037547 restraints weight = 122975.931| |-----------------------------------------------------------------------------| r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.7916 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= 0.239 Angle : 0.634 9.609 51451 Z= 0.329 Chirality : 0.044 0.202 5747 Planarity : 0.004 0.059 6629 Dihedral : 4.761 28.127 5076 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.07 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: 0.41 (0.12), residues: 4618 helix: 1.21 (0.13), residues: 1732 sheet: -0.26 (0.19), residues: 677 loop : -0.22 (0.14), residues: 2209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 760 HIS 0.015 0.001 HIS B1082 PHE 0.025 0.002 PHE F 143 TYR 0.024 0.002 TYR L 29 ARG 0.010 0.001 ARG A 834 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8797.95 seconds wall clock time: 163 minutes 57.61 seconds (9837.61 seconds total)