Starting phenix.real_space_refine on Fri Mar 22 07:29:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnx_9852/03_2024/6jnx_9852.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnx_9852/03_2024/6jnx_9852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnx_9852/03_2024/6jnx_9852.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnx_9852/03_2024/6jnx_9852.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnx_9852/03_2024/6jnx_9852.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnx_9852/03_2024/6jnx_9852.pdb" } resolution = 4.08 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 144 5.49 5 Mg 1 5.21 5 S 140 5.16 5 C 20038 2.51 5 N 5784 2.21 5 O 6530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "D TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 31": "NH1" <-> "NH2" Residue "P ARG 113": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32639 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1686 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 209} 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: "B" Number of atoms: 1681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1681 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1282} Chain: "D" Number of atoms: 10388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10388 Classifications: {'peptide': 1335} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1279} Chain breaks: 2 Chain: "E" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 2513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2513 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 6, 'TRANS': 300} Chain breaks: 2 Chain: "N" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1303 Classifications: {'DNA': 63} Link IDs: {'rna3p': 62} Chain: "R" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 394 Classifications: {'RNA': 18} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 10, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 14} Chain: "T" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1281 Classifications: {'DNA': 63} Link IDs: {'rna3p': 62} Chain: "P" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1179 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 141} 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: "Q" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1017 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain breaks: 1 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14383 SG CYS D 70 111.878 74.258 65.292 1.00223.00 S ATOM 14397 SG CYS D 72 112.736 73.289 61.949 1.00232.47 S ATOM 14505 SG CYS D 85 115.346 73.984 65.124 1.00231.39 S ATOM 20217 SG CYS D 814 88.075 90.596 127.947 1.00146.96 S ATOM 20782 SG CYS D 888 87.842 90.725 123.283 1.00139.40 S ATOM 20833 SG CYS D 895 86.868 88.075 125.508 1.00144.50 S ATOM 20854 SG CYS D 898 85.112 91.115 126.069 1.00145.73 S Time building chain proxies: 16.46, per 1000 atoms: 0.50 Number of scatterers: 32639 At special positions: 0 Unit cell: (172.524, 184.287, 164.682, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 140 16.00 P 144 15.00 Mg 1 11.99 O 6530 8.00 N 5784 7.00 C 20038 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: 14.27 Conformation dependent library (CDL) restraints added in 5.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " Number of angles added : 6 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6988 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 54 sheets defined 43.2% alpha, 13.1% beta 57 base pairs and 110 stacking pairs defined. Time for finding SS restraints: 12.25 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.787A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.902A pdb=" N ASP A 114 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE A 115 " --> pdb=" O ALA A 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 111 through 115' Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.700A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA B 42 " --> pdb=" O THR B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.709A pdb=" N LEU B 82 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 212 through 228 removed outlier: 3.869A pdb=" N ALA B 216 " --> pdb=" O ASP B 212 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 232 removed outlier: 3.567A pdb=" N VAL B 232 " --> pdb=" O GLU B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 229 through 232' Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'C' and resid 28 through 39 removed outlier: 3.503A pdb=" N ILE C 39 " --> pdb=" O PHE C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.511A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.610A pdb=" N CYS C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 213 Processing helix chain 'C' and resid 216 through 224 Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.581A pdb=" N ALA C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 289 through 294' Processing helix chain 'C' and resid 318 through 327 Processing helix chain 'C' and resid 345 through 354 removed outlier: 4.203A pdb=" N GLU C 349 " --> pdb=" O PRO C 345 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR C 350 " --> pdb=" O TYR C 346 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP C 354 " --> pdb=" O THR C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.996A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.789A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 481 removed outlier: 3.829A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 508 removed outlier: 4.387A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 removed outlier: 3.640A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 549 removed outlier: 3.678A pdb=" N ARG C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 667 removed outlier: 3.716A pdb=" N LEU C 667 " --> pdb=" O VAL C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 688 removed outlier: 3.754A pdb=" N GLN C 688 " --> pdb=" O ASN C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 826 Processing helix chain 'C' and resid 858 through 863 removed outlier: 3.905A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 Processing helix chain 'C' and resid 942 through 977 Processing helix chain 'C' and resid 993 through 998 removed outlier: 3.583A pdb=" N ARG C 996 " --> pdb=" O PRO C 993 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TRP C 997 " --> pdb=" O ARG C 994 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU C 998 " --> pdb=" O ASP C 995 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 993 through 998' Processing helix chain 'C' and resid 1005 through 1038 removed outlier: 3.504A pdb=" N ASN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN C1038 " --> pdb=" O ARG C1034 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1084 removed outlier: 3.597A pdb=" N ASP C1084 " --> pdb=" O PRO C1081 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1081 through 1084' Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 4.415A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.729A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.875A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU C1151 " --> pdb=" O ARG C1147 " (cutoff:3.500A) Processing helix chain 'C' and resid 1167 through 1177 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1242 removed outlier: 3.735A pdb=" N ASP C1241 " --> pdb=" O LEU C1238 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1281 Processing helix chain 'C' and resid 1283 through 1293 removed outlier: 4.426A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN C1288 " --> pdb=" O ALA C1284 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1309 Processing helix chain 'C' and resid 1320 through 1333 Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.546A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU D 100 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 163 through 172 Processing helix chain 'D' and resid 180 through 191 Processing helix chain 'D' and resid 194 through 208 Processing helix chain 'D' and resid 210 through 230 removed outlier: 3.593A pdb=" N GLN D 229 " --> pdb=" O GLU D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 removed outlier: 3.693A pdb=" N TRP D 236 " --> pdb=" O LYS D 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 233 through 236' Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 286 removed outlier: 3.566A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 336 through 342 removed outlier: 3.571A pdb=" N LEU D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 removed outlier: 3.514A pdb=" N ALA D 397 " --> pdb=" O THR D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 416 removed outlier: 4.251A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 452 through 458 removed outlier: 4.416A pdb=" N ALA D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 505 through 514 Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.569A pdb=" N ALA D 533 " --> pdb=" O GLY D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 580 Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.970A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.595A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 Processing helix chain 'D' and resid 674 through 702 Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 741 Processing helix chain 'D' and resid 769 through 805 removed outlier: 3.706A pdb=" N TYR D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP D 802 " --> pdb=" O ARG D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 840 Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 897 through 899 No H-bonds generated for 'chain 'D' and resid 897 through 899' Processing helix chain 'D' and resid 914 through 925 removed outlier: 4.119A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 928 No H-bonds generated for 'chain 'D' and resid 926 through 928' Processing helix chain 'D' and resid 1137 through 1147 removed outlier: 3.677A pdb=" N VAL D1141 " --> pdb=" O GLY D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1225 removed outlier: 3.608A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1245 removed outlier: 3.555A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 Processing helix chain 'D' and resid 1282 through 1293 Processing helix chain 'D' and resid 1308 through 1313 Processing helix chain 'D' and resid 1318 through 1325 removed outlier: 3.588A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1349 through 1354 Processing helix chain 'D' and resid 1360 through 1373 removed outlier: 3.987A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG D1373 " --> pdb=" O ARG D1369 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 32 removed outlier: 3.884A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 78 removed outlier: 3.722A pdb=" N LEU E 64 " --> pdb=" O ASN E 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 removed outlier: 3.801A pdb=" N MET F 100 " --> pdb=" O ASP F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 136 removed outlier: 3.578A pdb=" N GLU F 116 " --> pdb=" O THR F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 removed outlier: 3.657A pdb=" N ILE F 141 " --> pdb=" O TYR F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 234 removed outlier: 4.073A pdb=" N THR F 234 " --> pdb=" O VAL F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 258 removed outlier: 3.957A pdb=" N GLN F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 292 removed outlier: 3.744A pdb=" N PHE F 266 " --> pdb=" O VAL F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 306 removed outlier: 3.934A pdb=" N LEU F 305 " --> pdb=" O ASN F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 321 Processing helix chain 'F' and resid 324 through 330 Processing helix chain 'F' and resid 333 through 352 removed outlier: 4.107A pdb=" N LYS F 343 " --> pdb=" O ARG F 339 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 392 removed outlier: 5.963A pdb=" N ARG F 385 " --> pdb=" O GLU F 381 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU F 386 " --> pdb=" O ALA F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 418 removed outlier: 3.554A pdb=" N LEU F 404 " --> pdb=" O GLN F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 446 removed outlier: 4.085A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 29 Processing helix chain 'P' and resid 39 through 46 removed outlier: 4.366A pdb=" N SER P 46 " --> pdb=" O LYS P 42 " (cutoff:3.500A) Processing helix chain 'P' and resid 59 through 75 Processing helix chain 'P' and resid 77 through 89 Processing helix chain 'P' and resid 93 through 104 removed outlier: 3.738A pdb=" N VAL P 104 " --> pdb=" O TYR P 100 " (cutoff:3.500A) Processing helix chain 'P' and resid 122 through 153 removed outlier: 3.527A pdb=" N ARG P 127 " --> pdb=" O LEU P 123 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ARG P 128 " --> pdb=" O ALA P 124 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE P 133 " --> pdb=" O GLU P 129 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU P 134 " --> pdb=" O VAL P 130 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE P 139 " --> pdb=" O ASN P 135 " (cutoff:3.500A) Proline residue: P 143 - end of helix removed outlier: 3.708A pdb=" N LYS P 150 " --> pdb=" O ASP P 146 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 29 removed outlier: 3.897A pdb=" N SER Q 29 " --> pdb=" O ALA Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 37 through 45 Processing helix chain 'Q' and resid 61 through 74 Processing helix chain 'Q' and resid 78 through 88 Processing helix chain 'Q' and resid 93 through 104 Processing helix chain 'Q' and resid 122 through 142 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 17 removed outlier: 5.256A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 61 removed outlier: 5.560A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET A 142 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 110 removed outlier: 3.782A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 16 through 18 removed outlier: 3.502A pdb=" N GLU B 17 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N THR B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N VAL B 192 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG B 182 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 101 removed outlier: 3.585A pdb=" N VAL B 98 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AA9, first strand: chain 'B' and resid 104 through 105 Processing sheet with id=AB1, first strand: chain 'B' and resid 108 through 111 Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.786A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.786A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 453 Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 158 removed outlier: 3.759A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 227 through 231 Processing sheet with id=AB8, first strand: chain 'C' and resid 239 through 240 Processing sheet with id=AB9, first strand: chain 'C' and resid 255 through 257 removed outlier: 7.219A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 301 through 302 removed outlier: 3.863A pdb=" N TYR C 301 " --> pdb=" O CYS C 311 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.397A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.528A pdb=" N ILE C 616 " --> pdb=" O ARG C 637 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG C 637 " --> pdb=" O ILE C 616 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 716 through 718 removed outlier: 6.508A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP C 781 " --> pdb=" O ALA C 718 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 749 through 752 removed outlier: 6.881A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.536A pdb=" N THR C 757 " --> pdb=" O ILE C 765 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C 765 " --> pdb=" O THR C 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC8, first strand: chain 'C' and resid 1066 through 1067 removed outlier: 5.150A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 9.562A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1066 through 1067 Processing sheet with id=AD1, first strand: chain 'C' and resid 830 through 838 removed outlier: 6.805A pdb=" N ILE C1049 " --> pdb=" O VAL C 933 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL C 933 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LYS C1051 " --> pdb=" O VAL C 931 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL C 931 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.791A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1086 through 1087 Processing sheet with id=AD4, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.786A pdb=" N GLN D 435 " --> pdb=" O LEU D 423 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD6, first strand: chain 'C' and resid 1268 through 1270 removed outlier: 3.584A pdb=" N GLN C1268 " --> pdb=" O VAL D 347 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS D 345 " --> pdb=" O PHE C1270 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 1335 through 1339 Processing sheet with id=AD8, first strand: chain 'D' and resid 34 through 37 removed outlier: 4.374A pdb=" N SER D 34 " --> pdb=" O MET D 102 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N HIS D 104 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLY D 36 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU D 106 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.510A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.298A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 144 through 145 Processing sheet with id=AE1, first strand: chain 'D' and resid 253 through 254 removed outlier: 3.893A pdb=" N VAL D 253 " --> pdb=" O ALA D 261 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 366 through 369 removed outlier: 6.366A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.561A pdb=" N LEU D 527 " --> pdb=" O LYS D 549 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 552 through 554 removed outlier: 3.628A pdb=" N ILE D 552 " --> pdb=" O SER D 568 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 706 through 707 Processing sheet with id=AE6, first strand: chain 'D' and resid 809 through 811 removed outlier: 6.174A pdb=" N VAL D 894 " --> pdb=" O VAL D 809 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU D 811 " --> pdb=" O VAL D 894 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE8, first strand: chain 'D' and resid 825 through 826 removed outlier: 3.810A pdb=" N GLU D 833 " --> pdb=" O VAL D 825 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 848 through 849 removed outlier: 6.409A pdb=" N VAL D 848 " --> pdb=" O LEU D 857 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 957 through 961 removed outlier: 4.369A pdb=" N THR D 980 " --> pdb=" O VAL D 997 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AF3, first strand: chain 'D' and resid 1025 through 1026 Processing sheet with id=AF4, first strand: chain 'D' and resid 1077 through 1081 removed outlier: 4.206A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG D1036 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY D1033 " --> pdb=" O ILE D1115 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 1046 through 1049 removed outlier: 3.531A pdb=" N SER D1058 " --> pdb=" O GLN D1049 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 1162 through 1165 Processing sheet with id=AF7, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 6.332A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 162 through 165 removed outlier: 6.013A pdb=" N ARG F 260 " --> pdb=" O THR F 163 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Q' and resid 108 through 109 1311 hydrogen bonds defined for protein. 3732 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 138 hydrogen bonds 272 hydrogen bond angles 0 basepair planarities 57 basepair parallelities 110 stacking parallelities Total time for adding SS restraints: 15.80 Time building geometry restraints manager: 15.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7115 1.32 - 1.45: 7632 1.45 - 1.57: 18173 1.57 - 1.69: 285 1.69 - 1.81: 244 Bond restraints: 33449 Sorted by residual: bond pdb=" C SER A 178 " pdb=" N PRO A 179 " ideal model delta sigma weight residual 1.337 1.269 0.068 1.24e-02 6.50e+03 3.02e+01 bond pdb=" CA SER P 37 " pdb=" CB SER P 37 " ideal model delta sigma weight residual 1.542 1.508 0.035 8.90e-03 1.26e+04 1.51e+01 bond pdb=" C ASP C1084 " pdb=" N MET C1085 " ideal model delta sigma weight residual 1.331 1.278 0.052 1.48e-02 4.57e+03 1.26e+01 bond pdb=" C PRO C1093 " pdb=" N VAL C1094 " ideal model delta sigma weight residual 1.332 1.284 0.048 1.36e-02 5.41e+03 1.22e+01 bond pdb=" N ASP C 358 " pdb=" CA ASP C 358 " ideal model delta sigma weight residual 1.453 1.494 -0.040 1.22e-02 6.72e+03 1.10e+01 ... (remaining 33444 not shown) Histogram of bond angle deviations from ideal: 95.78 - 103.46: 758 103.46 - 111.14: 13781 111.14 - 118.82: 13751 118.82 - 126.50: 16775 126.50 - 134.18: 721 Bond angle restraints: 45786 Sorted by residual: angle pdb=" N ARG Q 113 " pdb=" CA ARG Q 113 " pdb=" C ARG Q 113 " ideal model delta sigma weight residual 111.36 101.38 9.98 1.09e+00 8.42e-01 8.38e+01 angle pdb=" N ASP D 710 " pdb=" CA ASP D 710 " pdb=" C ASP D 710 " ideal model delta sigma weight residual 113.38 104.26 9.12 1.17e+00 7.31e-01 6.07e+01 angle pdb=" N ILE D1210 " pdb=" CA ILE D1210 " pdb=" C ILE D1210 " ideal model delta sigma weight residual 112.12 106.72 5.40 8.40e-01 1.42e+00 4.14e+01 angle pdb=" O3' DT T 48 " pdb=" C3' DT T 48 " pdb=" C2' DT T 48 " ideal model delta sigma weight residual 111.50 102.07 9.43 1.50e+00 4.44e-01 3.96e+01 angle pdb=" N GLY D1171 " pdb=" CA GLY D1171 " pdb=" C GLY D1171 " ideal model delta sigma weight residual 115.08 107.97 7.11 1.19e+00 7.06e-01 3.57e+01 ... (remaining 45781 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.26: 19273 35.26 - 70.51: 931 70.51 - 105.77: 25 105.77 - 141.03: 3 141.03 - 176.28: 2 Dihedral angle restraints: 20234 sinusoidal: 9381 harmonic: 10853 Sorted by residual: dihedral pdb=" O4' U R 20 " pdb=" C1' U R 20 " pdb=" N1 U R 20 " pdb=" C2 U R 20 " ideal model delta sinusoidal sigma weight residual 200.00 77.41 122.59 1 1.50e+01 4.44e-03 6.56e+01 dihedral pdb=" CA VAL C 228 " pdb=" C VAL C 228 " pdb=" N ILE C 229 " pdb=" CA ILE C 229 " ideal model delta harmonic sigma weight residual -180.00 -150.12 -29.88 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA SER C1295 " pdb=" C SER C1295 " pdb=" N ASP C1296 " pdb=" CA ASP C1296 " ideal model delta harmonic sigma weight residual -180.00 -150.54 -29.46 0 5.00e+00 4.00e-02 3.47e+01 ... (remaining 20231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3992 0.072 - 0.144: 1060 0.144 - 0.216: 121 0.216 - 0.288: 21 0.288 - 0.360: 7 Chirality restraints: 5201 Sorted by residual: chirality pdb=" C3' U R 16 " pdb=" C4' U R 16 " pdb=" O3' U R 16 " pdb=" C2' U R 16 " both_signs ideal model delta sigma weight residual False -2.48 -2.12 -0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" C2' U R 16 " pdb=" C3' U R 16 " pdb=" O2' U R 16 " pdb=" C1' U R 16 " both_signs ideal model delta sigma weight residual False -2.75 -3.08 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CB ILE C 765 " pdb=" CA ILE C 765 " pdb=" CG1 ILE C 765 " pdb=" CG2 ILE C 765 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 5198 not shown) Planarity restraints: 5447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 357 " 0.021 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C ASN C 357 " -0.073 2.00e-02 2.50e+03 pdb=" O ASN C 357 " 0.028 2.00e-02 2.50e+03 pdb=" N ASP C 358 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 43 " -0.018 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C THR D 43 " 0.064 2.00e-02 2.50e+03 pdb=" O THR D 43 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE D 44 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 29 " 0.054 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO B 30 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO B 30 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 30 " 0.041 5.00e-02 4.00e+02 ... (remaining 5444 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 202 2.47 - 3.08: 22308 3.08 - 3.68: 53379 3.68 - 4.29: 73715 4.29 - 4.90: 115170 Nonbonded interactions: 264774 Sorted by model distance: nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1501 " model vdw 1.858 2.170 nonbonded pdb=" OP1 G R 19 " pdb="MG MG D1501 " model vdw 1.882 2.170 nonbonded pdb=" OD2 ASP D 462 " pdb="MG MG D1501 " model vdw 1.970 2.170 nonbonded pdb=" O GLY D1171 " pdb=" CD LYS D1172 " model vdw 2.014 3.440 nonbonded pdb=" N GLU P 33 " pdb=" OE1 GLU P 33 " model vdw 2.212 2.520 ... (remaining 264769 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 135 or (resid 136 and (name N or name CA or name \ C or name O or name CB )) or resid 137 through 158 or resid 170 through 232)) selection = (chain 'B' and (resid 8 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 232)) } ncs_group { reference = (chain 'P' and (resid 7 through 47 or resid 60 through 144)) selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 3.920 Check model and map are aligned: 0.470 Set scattering table: 0.300 Process input model: 100.260 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 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 : 0.012 0.095 33449 Z= 0.740 Angle : 1.232 12.295 45786 Z= 0.704 Chirality : 0.064 0.360 5201 Planarity : 0.008 0.082 5447 Dihedral : 16.708 176.282 13246 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.67 % Favored : 92.01 % Rotamer: Outliers : 0.90 % Allowed : 6.18 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % 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: -3.99 (0.11), residues: 3741 helix: -2.81 (0.10), residues: 1448 sheet: -2.00 (0.25), residues: 386 loop : -2.65 (0.12), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.005 TRP C 183 HIS 0.019 0.003 HIS D1252 PHE 0.032 0.004 PHE C 224 TYR 0.043 0.004 TYR C1251 ARG 0.021 0.001 ARG D 312 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 974 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 945 time to evaluate : 3.797 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: A 9 LEU cc_start: 0.6167 (mt) cc_final: 0.5877 (mm) REVERT: A 10 LYS cc_start: 0.8434 (mttp) cc_final: 0.8231 (mmtp) REVERT: A 29 GLU cc_start: 0.7019 (tt0) cc_final: 0.6763 (pm20) REVERT: A 41 ASN cc_start: 0.8731 (t0) cc_final: 0.8485 (t0) REVERT: A 97 GLU cc_start: 0.8034 (pp20) cc_final: 0.7669 (pm20) REVERT: A 206 GLU cc_start: 0.7535 (tp30) cc_final: 0.6554 (tm-30) REVERT: A 212 ASP cc_start: 0.8641 (m-30) cc_final: 0.7931 (p0) REVERT: B 18 GLN cc_start: 0.7531 (pt0) cc_final: 0.7318 (pm20) REVERT: B 59 VAL cc_start: 0.9323 (t) cc_final: 0.8872 (p) REVERT: B 77 ASP cc_start: 0.6194 (m-30) cc_final: 0.5449 (m-30) REVERT: B 79 LEU cc_start: 0.8041 (tp) cc_final: 0.7715 (pp) REVERT: B 81 ILE cc_start: 0.7982 (tt) cc_final: 0.7485 (tt) REVERT: B 205 MET cc_start: 0.7480 (ppp) cc_final: 0.7061 (ppp) REVERT: B 226 GLU cc_start: 0.8443 (mm-30) cc_final: 0.7899 (tt0) REVERT: B 227 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7743 (mm-40) REVERT: C 8 LYS cc_start: 0.8569 (mttt) cc_final: 0.8148 (mttp) REVERT: C 83 GLN cc_start: 0.5718 (pm20) cc_final: 0.5135 (tp40) REVERT: C 84 GLU cc_start: 0.8418 (tt0) cc_final: 0.8086 (tt0) REVERT: C 132 ASP cc_start: 0.8704 (m-30) cc_final: 0.8450 (t0) REVERT: C 214 ASN cc_start: 0.8517 (t0) cc_final: 0.8304 (p0) REVERT: C 256 GLU cc_start: 0.5352 (pt0) cc_final: 0.4931 (tt0) REVERT: C 265 LYS cc_start: 0.1851 (mtmp) cc_final: 0.0738 (tttt) REVERT: C 423 ASP cc_start: 0.6727 (m-30) cc_final: 0.6366 (t0) REVERT: C 549 ASP cc_start: 0.8680 (t0) cc_final: 0.8011 (m-30) REVERT: C 563 THR cc_start: 0.9221 (t) cc_final: 0.8876 (m) REVERT: C 645 PHE cc_start: 0.8218 (m-10) cc_final: 0.7486 (m-10) REVERT: C 694 ARG cc_start: 0.7748 (tpp80) cc_final: 0.6783 (mtm110) REVERT: C 706 ARG cc_start: 0.8092 (mmm-85) cc_final: 0.7026 (mmt180) REVERT: C 741 MET cc_start: 0.8057 (ttp) cc_final: 0.7557 (ttt) REVERT: C 768 MET cc_start: 0.6804 (mtp) cc_final: 0.6236 (mtm) REVERT: C 778 GLU cc_start: 0.7686 (tp30) cc_final: 0.7345 (mm-30) REVERT: C 779 ARG cc_start: 0.7298 (ttt-90) cc_final: 0.7064 (ttp80) REVERT: C 800 MET cc_start: 0.7977 (mtm) cc_final: 0.7748 (mtp) REVERT: C 835 GLU cc_start: 0.8902 (tt0) cc_final: 0.8094 (tm-30) REVERT: C 909 LYS cc_start: 0.8300 (pmmt) cc_final: 0.7664 (tmtt) REVERT: C 937 ASP cc_start: 0.8539 (t0) cc_final: 0.8267 (t0) REVERT: C 949 GLU cc_start: 0.9069 (tt0) cc_final: 0.8467 (mt-10) REVERT: C 1073 LYS cc_start: 0.8587 (mttt) cc_final: 0.8203 (mmtt) REVERT: C 1080 ASN cc_start: 0.8144 (t0) cc_final: 0.7920 (t0) REVERT: C 1089 GLU cc_start: 0.7781 (pp20) cc_final: 0.7426 (pt0) REVERT: C 1107 MET cc_start: 0.7067 (mtm) cc_final: 0.6775 (mtt) REVERT: C 1122 LYS cc_start: 0.8154 (tptp) cc_final: 0.7311 (tptt) REVERT: C 1126 ASP cc_start: 0.8680 (t70) cc_final: 0.8186 (t70) REVERT: C 1207 SER cc_start: 0.9198 (m) cc_final: 0.8869 (t) REVERT: C 1211 ARG cc_start: 0.8095 (ptp-170) cc_final: 0.7530 (ptp-170) REVERT: C 1296 ASP cc_start: 0.8557 (t0) cc_final: 0.7986 (t0) REVERT: C 1322 SER cc_start: 0.8417 (p) cc_final: 0.8117 (t) REVERT: D 155 GLU cc_start: 0.7566 (mm-30) cc_final: 0.6758 (mp0) REVERT: D 160 LEU cc_start: 0.7507 (mt) cc_final: 0.7306 (mt) REVERT: D 180 MET cc_start: 0.7935 (ptm) cc_final: 0.7575 (ttp) REVERT: D 190 LYS cc_start: 0.8661 (ttmt) cc_final: 0.8393 (tppt) REVERT: D 193 ASP cc_start: 0.7443 (t0) cc_final: 0.6687 (p0) REVERT: D 214 ARG cc_start: 0.6475 (ttm-80) cc_final: 0.6265 (mtp180) REVERT: D 308 ASP cc_start: 0.7651 (t0) cc_final: 0.7409 (t0) REVERT: D 314 ARG cc_start: 0.7812 (mtp180) cc_final: 0.7194 (tpp-160) REVERT: D 321 LYS cc_start: 0.7784 (mmpt) cc_final: 0.7202 (mttm) REVERT: D 322 ARG cc_start: 0.6147 (ttp-110) cc_final: 0.5664 (mmm160) REVERT: D 339 ARG cc_start: 0.8292 (mtm110) cc_final: 0.8025 (mtm110) REVERT: D 413 ASP cc_start: 0.8618 (t0) cc_final: 0.8365 (t0) REVERT: D 414 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7605 (tt0) REVERT: D 579 LEU cc_start: 0.7368 (pt) cc_final: 0.7063 (pt) REVERT: D 642 ASP cc_start: 0.8753 (m-30) cc_final: 0.8345 (t70) REVERT: D 660 GLU cc_start: 0.7379 (mm-30) cc_final: 0.7122 (mm-30) REVERT: D 684 ASP cc_start: 0.7895 (m-30) cc_final: 0.7620 (m-30) REVERT: D 723 TYR cc_start: 0.7842 (t80) cc_final: 0.7606 (t80) REVERT: D 805 GLN cc_start: 0.8104 (tp40) cc_final: 0.7859 (tp40) REVERT: D 822 MET cc_start: 0.7911 (mmt) cc_final: 0.6965 (mmm) REVERT: D 853 THR cc_start: 0.6779 (m) cc_final: 0.6381 (p) REVERT: D 860 ARG cc_start: 0.6933 (ptt-90) cc_final: 0.6672 (ptm160) REVERT: D 874 GLU cc_start: 0.8529 (mm-30) cc_final: 0.7939 (pt0) REVERT: D 929 GLN cc_start: 0.7507 (mt0) cc_final: 0.6898 (tm-30) REVERT: D 979 ASN cc_start: 0.7395 (m-40) cc_final: 0.6933 (p0) REVERT: D 1146 GLU cc_start: 0.7970 (tp30) cc_final: 0.7597 (tp30) REVERT: D 1151 LYS cc_start: 0.8507 (tptp) cc_final: 0.7730 (ttmt) REVERT: D 1189 MET cc_start: 0.7013 (mtt) cc_final: 0.6806 (mtm) REVERT: D 1205 GLU cc_start: 0.6227 (tp30) cc_final: 0.5957 (pm20) REVERT: D 1244 GLN cc_start: 0.8354 (mm-40) cc_final: 0.7992 (mm110) REVERT: E 8 ASP cc_start: 0.8389 (m-30) cc_final: 0.7196 (t0) REVERT: E 15 ASN cc_start: 0.7821 (t0) cc_final: 0.7419 (t0) REVERT: E 26 ARG cc_start: 0.8086 (tpt170) cc_final: 0.7028 (tpt-90) REVERT: E 30 MET cc_start: 0.7150 (mtm) cc_final: 0.6888 (mtp) REVERT: E 35 LYS cc_start: 0.7980 (mtmp) cc_final: 0.7596 (ttmt) REVERT: E 53 GLU cc_start: 0.8560 (mt-10) cc_final: 0.7963 (mt-10) REVERT: F 347 ILE cc_start: 0.5917 (mt) cc_final: 0.5709 (mt) REVERT: F 374 ARG cc_start: 0.7100 (mtt90) cc_final: 0.6716 (mtp-110) REVERT: F 379 MET cc_start: 0.7570 (tpp) cc_final: 0.7186 (tpt) REVERT: F 405 ILE cc_start: 0.8439 (pt) cc_final: 0.8236 (pt) REVERT: P 44 MET cc_start: 0.6697 (tpt) cc_final: 0.6195 (ttp) REVERT: P 45 GLU cc_start: 0.6521 (pp20) cc_final: 0.6083 (mt-10) REVERT: P 48 GLU cc_start: 0.6279 (tp30) cc_final: 0.5587 (tm-30) REVERT: P 53 MET cc_start: 0.2573 (mmm) cc_final: 0.1973 (tpt) REVERT: P 129 GLU cc_start: 0.8638 (mt-10) cc_final: 0.7961 (tp30) REVERT: Q 16 LEU cc_start: 0.8672 (tp) cc_final: 0.8407 (tt) REVERT: Q 19 TRP cc_start: 0.3422 (m100) cc_final: 0.2919 (m100) REVERT: Q 23 TRP cc_start: 0.7463 (t60) cc_final: 0.7162 (t60) REVERT: Q 60 ASP cc_start: 0.6524 (m-30) cc_final: 0.6077 (m-30) REVERT: Q 75 TYR cc_start: 0.6714 (t80) cc_final: 0.6417 (t80) outliers start: 29 outliers final: 4 residues processed: 965 average time/residue: 0.5008 time to fit residues: 734.3230 Evaluate side-chains 502 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 498 time to evaluate : 3.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 325 optimal weight: 8.9990 chunk 291 optimal weight: 0.1980 chunk 161 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 196 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 301 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 224 optimal weight: 7.9990 chunk 349 optimal weight: 6.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 HIS B 117 HIS ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN C 343 HIS C 437 ASN C 808 ASN C 824 GLN C1244 HIS C1264 GLN C1268 GLN C1313 HIS D 45 ASN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 ASN D 320 ASN D 365 GLN D 489 ASN D 805 GLN D 910 ASN D1197 ASN D1279 GLN D1295 ASN D1326 GLN E 15 ASN F 147 GLN P 13 HIS P 68 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 33449 Z= 0.258 Angle : 0.705 10.961 45786 Z= 0.378 Chirality : 0.045 0.185 5201 Planarity : 0.006 0.070 5447 Dihedral : 19.530 169.889 5824 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.67 % Favored : 94.25 % Rotamer: Outliers : 0.16 % Allowed : 4.54 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.13), residues: 3741 helix: -0.92 (0.12), residues: 1494 sheet: -1.65 (0.25), residues: 396 loop : -2.25 (0.13), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 409 HIS 0.005 0.001 HIS D 430 PHE 0.023 0.002 PHE C 972 TYR 0.024 0.002 TYR P 142 ARG 0.007 0.001 ARG D1258 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 705 time to evaluate : 3.637 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: A 29 GLU cc_start: 0.7139 (tt0) cc_final: 0.6775 (tt0) REVERT: A 41 ASN cc_start: 0.8751 (t0) cc_final: 0.8529 (t0) REVERT: A 51 MET cc_start: 0.8684 (mmm) cc_final: 0.8482 (mmm) REVERT: A 62 ASP cc_start: 0.8614 (t70) cc_final: 0.8084 (p0) REVERT: A 64 VAL cc_start: 0.9017 (t) cc_final: 0.8751 (p) REVERT: A 120 ASP cc_start: 0.8271 (p0) cc_final: 0.7963 (p0) REVERT: A 131 CYS cc_start: 0.8201 (p) cc_final: 0.7835 (p) REVERT: A 135 ASP cc_start: 0.7282 (t0) cc_final: 0.6947 (t0) REVERT: A 181 GLU cc_start: 0.8115 (tp30) cc_final: 0.7429 (tm-30) REVERT: A 206 GLU cc_start: 0.7850 (tp30) cc_final: 0.6928 (tm-30) REVERT: A 212 ASP cc_start: 0.8516 (m-30) cc_final: 0.7803 (p0) REVERT: B 77 ASP cc_start: 0.6239 (m-30) cc_final: 0.5491 (t0) REVERT: B 79 LEU cc_start: 0.8041 (tp) cc_final: 0.7486 (pp) REVERT: B 104 LYS cc_start: 0.6410 (tttt) cc_final: 0.5936 (tppt) REVERT: B 110 VAL cc_start: 0.7919 (t) cc_final: 0.7635 (t) REVERT: B 226 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7755 (tt0) REVERT: C 14 ASP cc_start: 0.9211 (t0) cc_final: 0.8955 (t0) REVERT: C 83 GLN cc_start: 0.5653 (pm20) cc_final: 0.5365 (tp40) REVERT: C 84 GLU cc_start: 0.8356 (tt0) cc_final: 0.8068 (tt0) REVERT: C 132 ASP cc_start: 0.8763 (m-30) cc_final: 0.8522 (t0) REVERT: C 189 ASP cc_start: 0.7482 (m-30) cc_final: 0.7103 (p0) REVERT: C 192 ASP cc_start: 0.7931 (m-30) cc_final: 0.7699 (m-30) REVERT: C 200 ARG cc_start: 0.8639 (mmm160) cc_final: 0.8383 (mmm160) REVERT: C 231 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7473 (tm-30) REVERT: C 256 GLU cc_start: 0.4703 (pt0) cc_final: 0.4157 (tt0) REVERT: C 479 LEU cc_start: 0.7370 (tp) cc_final: 0.7135 (tp) REVERT: C 488 MET cc_start: 0.7640 (mpp) cc_final: 0.7420 (ptt) REVERT: C 530 ILE cc_start: 0.8645 (mt) cc_final: 0.7961 (tt) REVERT: C 549 ASP cc_start: 0.8328 (t0) cc_final: 0.7853 (m-30) REVERT: C 573 ASN cc_start: 0.7820 (m110) cc_final: 0.7513 (m110) REVERT: C 588 GLU cc_start: 0.8295 (tt0) cc_final: 0.7595 (tt0) REVERT: C 645 PHE cc_start: 0.8065 (m-10) cc_final: 0.7618 (m-10) REVERT: C 651 ASP cc_start: 0.8093 (m-30) cc_final: 0.7798 (m-30) REVERT: C 686 GLN cc_start: 0.8754 (tm-30) cc_final: 0.8543 (tt0) REVERT: C 706 ARG cc_start: 0.7913 (mmm-85) cc_final: 0.7073 (mmt180) REVERT: C 741 MET cc_start: 0.8136 (ttp) cc_final: 0.7571 (ttt) REVERT: C 768 MET cc_start: 0.7107 (mtp) cc_final: 0.6475 (mtm) REVERT: C 778 GLU cc_start: 0.8009 (tp30) cc_final: 0.7499 (mm-30) REVERT: C 779 ARG cc_start: 0.7526 (ttt-90) cc_final: 0.7133 (ttp80) REVERT: C 785 ASP cc_start: 0.7712 (m-30) cc_final: 0.7307 (m-30) REVERT: C 813 GLU cc_start: 0.8469 (tp30) cc_final: 0.7708 (tt0) REVERT: C 843 THR cc_start: 0.7206 (p) cc_final: 0.7005 (t) REVERT: C 845 LEU cc_start: 0.5883 (tp) cc_final: 0.5602 (tp) REVERT: C 900 LYS cc_start: 0.6990 (tptm) cc_final: 0.6636 (tmtt) REVERT: C 949 GLU cc_start: 0.8956 (tt0) cc_final: 0.8245 (mt-10) REVERT: C 1066 MET cc_start: 0.8252 (ptm) cc_final: 0.7630 (ttm) REVERT: C 1078 LYS cc_start: 0.8401 (tttt) cc_final: 0.8078 (tttp) REVERT: C 1080 ASN cc_start: 0.8664 (t0) cc_final: 0.8042 (t0) REVERT: C 1084 ASP cc_start: 0.8541 (m-30) cc_final: 0.8303 (m-30) REVERT: C 1107 MET cc_start: 0.7148 (mtm) cc_final: 0.6616 (mtt) REVERT: C 1126 ASP cc_start: 0.8720 (t70) cc_final: 0.8207 (t70) REVERT: C 1207 SER cc_start: 0.9130 (m) cc_final: 0.8824 (t) REVERT: C 1211 ARG cc_start: 0.7982 (ptp-170) cc_final: 0.7395 (ptp-170) REVERT: C 1229 TYR cc_start: 0.8188 (m-10) cc_final: 0.7789 (m-80) REVERT: C 1230 MET cc_start: 0.7823 (ttp) cc_final: 0.7587 (ttt) REVERT: C 1273 MET cc_start: 0.6929 (mtp) cc_final: 0.6464 (mtp) REVERT: C 1290 MET cc_start: 0.8245 (tmm) cc_final: 0.7757 (ttm) REVERT: C 1291 LEU cc_start: 0.7506 (tp) cc_final: 0.6805 (tp) REVERT: C 1292 THR cc_start: 0.7916 (m) cc_final: 0.7650 (p) REVERT: C 1295 SER cc_start: 0.9098 (t) cc_final: 0.8779 (p) REVERT: C 1296 ASP cc_start: 0.8430 (t0) cc_final: 0.8153 (t0) REVERT: C 1329 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8069 (tm-30) REVERT: C 1338 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6903 (tt0) REVERT: D 154 LEU cc_start: 0.8047 (tt) cc_final: 0.7663 (pp) REVERT: D 155 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7328 (mp0) REVERT: D 190 LYS cc_start: 0.8789 (ttmt) cc_final: 0.8551 (tmmt) REVERT: D 192 MET cc_start: 0.8612 (ttp) cc_final: 0.7629 (tpp) REVERT: D 200 GLN cc_start: 0.7967 (tt0) cc_final: 0.7464 (tp40) REVERT: D 314 ARG cc_start: 0.7661 (mtp180) cc_final: 0.7135 (tpp-160) REVERT: D 321 LYS cc_start: 0.7914 (mmpt) cc_final: 0.7352 (mttp) REVERT: D 322 ARG cc_start: 0.6229 (ttp-110) cc_final: 0.5876 (mmm160) REVERT: D 349 TYR cc_start: 0.8061 (m-80) cc_final: 0.7735 (m-80) REVERT: D 414 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8173 (tt0) REVERT: D 442 ILE cc_start: 0.7550 (mm) cc_final: 0.7264 (tt) REVERT: D 458 ASN cc_start: 0.8264 (t0) cc_final: 0.8016 (t0) REVERT: D 462 ASP cc_start: 0.7656 (t0) cc_final: 0.7124 (m-30) REVERT: D 484 MET cc_start: 0.7844 (mmm) cc_final: 0.7594 (mmt) REVERT: D 505 ASP cc_start: 0.7817 (t70) cc_final: 0.7602 (t0) REVERT: D 596 LEU cc_start: 0.8524 (mt) cc_final: 0.8288 (mt) REVERT: D 642 ASP cc_start: 0.8712 (m-30) cc_final: 0.8435 (t70) REVERT: D 684 ASP cc_start: 0.7796 (m-30) cc_final: 0.7556 (m-30) REVERT: D 723 TYR cc_start: 0.8115 (t80) cc_final: 0.7769 (t80) REVERT: D 765 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7051 (mt-10) REVERT: D 805 GLN cc_start: 0.8114 (tp-100) cc_final: 0.7889 (tp40) REVERT: D 860 ARG cc_start: 0.6888 (ptt-90) cc_final: 0.6550 (ptm160) REVERT: D 928 THR cc_start: 0.9140 (m) cc_final: 0.8876 (t) REVERT: D 929 GLN cc_start: 0.7535 (mt0) cc_final: 0.7168 (tp40) REVERT: D 932 MET cc_start: 0.4003 (mmp) cc_final: 0.3679 (mmm) REVERT: D 979 ASN cc_start: 0.7298 (m-40) cc_final: 0.6962 (p0) REVERT: D 1146 GLU cc_start: 0.8248 (tp30) cc_final: 0.8003 (tp30) REVERT: D 1151 LYS cc_start: 0.8655 (tptp) cc_final: 0.7785 (mtmt) REVERT: D 1205 GLU cc_start: 0.6788 (tp30) cc_final: 0.6257 (pm20) REVERT: D 1244 GLN cc_start: 0.8279 (mm-40) cc_final: 0.8073 (mm-40) REVERT: D 1273 ASP cc_start: 0.7781 (m-30) cc_final: 0.7520 (t70) REVERT: D 1370 MET cc_start: 0.6719 (tpp) cc_final: 0.6359 (tpp) REVERT: E 15 ASN cc_start: 0.8022 (t0) cc_final: 0.7488 (t0) REVERT: E 35 LYS cc_start: 0.7936 (mtmt) cc_final: 0.7698 (tttt) REVERT: E 41 GLU cc_start: 0.7434 (pm20) cc_final: 0.6357 (pt0) REVERT: F 141 ILE cc_start: 0.8917 (mm) cc_final: 0.8548 (tt) REVERT: F 149 ASP cc_start: 0.6849 (t0) cc_final: 0.6464 (t70) REVERT: F 269 LEU cc_start: 0.8770 (mt) cc_final: 0.8309 (pp) REVERT: F 273 MET cc_start: 0.6520 (mmm) cc_final: 0.6278 (ttt) REVERT: F 365 MET cc_start: 0.8185 (ttp) cc_final: 0.7351 (tmm) REVERT: F 377 LYS cc_start: 0.7795 (mtpt) cc_final: 0.7467 (ttpt) REVERT: F 405 ILE cc_start: 0.8632 (pt) cc_final: 0.8311 (pt) REVERT: F 445 ASP cc_start: 0.7857 (m-30) cc_final: 0.7591 (m-30) REVERT: P 36 MET cc_start: 0.0420 (ttp) cc_final: 0.0102 (ttp) REVERT: P 44 MET cc_start: 0.6629 (tpt) cc_final: 0.5804 (ptt) REVERT: P 45 GLU cc_start: 0.6525 (pp20) cc_final: 0.6012 (mt-10) REVERT: P 48 GLU cc_start: 0.6350 (tp30) cc_final: 0.5567 (tm-30) REVERT: P 53 MET cc_start: 0.2316 (mmm) cc_final: 0.1464 (tpt) REVERT: P 57 MET cc_start: 0.8113 (pmm) cc_final: 0.7468 (pmm) REVERT: P 77 ASP cc_start: 0.6707 (t0) cc_final: 0.6409 (t0) REVERT: P 106 ARG cc_start: 0.5446 (mtp180) cc_final: 0.4810 (ttm170) REVERT: P 129 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7766 (tp30) REVERT: P 142 TYR cc_start: 0.8679 (t80) cc_final: 0.8439 (t80) REVERT: Q 16 LEU cc_start: 0.8548 (tp) cc_final: 0.8245 (tp) REVERT: Q 33 GLU cc_start: 0.6363 (mp0) cc_final: 0.6158 (mp0) REVERT: Q 128 ARG cc_start: 0.8188 (mtt180) cc_final: 0.7715 (mtt180) outliers start: 5 outliers final: 0 residues processed: 708 average time/residue: 0.4384 time to fit residues: 495.4113 Evaluate side-chains 502 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 502 time to evaluate : 3.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 194 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 chunk 290 optimal weight: 4.9990 chunk 238 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 350 optimal weight: 10.0000 chunk 378 optimal weight: 20.0000 chunk 311 optimal weight: 7.9990 chunk 347 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 280 optimal weight: 40.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 HIS ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 ASN C 462 ASN C 580 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN D 294 ASN ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1197 ASN F 227 GLN Q 90 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.125 33449 Z= 0.438 Angle : 0.820 10.032 45786 Z= 0.436 Chirality : 0.048 0.229 5201 Planarity : 0.006 0.055 5447 Dihedral : 19.164 169.499 5824 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.81 % Favored : 92.11 % Rotamer: Outliers : 0.12 % Allowed : 6.65 % Favored : 93.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.15 (0.13), residues: 3741 helix: -0.46 (0.13), residues: 1501 sheet: -1.50 (0.23), residues: 425 loop : -2.26 (0.13), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP Q 15 HIS 0.010 0.002 HIS D 469 PHE 0.029 0.002 PHE F 427 TYR 0.027 0.002 TYR A 177 ARG 0.006 0.001 ARG D 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 575 time to evaluate : 3.499 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: A 29 GLU cc_start: 0.7337 (tt0) cc_final: 0.6934 (tt0) REVERT: A 51 MET cc_start: 0.8922 (mmm) cc_final: 0.8595 (mmm) REVERT: A 57 THR cc_start: 0.7890 (m) cc_final: 0.7633 (m) REVERT: A 62 ASP cc_start: 0.8609 (t70) cc_final: 0.8176 (p0) REVERT: A 64 VAL cc_start: 0.8996 (t) cc_final: 0.8784 (p) REVERT: A 135 ASP cc_start: 0.7544 (t0) cc_final: 0.7180 (t70) REVERT: A 181 GLU cc_start: 0.8180 (tp30) cc_final: 0.7437 (tm-30) REVERT: A 185 TYR cc_start: 0.8434 (p90) cc_final: 0.8176 (p90) REVERT: A 197 ASP cc_start: 0.6345 (t0) cc_final: 0.6122 (t0) REVERT: A 206 GLU cc_start: 0.8211 (tp30) cc_final: 0.7302 (tm-30) REVERT: A 212 ASP cc_start: 0.8549 (m-30) cc_final: 0.7670 (p0) REVERT: B 33 ARG cc_start: 0.7437 (tmm-80) cc_final: 0.6928 (ttt180) REVERT: B 77 ASP cc_start: 0.6812 (m-30) cc_final: 0.5460 (p0) REVERT: B 226 GLU cc_start: 0.8556 (mm-30) cc_final: 0.7894 (tt0) REVERT: C 8 LYS cc_start: 0.8720 (mttt) cc_final: 0.8397 (mttp) REVERT: C 17 LYS cc_start: 0.7979 (mptt) cc_final: 0.7418 (mmmt) REVERT: C 200 ARG cc_start: 0.8433 (mmm160) cc_final: 0.8112 (mmm160) REVERT: C 479 LEU cc_start: 0.7717 (tp) cc_final: 0.7509 (tp) REVERT: C 488 MET cc_start: 0.7624 (mpp) cc_final: 0.7173 (ptm) REVERT: C 549 ASP cc_start: 0.8301 (t0) cc_final: 0.7940 (m-30) REVERT: C 588 GLU cc_start: 0.8352 (tt0) cc_final: 0.7721 (tt0) REVERT: C 645 PHE cc_start: 0.8442 (m-10) cc_final: 0.8173 (m-10) REVERT: C 686 GLN cc_start: 0.8863 (tm-30) cc_final: 0.8467 (tt0) REVERT: C 694 ARG cc_start: 0.7431 (tpp80) cc_final: 0.6718 (mtm110) REVERT: C 706 ARG cc_start: 0.8065 (mmm-85) cc_final: 0.7181 (mmt180) REVERT: C 741 MET cc_start: 0.8141 (ttp) cc_final: 0.7673 (ttt) REVERT: C 768 MET cc_start: 0.7098 (mtp) cc_final: 0.6479 (mtm) REVERT: C 778 GLU cc_start: 0.8361 (tp30) cc_final: 0.7751 (mm-30) REVERT: C 779 ARG cc_start: 0.7929 (ttt-90) cc_final: 0.7393 (ttp80) REVERT: C 800 MET cc_start: 0.7223 (mtp) cc_final: 0.6813 (mtp) REVERT: C 811 ASN cc_start: 0.8610 (p0) cc_final: 0.8074 (p0) REVERT: C 843 THR cc_start: 0.7044 (p) cc_final: 0.6836 (t) REVERT: C 844 LYS cc_start: 0.8000 (mppt) cc_final: 0.7780 (mppt) REVERT: C 900 LYS cc_start: 0.7213 (tppt) cc_final: 0.6838 (tmtt) REVERT: C 937 ASP cc_start: 0.8824 (t0) cc_final: 0.8567 (t0) REVERT: C 949 GLU cc_start: 0.8998 (tt0) cc_final: 0.8479 (mt-10) REVERT: C 1095 ASP cc_start: 0.8508 (m-30) cc_final: 0.7367 (t0) REVERT: C 1122 LYS cc_start: 0.8296 (tptp) cc_final: 0.8094 (tppt) REVERT: C 1126 ASP cc_start: 0.8620 (t70) cc_final: 0.8091 (t70) REVERT: C 1174 GLU cc_start: 0.8529 (tt0) cc_final: 0.7990 (tp30) REVERT: C 1194 GLU cc_start: 0.7211 (mp0) cc_final: 0.6830 (mp0) REVERT: C 1211 ARG cc_start: 0.8102 (ptp-170) cc_final: 0.7373 (ptm-80) REVERT: C 1274 GLU cc_start: 0.6815 (pm20) cc_final: 0.6469 (pm20) REVERT: C 1291 LEU cc_start: 0.7840 (tp) cc_final: 0.7626 (tp) REVERT: C 1296 ASP cc_start: 0.8501 (t0) cc_final: 0.8229 (t0) REVERT: C 1329 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7734 (tm-30) REVERT: C 1338 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6996 (tt0) REVERT: D 154 LEU cc_start: 0.7764 (tt) cc_final: 0.7253 (pp) REVERT: D 155 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7390 (mp0) REVERT: D 190 LYS cc_start: 0.8882 (ttmt) cc_final: 0.8604 (tmmt) REVERT: D 193 ASP cc_start: 0.7963 (t0) cc_final: 0.6950 (p0) REVERT: D 200 GLN cc_start: 0.8047 (tt0) cc_final: 0.7554 (tp40) REVERT: D 314 ARG cc_start: 0.7924 (mtp180) cc_final: 0.7298 (ttt-90) REVERT: D 321 LYS cc_start: 0.7889 (mmpt) cc_final: 0.7276 (mttm) REVERT: D 322 ARG cc_start: 0.6569 (ttp-110) cc_final: 0.6033 (mmm160) REVERT: D 329 ASP cc_start: 0.8155 (t0) cc_final: 0.7535 (m-30) REVERT: D 375 GLU cc_start: 0.8143 (tp30) cc_final: 0.7689 (tp30) REVERT: D 400 MET cc_start: 0.8206 (ttm) cc_final: 0.7918 (ttm) REVERT: D 418 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8422 (mm-30) REVERT: D 429 LEU cc_start: 0.9413 (tp) cc_final: 0.9147 (tt) REVERT: D 443 GLU cc_start: 0.8485 (tp30) cc_final: 0.8037 (tt0) REVERT: D 458 ASN cc_start: 0.8582 (t0) cc_final: 0.8266 (t0) REVERT: D 484 MET cc_start: 0.7854 (mmm) cc_final: 0.7488 (mmm) REVERT: D 485 MET cc_start: 0.8963 (tpp) cc_final: 0.8724 (tpp) REVERT: D 521 LYS cc_start: 0.8380 (mttt) cc_final: 0.7854 (tttt) REVERT: D 579 LEU cc_start: 0.7186 (pt) cc_final: 0.6956 (pt) REVERT: D 596 LEU cc_start: 0.8940 (mt) cc_final: 0.8596 (mt) REVERT: D 642 ASP cc_start: 0.8828 (m-30) cc_final: 0.8571 (t70) REVERT: D 684 ASP cc_start: 0.7782 (m-30) cc_final: 0.7542 (m-30) REVERT: D 805 GLN cc_start: 0.8095 (tp-100) cc_final: 0.7753 (tp40) REVERT: D 929 GLN cc_start: 0.8079 (mt0) cc_final: 0.7332 (tm-30) REVERT: D 932 MET cc_start: 0.2927 (mmp) cc_final: 0.2575 (mmm) REVERT: D 995 TYR cc_start: 0.6607 (m-80) cc_final: 0.5885 (m-80) REVERT: D 1146 GLU cc_start: 0.8174 (tp30) cc_final: 0.7640 (tp30) REVERT: D 1151 LYS cc_start: 0.8571 (tptp) cc_final: 0.7719 (mtmt) REVERT: D 1186 TYR cc_start: 0.7357 (t80) cc_final: 0.7128 (t80) REVERT: D 1250 ASP cc_start: 0.8502 (m-30) cc_final: 0.7391 (p0) REVERT: D 1260 MET cc_start: 0.8451 (ttp) cc_final: 0.8196 (ttp) REVERT: D 1273 ASP cc_start: 0.8034 (m-30) cc_final: 0.7545 (t70) REVERT: E 8 ASP cc_start: 0.8654 (m-30) cc_final: 0.7695 (t0) REVERT: E 10 VAL cc_start: 0.8463 (t) cc_final: 0.8128 (p) REVERT: E 15 ASN cc_start: 0.8033 (t0) cc_final: 0.7765 (t0) REVERT: E 30 MET cc_start: 0.7654 (mtp) cc_final: 0.7435 (mtt) REVERT: E 41 GLU cc_start: 0.7183 (pm20) cc_final: 0.6436 (pt0) REVERT: E 42 GLU cc_start: 0.6972 (mp0) cc_final: 0.6528 (mp0) REVERT: E 44 ASP cc_start: 0.8408 (m-30) cc_final: 0.8018 (m-30) REVERT: E 56 GLU cc_start: 0.6893 (mm-30) cc_final: 0.6541 (mp0) REVERT: E 67 ARG cc_start: 0.7473 (ttm170) cc_final: 0.7242 (ttm110) REVERT: F 141 ILE cc_start: 0.8623 (mm) cc_final: 0.8264 (tt) REVERT: F 150 ARG cc_start: 0.6277 (ttt90) cc_final: 0.6045 (mtt90) REVERT: F 269 LEU cc_start: 0.8700 (mt) cc_final: 0.8113 (pp) REVERT: F 273 MET cc_start: 0.6566 (mmm) cc_final: 0.6332 (ttt) REVERT: F 365 MET cc_start: 0.8002 (ttp) cc_final: 0.7261 (tmm) REVERT: P 44 MET cc_start: 0.6835 (tpt) cc_final: 0.6251 (ptt) REVERT: P 45 GLU cc_start: 0.6549 (pp20) cc_final: 0.6001 (mt-10) REVERT: P 48 GLU cc_start: 0.6443 (tp30) cc_final: 0.5680 (tm-30) REVERT: P 57 MET cc_start: 0.8317 (pmm) cc_final: 0.7689 (pmm) REVERT: P 77 ASP cc_start: 0.7340 (t0) cc_final: 0.7051 (t0) REVERT: P 106 ARG cc_start: 0.5532 (mtp180) cc_final: 0.4868 (ttm170) REVERT: P 142 TYR cc_start: 0.8476 (t80) cc_final: 0.8142 (t80) REVERT: Q 106 ARG cc_start: 0.8518 (mtp180) cc_final: 0.8242 (mtm180) outliers start: 4 outliers final: 2 residues processed: 578 average time/residue: 0.4356 time to fit residues: 405.8576 Evaluate side-chains 437 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 435 time to evaluate : 3.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 346 optimal weight: 10.0000 chunk 263 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 235 optimal weight: 1.9990 chunk 351 optimal weight: 10.0000 chunk 372 optimal weight: 9.9990 chunk 183 optimal weight: 7.9990 chunk 333 optimal weight: 20.0000 chunk 100 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 HIS ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 462 ASN C 580 GLN C 808 ASN C1157 GLN D 45 ASN ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1195 GLN D1197 ASN F 227 GLN F 383 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 33449 Z= 0.219 Angle : 0.640 8.776 45786 Z= 0.341 Chirality : 0.043 0.182 5201 Planarity : 0.004 0.048 5447 Dihedral : 18.839 170.692 5824 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.04 % Favored : 93.88 % Rotamer: Outliers : 0.03 % Allowed : 2.76 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.13), residues: 3741 helix: 0.13 (0.13), residues: 1494 sheet: -1.40 (0.23), residues: 449 loop : -2.07 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP Q 15 HIS 0.006 0.001 HIS Q 95 PHE 0.022 0.001 PHE C1025 TYR 0.018 0.001 TYR Q 100 ARG 0.005 0.000 ARG D 293 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 585 time to evaluate : 3.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7279 (tt0) cc_final: 0.6919 (tt0) REVERT: A 51 MET cc_start: 0.8875 (mmm) cc_final: 0.8588 (mmm) REVERT: A 57 THR cc_start: 0.7522 (m) cc_final: 0.7264 (m) REVERT: A 62 ASP cc_start: 0.8497 (t70) cc_final: 0.8060 (p0) REVERT: A 135 ASP cc_start: 0.7634 (t0) cc_final: 0.7341 (t0) REVERT: A 181 GLU cc_start: 0.8196 (tp30) cc_final: 0.7512 (tm-30) REVERT: A 197 ASP cc_start: 0.6314 (t0) cc_final: 0.5974 (t0) REVERT: A 199 ASP cc_start: 0.7712 (m-30) cc_final: 0.7503 (m-30) REVERT: A 206 GLU cc_start: 0.8279 (tp30) cc_final: 0.7589 (tm-30) REVERT: B 33 ARG cc_start: 0.7397 (tmm-80) cc_final: 0.6861 (ttt180) REVERT: B 75 GLN cc_start: 0.5645 (mp-120) cc_final: 0.5340 (mp-120) REVERT: B 77 ASP cc_start: 0.6421 (m-30) cc_final: 0.5753 (t0) REVERT: B 81 ILE cc_start: 0.8213 (tt) cc_final: 0.7904 (pt) REVERT: B 147 GLN cc_start: 0.6008 (mt0) cc_final: 0.5706 (mt0) REVERT: B 226 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7905 (tt0) REVERT: C 8 LYS cc_start: 0.8632 (mttt) cc_final: 0.8288 (mttp) REVERT: C 158 ASP cc_start: 0.8255 (t0) cc_final: 0.7960 (t0) REVERT: C 200 ARG cc_start: 0.8403 (mmm160) cc_final: 0.7888 (mmm160) REVERT: C 479 LEU cc_start: 0.7695 (tp) cc_final: 0.7471 (tp) REVERT: C 488 MET cc_start: 0.7597 (mpp) cc_final: 0.7388 (ttm) REVERT: C 510 GLN cc_start: 0.8738 (mt0) cc_final: 0.8432 (mt0) REVERT: C 542 ARG cc_start: 0.7534 (mtt180) cc_final: 0.7323 (mpt-90) REVERT: C 549 ASP cc_start: 0.8271 (t0) cc_final: 0.7670 (m-30) REVERT: C 588 GLU cc_start: 0.8376 (tt0) cc_final: 0.7741 (tt0) REVERT: C 645 PHE cc_start: 0.8280 (m-10) cc_final: 0.7970 (m-10) REVERT: C 686 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8517 (tt0) REVERT: C 694 ARG cc_start: 0.7178 (tpp80) cc_final: 0.6509 (mtm110) REVERT: C 706 ARG cc_start: 0.7981 (mmm-85) cc_final: 0.6993 (mmt180) REVERT: C 741 MET cc_start: 0.8004 (ttp) cc_final: 0.7594 (ttt) REVERT: C 768 MET cc_start: 0.7063 (mtp) cc_final: 0.6479 (mtm) REVERT: C 779 ARG cc_start: 0.7836 (ttt-90) cc_final: 0.7401 (ttp-110) REVERT: C 800 MET cc_start: 0.7200 (mtp) cc_final: 0.6932 (mtp) REVERT: C 900 LYS cc_start: 0.7183 (tppt) cc_final: 0.6879 (tmtt) REVERT: C 949 GLU cc_start: 0.9070 (tt0) cc_final: 0.8558 (mt-10) REVERT: C 1018 TYR cc_start: 0.7191 (t80) cc_final: 0.6903 (t80) REVERT: C 1107 MET cc_start: 0.7314 (mtm) cc_final: 0.6815 (mtt) REVERT: C 1119 MET cc_start: 0.8200 (tpp) cc_final: 0.7935 (tpp) REVERT: C 1122 LYS cc_start: 0.8112 (tptp) cc_final: 0.7736 (tppt) REVERT: C 1126 ASP cc_start: 0.8619 (t70) cc_final: 0.8205 (t70) REVERT: C 1174 GLU cc_start: 0.8496 (tt0) cc_final: 0.8021 (tp30) REVERT: C 1194 GLU cc_start: 0.7715 (mp0) cc_final: 0.7412 (mp0) REVERT: C 1211 ARG cc_start: 0.8015 (ptp-170) cc_final: 0.7327 (ptm-80) REVERT: C 1229 TYR cc_start: 0.8239 (m-10) cc_final: 0.7974 (m-10) REVERT: C 1230 MET cc_start: 0.7986 (ttp) cc_final: 0.7659 (ttt) REVERT: C 1274 GLU cc_start: 0.6568 (pm20) cc_final: 0.5853 (pm20) REVERT: C 1291 LEU cc_start: 0.7703 (tp) cc_final: 0.7106 (tp) REVERT: C 1295 SER cc_start: 0.9309 (t) cc_final: 0.8966 (p) REVERT: C 1329 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7861 (tm-30) REVERT: D 155 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7517 (mp0) REVERT: D 190 LYS cc_start: 0.8956 (ttmt) cc_final: 0.8679 (tmmt) REVERT: D 193 ASP cc_start: 0.8074 (t0) cc_final: 0.7085 (p0) REVERT: D 196 GLN cc_start: 0.7894 (mt0) cc_final: 0.7303 (mt0) REVERT: D 200 GLN cc_start: 0.7835 (tt0) cc_final: 0.7412 (tp40) REVERT: D 314 ARG cc_start: 0.7823 (mtp180) cc_final: 0.6941 (tpp-160) REVERT: D 321 LYS cc_start: 0.8013 (mmpt) cc_final: 0.7340 (mttt) REVERT: D 322 ARG cc_start: 0.6488 (ttp-110) cc_final: 0.5999 (mmm160) REVERT: D 329 ASP cc_start: 0.8008 (t0) cc_final: 0.7634 (m-30) REVERT: D 349 TYR cc_start: 0.8153 (m-80) cc_final: 0.7765 (m-80) REVERT: D 400 MET cc_start: 0.8235 (ttm) cc_final: 0.7979 (ttm) REVERT: D 414 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8393 (tm-30) REVERT: D 458 ASN cc_start: 0.8652 (t0) cc_final: 0.8384 (t0) REVERT: D 596 LEU cc_start: 0.8845 (mt) cc_final: 0.8622 (mt) REVERT: D 684 ASP cc_start: 0.7753 (m-30) cc_final: 0.7522 (m-30) REVERT: D 720 ASN cc_start: 0.7188 (t0) cc_final: 0.6821 (t0) REVERT: D 805 GLN cc_start: 0.8005 (tp-100) cc_final: 0.7693 (tp40) REVERT: D 929 GLN cc_start: 0.7740 (mt0) cc_final: 0.7124 (tm-30) REVERT: D 932 MET cc_start: 0.3314 (mmp) cc_final: 0.3086 (mmm) REVERT: D 995 TYR cc_start: 0.6536 (m-80) cc_final: 0.5733 (m-80) REVERT: D 1146 GLU cc_start: 0.8116 (tp30) cc_final: 0.7680 (tp30) REVERT: D 1151 LYS cc_start: 0.8544 (tptp) cc_final: 0.7674 (mtmt) REVERT: D 1231 ARG cc_start: 0.6795 (ttm170) cc_final: 0.6565 (ttm170) REVERT: D 1273 ASP cc_start: 0.8052 (m-30) cc_final: 0.7520 (t70) REVERT: E 10 VAL cc_start: 0.8433 (t) cc_final: 0.8130 (p) REVERT: E 15 ASN cc_start: 0.8389 (t0) cc_final: 0.7953 (t0) REVERT: E 30 MET cc_start: 0.7437 (mtp) cc_final: 0.7018 (mtt) REVERT: E 41 GLU cc_start: 0.7185 (pm20) cc_final: 0.6305 (pt0) REVERT: E 42 GLU cc_start: 0.7127 (mp0) cc_final: 0.6641 (mp0) REVERT: E 43 ASN cc_start: 0.8494 (t0) cc_final: 0.8237 (t0) REVERT: E 53 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7500 (mt-10) REVERT: E 56 GLU cc_start: 0.6934 (mm-30) cc_final: 0.6694 (mm-30) REVERT: E 62 GLN cc_start: 0.7984 (tp-100) cc_final: 0.7769 (tp40) REVERT: F 141 ILE cc_start: 0.8593 (mm) cc_final: 0.8386 (tp) REVERT: F 269 LEU cc_start: 0.8623 (mt) cc_final: 0.8004 (pp) REVERT: F 365 MET cc_start: 0.8203 (ttp) cc_final: 0.7253 (tmm) REVERT: P 45 GLU cc_start: 0.6541 (pp20) cc_final: 0.5989 (mt-10) REVERT: P 48 GLU cc_start: 0.6277 (tp30) cc_final: 0.5744 (tm-30) REVERT: P 53 MET cc_start: 0.4102 (mmm) cc_final: 0.2055 (tpp) REVERT: P 57 MET cc_start: 0.8106 (pmm) cc_final: 0.7747 (pmm) REVERT: P 77 ASP cc_start: 0.6841 (t0) cc_final: 0.6413 (t0) REVERT: P 142 TYR cc_start: 0.8655 (t80) cc_final: 0.8386 (t80) REVERT: Q 106 ARG cc_start: 0.8421 (mtp180) cc_final: 0.8212 (mtm180) outliers start: 1 outliers final: 0 residues processed: 586 average time/residue: 0.4311 time to fit residues: 410.7651 Evaluate side-chains 435 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 435 time to evaluate : 3.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 309 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 277 optimal weight: 0.0040 chunk 153 optimal weight: 0.9990 chunk 317 optimal weight: 10.0000 chunk 257 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 190 optimal weight: 8.9990 chunk 334 optimal weight: 0.0470 chunk 93 optimal weight: 0.6980 overall best weight: 0.7494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS B 23 HIS ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 808 ASN D 45 ASN ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN D1197 ASN Q 90 HIS Q 95 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33449 Z= 0.158 Angle : 0.591 9.150 45786 Z= 0.311 Chirality : 0.041 0.213 5201 Planarity : 0.004 0.050 5447 Dihedral : 18.527 174.058 5824 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.51 % Favored : 94.41 % Rotamer: Outliers : 0.03 % Allowed : 2.30 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.13), residues: 3741 helix: 0.53 (0.13), residues: 1512 sheet: -1.07 (0.24), residues: 445 loop : -1.94 (0.14), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP Q 15 HIS 0.005 0.001 HIS B 117 PHE 0.013 0.001 PHE F 316 TYR 0.021 0.001 TYR Q 100 ARG 0.007 0.000 ARG C 378 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 596 time to evaluate : 3.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7302 (tt0) cc_final: 0.6948 (tt0) REVERT: A 51 MET cc_start: 0.8824 (mmm) cc_final: 0.8530 (mmm) REVERT: A 62 ASP cc_start: 0.8425 (t70) cc_final: 0.8007 (p0) REVERT: A 135 ASP cc_start: 0.7608 (t0) cc_final: 0.7271 (t0) REVERT: A 158 ARG cc_start: 0.6732 (mtt180) cc_final: 0.6242 (ptp-170) REVERT: A 181 GLU cc_start: 0.8129 (tp30) cc_final: 0.7473 (tm-30) REVERT: A 197 ASP cc_start: 0.6383 (t0) cc_final: 0.6080 (t0) REVERT: A 199 ASP cc_start: 0.7617 (m-30) cc_final: 0.7346 (m-30) REVERT: A 206 GLU cc_start: 0.8342 (tp30) cc_final: 0.7586 (tm-30) REVERT: A 212 ASP cc_start: 0.8284 (m-30) cc_final: 0.8051 (m-30) REVERT: B 33 ARG cc_start: 0.7396 (tmm-80) cc_final: 0.6874 (ttt180) REVERT: B 75 GLN cc_start: 0.6157 (mp-120) cc_final: 0.5832 (mp-120) REVERT: B 77 ASP cc_start: 0.6647 (m-30) cc_final: 0.5949 (t0) REVERT: B 147 GLN cc_start: 0.6455 (mt0) cc_final: 0.6113 (mt0) REVERT: B 215 GLU cc_start: 0.7707 (tt0) cc_final: 0.7347 (mm-30) REVERT: B 226 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7777 (tt0) REVERT: C 8 LYS cc_start: 0.8603 (mttt) cc_final: 0.8145 (mttp) REVERT: C 47 TYR cc_start: 0.3649 (m-80) cc_final: 0.2224 (m-80) REVERT: C 158 ASP cc_start: 0.8198 (t0) cc_final: 0.7924 (t0) REVERT: C 200 ARG cc_start: 0.8398 (mmm160) cc_final: 0.7903 (mmm160) REVERT: C 479 LEU cc_start: 0.7803 (tp) cc_final: 0.7579 (tp) REVERT: C 510 GLN cc_start: 0.8713 (mt0) cc_final: 0.8397 (mt0) REVERT: C 515 MET cc_start: 0.7290 (ttp) cc_final: 0.6962 (ttt) REVERT: C 549 ASP cc_start: 0.8439 (t0) cc_final: 0.7600 (m-30) REVERT: C 588 GLU cc_start: 0.7397 (tt0) cc_final: 0.7034 (tt0) REVERT: C 606 LEU cc_start: 0.8042 (mm) cc_final: 0.7741 (mp) REVERT: C 645 PHE cc_start: 0.8264 (m-10) cc_final: 0.7944 (m-10) REVERT: C 694 ARG cc_start: 0.7077 (tpp80) cc_final: 0.6452 (ttp80) REVERT: C 741 MET cc_start: 0.7977 (ttp) cc_final: 0.7770 (ttt) REVERT: C 768 MET cc_start: 0.7227 (mtp) cc_final: 0.6665 (mtm) REVERT: C 779 ARG cc_start: 0.7811 (ttt-90) cc_final: 0.7380 (ttp-110) REVERT: C 845 LEU cc_start: 0.5982 (tp) cc_final: 0.5472 (tp) REVERT: C 881 ASP cc_start: 0.7516 (t70) cc_final: 0.6601 (t0) REVERT: C 900 LYS cc_start: 0.7279 (tppt) cc_final: 0.6756 (tmtt) REVERT: C 949 GLU cc_start: 0.9032 (tt0) cc_final: 0.8460 (mt-10) REVERT: C 1095 ASP cc_start: 0.8268 (m-30) cc_final: 0.7178 (t0) REVERT: C 1107 MET cc_start: 0.7314 (mtm) cc_final: 0.6780 (mtt) REVERT: C 1119 MET cc_start: 0.8089 (tpp) cc_final: 0.7832 (tpp) REVERT: C 1122 LYS cc_start: 0.8007 (tptp) cc_final: 0.6898 (tptt) REVERT: C 1126 ASP cc_start: 0.8614 (t70) cc_final: 0.8227 (t70) REVERT: C 1134 GLN cc_start: 0.8422 (tt0) cc_final: 0.8198 (pp30) REVERT: C 1174 GLU cc_start: 0.8376 (tt0) cc_final: 0.7996 (tp30) REVERT: C 1194 GLU cc_start: 0.7671 (mp0) cc_final: 0.7265 (mp0) REVERT: C 1211 ARG cc_start: 0.8034 (ptp-170) cc_final: 0.7337 (ptm-80) REVERT: C 1229 TYR cc_start: 0.8167 (m-10) cc_final: 0.7723 (m-10) REVERT: C 1230 MET cc_start: 0.7943 (ttp) cc_final: 0.7719 (ttt) REVERT: C 1273 MET cc_start: 0.7237 (mtt) cc_final: 0.7008 (mmm) REVERT: C 1291 LEU cc_start: 0.7432 (tp) cc_final: 0.6951 (tp) REVERT: C 1295 SER cc_start: 0.9383 (t) cc_final: 0.9091 (p) REVERT: C 1329 GLU cc_start: 0.8349 (tm-30) cc_final: 0.7931 (tm-30) REVERT: D 50 LYS cc_start: 0.7977 (tttm) cc_final: 0.7738 (tttm) REVERT: D 155 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7496 (mp0) REVERT: D 180 MET cc_start: 0.7375 (ttp) cc_final: 0.7173 (ttm) REVERT: D 190 LYS cc_start: 0.8937 (ttmt) cc_final: 0.8661 (tmmt) REVERT: D 193 ASP cc_start: 0.8008 (t0) cc_final: 0.6768 (p0) REVERT: D 196 GLN cc_start: 0.7938 (mt0) cc_final: 0.7403 (mt0) REVERT: D 200 GLN cc_start: 0.7705 (tt0) cc_final: 0.7477 (tp40) REVERT: D 207 GLU cc_start: 0.7054 (tp30) cc_final: 0.6556 (mm-30) REVERT: D 289 ASP cc_start: 0.7598 (t70) cc_final: 0.7378 (t0) REVERT: D 314 ARG cc_start: 0.7879 (mtp180) cc_final: 0.6997 (tpp-160) REVERT: D 321 LYS cc_start: 0.7988 (mmpt) cc_final: 0.7265 (mttm) REVERT: D 329 ASP cc_start: 0.8002 (t0) cc_final: 0.7646 (m-30) REVERT: D 349 TYR cc_start: 0.8037 (m-80) cc_final: 0.7727 (m-80) REVERT: D 353 SER cc_start: 0.9222 (t) cc_final: 0.8567 (p) REVERT: D 387 LEU cc_start: 0.7446 (tp) cc_final: 0.7235 (mm) REVERT: D 414 GLU cc_start: 0.8556 (tm-30) cc_final: 0.7707 (tp30) REVERT: D 720 ASN cc_start: 0.7078 (t0) cc_final: 0.6740 (t0) REVERT: D 765 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7004 (mt-10) REVERT: D 805 GLN cc_start: 0.8104 (tp-100) cc_final: 0.7702 (tp40) REVERT: D 925 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8250 (tm-30) REVERT: D 929 GLN cc_start: 0.7787 (mt0) cc_final: 0.7119 (tm-30) REVERT: D 995 TYR cc_start: 0.6579 (m-80) cc_final: 0.5501 (m-80) REVERT: D 1151 LYS cc_start: 0.8512 (tptp) cc_final: 0.7657 (mtmt) REVERT: D 1189 MET cc_start: 0.7589 (mpp) cc_final: 0.7272 (mpp) REVERT: D 1239 ASP cc_start: 0.7065 (t0) cc_final: 0.6711 (m-30) REVERT: D 1250 ASP cc_start: 0.8109 (m-30) cc_final: 0.7306 (p0) REVERT: D 1273 ASP cc_start: 0.7988 (m-30) cc_final: 0.7490 (t70) REVERT: E 15 ASN cc_start: 0.8221 (t0) cc_final: 0.7888 (t0) REVERT: E 26 ARG cc_start: 0.8503 (tpp80) cc_final: 0.8032 (tpt-90) REVERT: E 30 MET cc_start: 0.7295 (mtp) cc_final: 0.7042 (mtp) REVERT: E 35 LYS cc_start: 0.7103 (ttpt) cc_final: 0.6746 (ttpt) REVERT: E 41 GLU cc_start: 0.7006 (pm20) cc_final: 0.6264 (pt0) REVERT: E 44 ASP cc_start: 0.8791 (m-30) cc_final: 0.8516 (m-30) REVERT: E 53 GLU cc_start: 0.7826 (mt-10) cc_final: 0.6958 (mt-10) REVERT: E 56 GLU cc_start: 0.6820 (mm-30) cc_final: 0.6549 (mm-30) REVERT: E 62 GLN cc_start: 0.7906 (tp-100) cc_final: 0.7498 (tm-30) REVERT: E 66 VAL cc_start: 0.7947 (t) cc_final: 0.7745 (t) REVERT: F 269 LEU cc_start: 0.8582 (mt) cc_final: 0.8014 (pp) REVERT: F 365 MET cc_start: 0.8032 (ttp) cc_final: 0.7157 (tmm) REVERT: P 36 MET cc_start: 0.1190 (ttm) cc_final: 0.0931 (tpp) REVERT: P 45 GLU cc_start: 0.6073 (pp20) cc_final: 0.5834 (mt-10) REVERT: P 48 GLU cc_start: 0.6516 (tp30) cc_final: 0.5885 (tm-30) REVERT: P 53 MET cc_start: 0.3828 (mmm) cc_final: 0.1643 (tpt) REVERT: P 57 MET cc_start: 0.7996 (pmm) cc_final: 0.7637 (pmm) REVERT: P 77 ASP cc_start: 0.6462 (t0) cc_final: 0.6197 (t0) REVERT: P 120 LYS cc_start: 0.5432 (mptt) cc_final: 0.5143 (mmtt) REVERT: P 129 GLU cc_start: 0.7790 (pt0) cc_final: 0.6976 (tp30) REVERT: Q 130 VAL cc_start: 0.8333 (t) cc_final: 0.7938 (p) outliers start: 1 outliers final: 1 residues processed: 597 average time/residue: 0.4320 time to fit residues: 415.2101 Evaluate side-chains 450 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 449 time to evaluate : 4.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 125 optimal weight: 10.0000 chunk 335 optimal weight: 8.9990 chunk 73 optimal weight: 7.9990 chunk 218 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 372 optimal weight: 1.9990 chunk 309 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 30 optimal weight: 0.0370 chunk 123 optimal weight: 3.9990 chunk 195 optimal weight: 7.9990 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 HIS C 314 ASN C 686 GLN D 45 ASN D 458 ASN ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 921 GLN D1197 ASN E 43 ASN Q 90 HIS ** Q 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 33449 Z= 0.247 Angle : 0.640 15.939 45786 Z= 0.336 Chirality : 0.043 0.171 5201 Planarity : 0.004 0.056 5447 Dihedral : 18.469 175.520 5824 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.50 % Favored : 93.42 % Rotamer: Outliers : 0.06 % Allowed : 2.76 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.13), residues: 3741 helix: 0.56 (0.13), residues: 1509 sheet: -0.89 (0.24), residues: 415 loop : -1.97 (0.14), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP Q 19 HIS 0.005 0.001 HIS Q 95 PHE 0.022 0.002 PHE C1025 TYR 0.016 0.001 TYR Q 100 ARG 0.006 0.000 ARG Q 31 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 539 time to evaluate : 3.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7321 (tt0) cc_final: 0.6955 (tt0) REVERT: A 51 MET cc_start: 0.8903 (mmm) cc_final: 0.8590 (mmm) REVERT: A 62 ASP cc_start: 0.8407 (t70) cc_final: 0.7995 (p0) REVERT: A 158 ARG cc_start: 0.6713 (mtt180) cc_final: 0.6419 (ptp-170) REVERT: A 181 GLU cc_start: 0.8189 (tp30) cc_final: 0.7553 (tm-30) REVERT: A 199 ASP cc_start: 0.7660 (m-30) cc_final: 0.7336 (m-30) REVERT: A 206 GLU cc_start: 0.8324 (tp30) cc_final: 0.7688 (tm-30) REVERT: B 33 ARG cc_start: 0.7447 (tmm-80) cc_final: 0.6862 (ttt180) REVERT: B 77 ASP cc_start: 0.6739 (m-30) cc_final: 0.5980 (t0) REVERT: B 147 GLN cc_start: 0.6578 (mt0) cc_final: 0.6205 (mt0) REVERT: B 215 GLU cc_start: 0.7691 (tt0) cc_final: 0.7343 (tm-30) REVERT: B 226 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7846 (tt0) REVERT: C 8 LYS cc_start: 0.8679 (mttt) cc_final: 0.8249 (mttp) REVERT: C 47 TYR cc_start: 0.3800 (m-80) cc_final: 0.2256 (m-80) REVERT: C 158 ASP cc_start: 0.8196 (t0) cc_final: 0.7901 (t0) REVERT: C 200 ARG cc_start: 0.8438 (mmm160) cc_final: 0.8077 (mmm160) REVERT: C 365 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7852 (tm-30) REVERT: C 459 MET cc_start: 0.7733 (mtp) cc_final: 0.7483 (mtp) REVERT: C 510 GLN cc_start: 0.8812 (mt0) cc_final: 0.8369 (mt0) REVERT: C 515 MET cc_start: 0.7979 (ttp) cc_final: 0.7738 (ttt) REVERT: C 542 ARG cc_start: 0.7714 (mpt-90) cc_final: 0.7162 (mmt90) REVERT: C 549 ASP cc_start: 0.8466 (t0) cc_final: 0.7729 (m-30) REVERT: C 580 GLN cc_start: 0.7568 (mt0) cc_final: 0.7297 (mt0) REVERT: C 588 GLU cc_start: 0.7569 (tt0) cc_final: 0.7107 (tt0) REVERT: C 628 HIS cc_start: 0.7632 (m90) cc_final: 0.7396 (m90) REVERT: C 645 PHE cc_start: 0.8231 (m-10) cc_final: 0.7902 (m-10) REVERT: C 694 ARG cc_start: 0.7312 (tpp80) cc_final: 0.6582 (ttp-110) REVERT: C 768 MET cc_start: 0.7292 (mtp) cc_final: 0.6739 (mtm) REVERT: C 779 ARG cc_start: 0.7992 (ttt-90) cc_final: 0.7517 (ttp-110) REVERT: C 900 LYS cc_start: 0.7085 (tppt) cc_final: 0.6635 (tmtt) REVERT: C 930 ASP cc_start: 0.8430 (t0) cc_final: 0.8158 (m-30) REVERT: C 949 GLU cc_start: 0.8974 (tt0) cc_final: 0.8483 (mt-10) REVERT: C 1018 TYR cc_start: 0.7462 (t80) cc_final: 0.7192 (t80) REVERT: C 1107 MET cc_start: 0.7144 (mtm) cc_final: 0.6667 (mtt) REVERT: C 1119 MET cc_start: 0.8142 (tpp) cc_final: 0.7796 (tpp) REVERT: C 1122 LYS cc_start: 0.8096 (tptp) cc_final: 0.7678 (tppt) REVERT: C 1126 ASP cc_start: 0.8548 (t70) cc_final: 0.7951 (t70) REVERT: C 1134 GLN cc_start: 0.8507 (tt0) cc_final: 0.8221 (pp30) REVERT: C 1174 GLU cc_start: 0.8399 (tt0) cc_final: 0.7940 (tp30) REVERT: C 1194 GLU cc_start: 0.7698 (mp0) cc_final: 0.7318 (mp0) REVERT: C 1211 ARG cc_start: 0.8060 (ptp-170) cc_final: 0.7332 (ptm-80) REVERT: C 1229 TYR cc_start: 0.8278 (m-10) cc_final: 0.8036 (m-10) REVERT: C 1274 GLU cc_start: 0.6498 (pm20) cc_final: 0.5804 (pm20) REVERT: C 1291 LEU cc_start: 0.7811 (tp) cc_final: 0.6856 (tp) REVERT: C 1295 SER cc_start: 0.9512 (t) cc_final: 0.8672 (p) REVERT: C 1296 ASP cc_start: 0.8325 (t70) cc_final: 0.7747 (m-30) REVERT: C 1322 SER cc_start: 0.8602 (p) cc_final: 0.8250 (p) REVERT: C 1329 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7746 (tm-30) REVERT: D 50 LYS cc_start: 0.7827 (tttm) cc_final: 0.7588 (tttm) REVERT: D 155 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7502 (mp0) REVERT: D 180 MET cc_start: 0.7188 (ttp) cc_final: 0.6882 (ttm) REVERT: D 193 ASP cc_start: 0.8149 (t0) cc_final: 0.7418 (p0) REVERT: D 314 ARG cc_start: 0.7721 (mtp180) cc_final: 0.7429 (mtp180) REVERT: D 321 LYS cc_start: 0.8037 (mmpt) cc_final: 0.7306 (mttt) REVERT: D 329 ASP cc_start: 0.8049 (t0) cc_final: 0.7662 (m-30) REVERT: D 414 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8460 (tm-30) REVERT: D 479 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7592 (tp30) REVERT: D 596 LEU cc_start: 0.8873 (mt) cc_final: 0.8616 (mt) REVERT: D 697 MET cc_start: 0.7064 (tmm) cc_final: 0.6836 (tmm) REVERT: D 720 ASN cc_start: 0.7455 (t0) cc_final: 0.6936 (t0) REVERT: D 805 GLN cc_start: 0.8159 (tp-100) cc_final: 0.7644 (tp40) REVERT: D 821 MET cc_start: 0.8419 (ttm) cc_final: 0.8148 (ttp) REVERT: D 929 GLN cc_start: 0.7835 (mt0) cc_final: 0.7185 (tm-30) REVERT: D 932 MET cc_start: 0.2031 (mmm) cc_final: 0.1339 (mmm) REVERT: D 979 ASN cc_start: 0.7681 (m-40) cc_final: 0.7188 (p0) REVERT: D 995 TYR cc_start: 0.6594 (m-80) cc_final: 0.5635 (m-80) REVERT: D 1151 LYS cc_start: 0.8530 (tptp) cc_final: 0.7679 (mtmt) REVERT: D 1186 TYR cc_start: 0.7378 (t80) cc_final: 0.7118 (t80) REVERT: D 1250 ASP cc_start: 0.8251 (m-30) cc_final: 0.7299 (p0) REVERT: D 1273 ASP cc_start: 0.8108 (m-30) cc_final: 0.7559 (t70) REVERT: E 15 ASN cc_start: 0.8182 (t0) cc_final: 0.7835 (t0) REVERT: E 26 ARG cc_start: 0.8646 (tpp80) cc_final: 0.8164 (tpt-90) REVERT: E 30 MET cc_start: 0.7470 (mtp) cc_final: 0.7236 (mtp) REVERT: E 41 GLU cc_start: 0.7411 (pm20) cc_final: 0.6360 (pt0) REVERT: E 62 GLN cc_start: 0.7753 (tp-100) cc_final: 0.7390 (tm-30) REVERT: E 66 VAL cc_start: 0.7974 (t) cc_final: 0.7768 (t) REVERT: F 256 PHE cc_start: 0.7167 (t80) cc_final: 0.6942 (t80) REVERT: F 261 LEU cc_start: 0.7905 (pp) cc_final: 0.7013 (tp) REVERT: F 266 PHE cc_start: 0.8030 (m-80) cc_final: 0.7456 (t80) REVERT: F 365 MET cc_start: 0.7966 (ttp) cc_final: 0.7239 (tmm) REVERT: P 36 MET cc_start: 0.1228 (ttm) cc_final: 0.0976 (tpp) REVERT: P 48 GLU cc_start: 0.6576 (tp30) cc_final: 0.5984 (tm-30) REVERT: P 53 MET cc_start: 0.4380 (mmm) cc_final: 0.2535 (tpt) REVERT: P 57 MET cc_start: 0.8137 (pmm) cc_final: 0.7780 (pmm) REVERT: P 77 ASP cc_start: 0.6574 (t0) cc_final: 0.6147 (t0) REVERT: P 120 LYS cc_start: 0.5435 (mptt) cc_final: 0.4996 (mmtt) REVERT: P 142 TYR cc_start: 0.8672 (t80) cc_final: 0.8395 (t80) outliers start: 2 outliers final: 0 residues processed: 539 average time/residue: 0.4223 time to fit residues: 371.3152 Evaluate side-chains 434 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 434 time to evaluate : 3.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 359 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 212 optimal weight: 0.9990 chunk 272 optimal weight: 20.0000 chunk 210 optimal weight: 0.3980 chunk 313 optimal weight: 2.9990 chunk 208 optimal weight: 0.7980 chunk 371 optimal weight: 10.0000 chunk 232 optimal weight: 5.9990 chunk 226 optimal weight: 5.9990 chunk 171 optimal weight: 6.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 314 ASN C 808 ASN ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN D 458 ASN ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1197 ASN E 43 ASN F 446 GLN Q 90 HIS Q 95 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.5439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33449 Z= 0.185 Angle : 0.605 15.088 45786 Z= 0.315 Chirality : 0.042 0.173 5201 Planarity : 0.004 0.051 5447 Dihedral : 18.369 176.616 5824 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.59 % Favored : 94.33 % Rotamer: Outliers : 0.09 % Allowed : 1.93 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.13), residues: 3741 helix: 0.77 (0.13), residues: 1509 sheet: -0.73 (0.25), residues: 412 loop : -1.88 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP Q 19 HIS 0.005 0.001 HIS Q 95 PHE 0.029 0.001 PHE C1025 TYR 0.017 0.001 TYR Q 100 ARG 0.007 0.000 ARG C1033 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 547 time to evaluate : 3.354 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: A 29 GLU cc_start: 0.7316 (tt0) cc_final: 0.6949 (tt0) REVERT: A 51 MET cc_start: 0.8851 (mmm) cc_final: 0.8557 (mmm) REVERT: A 62 ASP cc_start: 0.8401 (t70) cc_final: 0.7983 (p0) REVERT: A 135 ASP cc_start: 0.7675 (t70) cc_final: 0.7463 (t0) REVERT: A 181 GLU cc_start: 0.8172 (tp30) cc_final: 0.7558 (tm-30) REVERT: A 199 ASP cc_start: 0.7680 (m-30) cc_final: 0.7354 (m-30) REVERT: A 206 GLU cc_start: 0.8313 (tp30) cc_final: 0.7687 (tm-30) REVERT: B 33 ARG cc_start: 0.7430 (tmm-80) cc_final: 0.6894 (ttt180) REVERT: B 77 ASP cc_start: 0.6675 (m-30) cc_final: 0.6078 (t0) REVERT: B 147 GLN cc_start: 0.6435 (mt0) cc_final: 0.6033 (mt0) REVERT: B 215 GLU cc_start: 0.7803 (tt0) cc_final: 0.7115 (tm-30) REVERT: B 226 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7836 (tt0) REVERT: C 8 LYS cc_start: 0.8607 (mttt) cc_final: 0.8199 (mttp) REVERT: C 47 TYR cc_start: 0.3564 (m-80) cc_final: 0.2111 (m-80) REVERT: C 158 ASP cc_start: 0.8253 (t0) cc_final: 0.7918 (t70) REVERT: C 163 LYS cc_start: 0.7623 (ptmm) cc_final: 0.7090 (ptmt) REVERT: C 200 ARG cc_start: 0.8425 (mmm160) cc_final: 0.8074 (mmm160) REVERT: C 214 ASN cc_start: 0.8824 (t0) cc_final: 0.8616 (t0) REVERT: C 459 MET cc_start: 0.7629 (mtp) cc_final: 0.7397 (mtp) REVERT: C 479 LEU cc_start: 0.7884 (tp) cc_final: 0.7649 (tp) REVERT: C 492 MET cc_start: 0.7589 (ptp) cc_final: 0.7054 (pmm) REVERT: C 510 GLN cc_start: 0.8795 (mt0) cc_final: 0.8372 (mt0) REVERT: C 542 ARG cc_start: 0.7764 (mpt-90) cc_final: 0.7441 (mtt90) REVERT: C 549 ASP cc_start: 0.8417 (t0) cc_final: 0.7640 (m-30) REVERT: C 580 GLN cc_start: 0.7702 (mt0) cc_final: 0.7440 (mt0) REVERT: C 588 GLU cc_start: 0.7649 (tt0) cc_final: 0.7212 (tt0) REVERT: C 628 HIS cc_start: 0.7600 (m90) cc_final: 0.7396 (m90) REVERT: C 645 PHE cc_start: 0.8292 (m-10) cc_final: 0.7915 (m-10) REVERT: C 694 ARG cc_start: 0.7371 (tpp80) cc_final: 0.6586 (ttp-110) REVERT: C 768 MET cc_start: 0.7244 (mtp) cc_final: 0.6710 (mtm) REVERT: C 779 ARG cc_start: 0.8200 (ttt-90) cc_final: 0.7540 (ttp-110) REVERT: C 900 LYS cc_start: 0.7153 (tppt) cc_final: 0.6784 (tmtt) REVERT: C 930 ASP cc_start: 0.8371 (t0) cc_final: 0.8065 (m-30) REVERT: C 949 GLU cc_start: 0.8999 (tt0) cc_final: 0.8535 (mt-10) REVERT: C 1066 MET cc_start: 0.8717 (ptp) cc_final: 0.8431 (ptp) REVERT: C 1107 MET cc_start: 0.7107 (mtm) cc_final: 0.6641 (mtt) REVERT: C 1119 MET cc_start: 0.8088 (tpp) cc_final: 0.7832 (tpp) REVERT: C 1122 LYS cc_start: 0.8040 (tptp) cc_final: 0.7729 (tptt) REVERT: C 1126 ASP cc_start: 0.8601 (t70) cc_final: 0.8028 (t70) REVERT: C 1134 GLN cc_start: 0.8503 (tt0) cc_final: 0.8225 (pp30) REVERT: C 1174 GLU cc_start: 0.8375 (tt0) cc_final: 0.7889 (tp30) REVERT: C 1194 GLU cc_start: 0.7712 (mp0) cc_final: 0.7278 (mp0) REVERT: C 1211 ARG cc_start: 0.8131 (ptp-170) cc_final: 0.7405 (ptm-80) REVERT: C 1229 TYR cc_start: 0.8264 (m-10) cc_final: 0.7939 (m-10) REVERT: C 1230 MET cc_start: 0.7923 (ttp) cc_final: 0.7622 (ttt) REVERT: C 1291 LEU cc_start: 0.7645 (tp) cc_final: 0.6941 (tp) REVERT: C 1295 SER cc_start: 0.9551 (t) cc_final: 0.8994 (p) REVERT: C 1296 ASP cc_start: 0.8293 (t70) cc_final: 0.7769 (m-30) REVERT: C 1322 SER cc_start: 0.8472 (p) cc_final: 0.8073 (p) REVERT: C 1329 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7806 (tm-30) REVERT: D 155 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7586 (mp0) REVERT: D 180 MET cc_start: 0.7066 (ttp) cc_final: 0.6836 (ttm) REVERT: D 260 PHE cc_start: 0.7679 (m-80) cc_final: 0.7197 (m-80) REVERT: D 314 ARG cc_start: 0.7654 (mtp180) cc_final: 0.7394 (mtp-110) REVERT: D 321 LYS cc_start: 0.8148 (mmpt) cc_final: 0.7751 (mttt) REVERT: D 329 ASP cc_start: 0.7848 (t0) cc_final: 0.7449 (m-30) REVERT: D 349 TYR cc_start: 0.8173 (m-80) cc_final: 0.7794 (m-80) REVERT: D 387 LEU cc_start: 0.7483 (tp) cc_final: 0.7211 (mm) REVERT: D 414 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8439 (tm-30) REVERT: D 429 LEU cc_start: 0.9015 (tt) cc_final: 0.8807 (tt) REVERT: D 479 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7595 (tp30) REVERT: D 497 GLU cc_start: 0.8528 (tt0) cc_final: 0.8214 (mt-10) REVERT: D 596 LEU cc_start: 0.8843 (mt) cc_final: 0.8583 (mt) REVERT: D 720 ASN cc_start: 0.7366 (t0) cc_final: 0.6829 (t0) REVERT: D 805 GLN cc_start: 0.8101 (tp-100) cc_final: 0.7728 (tp40) REVERT: D 821 MET cc_start: 0.8410 (ttm) cc_final: 0.8208 (ttp) REVERT: D 929 GLN cc_start: 0.7915 (mt0) cc_final: 0.7269 (tm-30) REVERT: D 932 MET cc_start: 0.2051 (mmm) cc_final: 0.1489 (mmm) REVERT: D 979 ASN cc_start: 0.7689 (m-40) cc_final: 0.7234 (p0) REVERT: D 995 TYR cc_start: 0.6606 (m-80) cc_final: 0.5642 (m-80) REVERT: D 1151 LYS cc_start: 0.8398 (tptp) cc_final: 0.7577 (mtmt) REVERT: D 1186 TYR cc_start: 0.7516 (t80) cc_final: 0.7231 (t80) REVERT: D 1243 LEU cc_start: 0.9016 (tp) cc_final: 0.8813 (tp) REVERT: D 1250 ASP cc_start: 0.8226 (m-30) cc_final: 0.7381 (p0) REVERT: D 1273 ASP cc_start: 0.8054 (m-30) cc_final: 0.7491 (t70) REVERT: E 15 ASN cc_start: 0.8222 (t0) cc_final: 0.7820 (t0) REVERT: E 26 ARG cc_start: 0.8558 (tpp80) cc_final: 0.8150 (tpt-90) REVERT: E 41 GLU cc_start: 0.7072 (pm20) cc_final: 0.6359 (pt0) REVERT: E 62 GLN cc_start: 0.7907 (tp-100) cc_final: 0.7501 (tm-30) REVERT: F 221 PHE cc_start: 0.3268 (m-80) cc_final: 0.3029 (m-80) REVERT: F 261 LEU cc_start: 0.8034 (pp) cc_final: 0.7207 (tp) REVERT: F 266 PHE cc_start: 0.7994 (m-80) cc_final: 0.7435 (t80) REVERT: F 365 MET cc_start: 0.8570 (ttp) cc_final: 0.7805 (tmm) REVERT: P 48 GLU cc_start: 0.6584 (tp30) cc_final: 0.6035 (tm-30) REVERT: P 53 MET cc_start: 0.4777 (mmm) cc_final: 0.3353 (tpt) REVERT: P 57 MET cc_start: 0.8045 (pmm) cc_final: 0.7707 (pmm) REVERT: P 77 ASP cc_start: 0.6590 (t0) cc_final: 0.6178 (t0) REVERT: P 120 LYS cc_start: 0.5598 (mptt) cc_final: 0.5105 (mmtt) REVERT: Q 33 GLU cc_start: 0.7047 (mp0) cc_final: 0.6837 (mp0) outliers start: 3 outliers final: 1 residues processed: 548 average time/residue: 0.4242 time to fit residues: 380.5864 Evaluate side-chains 447 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 446 time to evaluate : 3.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 229 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 221 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 235 optimal weight: 9.9990 chunk 252 optimal weight: 7.9990 chunk 183 optimal weight: 5.9990 chunk 34 optimal weight: 40.0000 chunk 291 optimal weight: 9.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS C 314 ASN C1061 GLN D 45 ASN D 458 ASN ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 736 GLN D1197 ASN F 446 GLN Q 90 HIS Q 95 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.5642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 33449 Z= 0.336 Angle : 0.708 10.830 45786 Z= 0.372 Chirality : 0.045 0.193 5201 Planarity : 0.005 0.082 5447 Dihedral : 18.470 177.693 5824 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.81 % Favored : 92.11 % Rotamer: Outliers : 0.06 % Allowed : 1.49 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.13), residues: 3741 helix: 0.57 (0.13), residues: 1498 sheet: -0.78 (0.25), residues: 411 loop : -2.00 (0.13), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP Q 19 HIS 0.007 0.002 HIS Q 95 PHE 0.022 0.002 PHE D 49 TYR 0.021 0.002 TYR C1018 ARG 0.005 0.001 ARG D 337 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 520 time to evaluate : 3.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7414 (tt0) cc_final: 0.7040 (tt0) REVERT: A 51 MET cc_start: 0.8942 (mmm) cc_final: 0.8640 (mmm) REVERT: A 57 THR cc_start: 0.7212 (m) cc_final: 0.6915 (m) REVERT: A 62 ASP cc_start: 0.8483 (t70) cc_final: 0.8023 (p0) REVERT: A 135 ASP cc_start: 0.7747 (t70) cc_final: 0.7541 (t0) REVERT: A 181 GLU cc_start: 0.8296 (tp30) cc_final: 0.7722 (tm-30) REVERT: A 199 ASP cc_start: 0.7488 (m-30) cc_final: 0.7219 (m-30) REVERT: A 206 GLU cc_start: 0.8305 (tp30) cc_final: 0.7804 (tm-30) REVERT: B 77 ASP cc_start: 0.6501 (m-30) cc_final: 0.5978 (t0) REVERT: B 147 GLN cc_start: 0.6451 (mt0) cc_final: 0.6105 (mt0) REVERT: B 215 GLU cc_start: 0.7838 (tt0) cc_final: 0.7131 (tm-30) REVERT: B 226 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7935 (tt0) REVERT: C 8 LYS cc_start: 0.8697 (mttt) cc_final: 0.8207 (mtmm) REVERT: C 17 LYS cc_start: 0.8041 (mptt) cc_final: 0.7341 (mmmt) REVERT: C 47 TYR cc_start: 0.3639 (m-80) cc_final: 0.2872 (m-80) REVERT: C 158 ASP cc_start: 0.8218 (t0) cc_final: 0.7847 (t0) REVERT: C 163 LYS cc_start: 0.7619 (ptmm) cc_final: 0.7159 (ptmt) REVERT: C 200 ARG cc_start: 0.8456 (mmm160) cc_final: 0.8077 (mmm160) REVERT: C 337 PHE cc_start: 0.5638 (t80) cc_final: 0.5435 (t80) REVERT: C 349 GLU cc_start: 0.7286 (mp0) cc_final: 0.7070 (mt-10) REVERT: C 365 GLU cc_start: 0.8268 (tm-30) cc_final: 0.8053 (tp30) REVERT: C 492 MET cc_start: 0.7644 (ptp) cc_final: 0.7116 (pmm) REVERT: C 510 GLN cc_start: 0.8841 (mt0) cc_final: 0.8390 (mt0) REVERT: C 546 GLU cc_start: 0.7038 (pm20) cc_final: 0.5992 (tp30) REVERT: C 549 ASP cc_start: 0.8501 (t0) cc_final: 0.7789 (m-30) REVERT: C 588 GLU cc_start: 0.7824 (tt0) cc_final: 0.7346 (tt0) REVERT: C 628 HIS cc_start: 0.7712 (m90) cc_final: 0.7410 (m90) REVERT: C 645 PHE cc_start: 0.8368 (m-10) cc_final: 0.8076 (m-10) REVERT: C 694 ARG cc_start: 0.7468 (tpp80) cc_final: 0.6489 (ttp80) REVERT: C 768 MET cc_start: 0.7239 (mtp) cc_final: 0.6721 (mtm) REVERT: C 779 ARG cc_start: 0.8235 (ttt-90) cc_final: 0.7604 (ttp-110) REVERT: C 811 ASN cc_start: 0.8513 (p0) cc_final: 0.7970 (p0) REVERT: C 900 LYS cc_start: 0.7203 (tppt) cc_final: 0.6922 (tmtt) REVERT: C 930 ASP cc_start: 0.8372 (t0) cc_final: 0.7983 (m-30) REVERT: C 949 GLU cc_start: 0.9018 (tt0) cc_final: 0.8713 (mt-10) REVERT: C 1018 TYR cc_start: 0.7151 (t80) cc_final: 0.6924 (t80) REVERT: C 1066 MET cc_start: 0.8881 (ptp) cc_final: 0.8606 (ptp) REVERT: C 1107 MET cc_start: 0.7295 (mtm) cc_final: 0.6838 (mtt) REVERT: C 1119 MET cc_start: 0.8454 (tpp) cc_final: 0.8093 (tpp) REVERT: C 1122 LYS cc_start: 0.8079 (tptp) cc_final: 0.7726 (tppt) REVERT: C 1126 ASP cc_start: 0.8574 (t70) cc_final: 0.7969 (t70) REVERT: C 1134 GLN cc_start: 0.8436 (tt0) cc_final: 0.8184 (pp30) REVERT: C 1174 GLU cc_start: 0.8460 (tt0) cc_final: 0.7926 (tp30) REVERT: C 1194 GLU cc_start: 0.7729 (mp0) cc_final: 0.7351 (mp0) REVERT: C 1211 ARG cc_start: 0.7989 (ptp-170) cc_final: 0.7257 (ptm-80) REVERT: C 1230 MET cc_start: 0.7823 (ttp) cc_final: 0.7542 (ttt) REVERT: C 1274 GLU cc_start: 0.6545 (pm20) cc_final: 0.5792 (pm20) REVERT: C 1291 LEU cc_start: 0.7573 (tp) cc_final: 0.7129 (tp) REVERT: C 1295 SER cc_start: 0.9579 (t) cc_final: 0.8836 (p) REVERT: C 1296 ASP cc_start: 0.8483 (t70) cc_final: 0.7988 (m-30) REVERT: C 1322 SER cc_start: 0.8596 (p) cc_final: 0.8258 (p) REVERT: C 1329 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7778 (tm-30) REVERT: D 155 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7557 (mp0) REVERT: D 314 ARG cc_start: 0.7628 (mtp180) cc_final: 0.7389 (mtp180) REVERT: D 321 LYS cc_start: 0.8227 (mmpt) cc_final: 0.7722 (mttm) REVERT: D 375 GLU cc_start: 0.8177 (tp30) cc_final: 0.7892 (tp30) REVERT: D 414 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8604 (tm-30) REVERT: D 497 GLU cc_start: 0.8537 (tt0) cc_final: 0.8206 (mt-10) REVERT: D 556 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8064 (mt-10) REVERT: D 596 LEU cc_start: 0.8943 (mt) cc_final: 0.8658 (mt) REVERT: D 708 ASN cc_start: 0.7164 (p0) cc_final: 0.6952 (p0) REVERT: D 720 ASN cc_start: 0.7644 (t0) cc_final: 0.7151 (t0) REVERT: D 759 ILE cc_start: 0.8663 (mm) cc_final: 0.8461 (mp) REVERT: D 805 GLN cc_start: 0.8346 (tp-100) cc_final: 0.7728 (tp40) REVERT: D 821 MET cc_start: 0.8425 (ttm) cc_final: 0.8209 (ttp) REVERT: D 929 GLN cc_start: 0.7985 (mt0) cc_final: 0.7514 (tm-30) REVERT: D 979 ASN cc_start: 0.7706 (m-40) cc_final: 0.7232 (p0) REVERT: D 995 TYR cc_start: 0.6168 (m-80) cc_final: 0.5395 (m-80) REVERT: D 1151 LYS cc_start: 0.8408 (tptp) cc_final: 0.7595 (mtmt) REVERT: D 1186 TYR cc_start: 0.7709 (t80) cc_final: 0.7472 (t80) REVERT: D 1215 GLU cc_start: 0.6637 (tt0) cc_final: 0.6393 (tp30) REVERT: D 1250 ASP cc_start: 0.8292 (m-30) cc_final: 0.7347 (p0) REVERT: D 1273 ASP cc_start: 0.8252 (m-30) cc_final: 0.7605 (t70) REVERT: D 1370 MET cc_start: 0.6243 (tpp) cc_final: 0.5992 (tpp) REVERT: E 8 ASP cc_start: 0.8479 (m-30) cc_final: 0.7585 (t0) REVERT: E 15 ASN cc_start: 0.8182 (t0) cc_final: 0.7804 (t0) REVERT: E 30 MET cc_start: 0.7506 (mtp) cc_final: 0.7303 (mtt) REVERT: E 41 GLU cc_start: 0.7332 (pm20) cc_final: 0.6622 (pt0) REVERT: E 53 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7588 (mt-10) REVERT: E 62 GLN cc_start: 0.7766 (tp-100) cc_final: 0.7390 (tm-30) REVERT: E 66 VAL cc_start: 0.7935 (t) cc_final: 0.7730 (t) REVERT: F 221 PHE cc_start: 0.3397 (m-80) cc_final: 0.3179 (m-80) REVERT: F 261 LEU cc_start: 0.7973 (pp) cc_final: 0.7257 (tp) REVERT: F 266 PHE cc_start: 0.8016 (m-80) cc_final: 0.7626 (m-80) REVERT: F 365 MET cc_start: 0.8687 (ttp) cc_final: 0.7856 (tmm) REVERT: P 48 GLU cc_start: 0.6614 (tp30) cc_final: 0.6151 (tm-30) REVERT: P 53 MET cc_start: 0.4455 (mmm) cc_final: 0.3487 (tpt) REVERT: P 57 MET cc_start: 0.8263 (pmm) cc_final: 0.7989 (pmm) REVERT: P 77 ASP cc_start: 0.6608 (t0) cc_final: 0.6102 (t0) REVERT: P 120 LYS cc_start: 0.5525 (mptt) cc_final: 0.5293 (mptt) REVERT: P 142 TYR cc_start: 0.8268 (t80) cc_final: 0.8035 (t80) REVERT: Q 33 GLU cc_start: 0.7074 (mp0) cc_final: 0.6811 (mp0) outliers start: 2 outliers final: 0 residues processed: 520 average time/residue: 0.4107 time to fit residues: 348.5904 Evaluate side-chains 423 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 423 time to evaluate : 3.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 337 optimal weight: 7.9990 chunk 355 optimal weight: 10.0000 chunk 324 optimal weight: 7.9990 chunk 345 optimal weight: 7.9990 chunk 208 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 chunk 271 optimal weight: 7.9990 chunk 106 optimal weight: 8.9990 chunk 312 optimal weight: 7.9990 chunk 327 optimal weight: 3.9990 chunk 344 optimal weight: 0.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 314 ASN C 808 ASN ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN D 196 GLN D 488 ASN ** D 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 90 HIS Q 95 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.5839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 33449 Z= 0.300 Angle : 0.688 11.345 45786 Z= 0.361 Chirality : 0.044 0.180 5201 Planarity : 0.005 0.077 5447 Dihedral : 18.442 177.841 5824 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.71 % Favored : 93.21 % Rotamer: Outliers : 0.03 % Allowed : 0.96 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.13), residues: 3741 helix: 0.52 (0.13), residues: 1496 sheet: -0.80 (0.25), residues: 411 loop : -2.04 (0.13), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP Q 19 HIS 0.008 0.001 HIS Q 95 PHE 0.017 0.002 PHE F 316 TYR 0.024 0.002 TYR C1018 ARG 0.005 0.000 ARG C 275 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 510 time to evaluate : 2.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.7844 (t0) cc_final: 0.7636 (t0) REVERT: A 29 GLU cc_start: 0.7351 (tt0) cc_final: 0.6985 (tt0) REVERT: A 51 MET cc_start: 0.8919 (mmm) cc_final: 0.8632 (mmm) REVERT: A 62 ASP cc_start: 0.8486 (t70) cc_final: 0.8025 (p0) REVERT: A 68 TYR cc_start: 0.7556 (m-80) cc_final: 0.6920 (m-80) REVERT: A 181 GLU cc_start: 0.8257 (tp30) cc_final: 0.7799 (tm-30) REVERT: A 199 ASP cc_start: 0.7703 (m-30) cc_final: 0.7477 (m-30) REVERT: A 206 GLU cc_start: 0.8309 (tp30) cc_final: 0.7811 (tm-30) REVERT: A 212 ASP cc_start: 0.8157 (m-30) cc_final: 0.7957 (m-30) REVERT: B 10 LYS cc_start: 0.9151 (mtmm) cc_final: 0.8672 (mtpt) REVERT: B 33 ARG cc_start: 0.7429 (tmm-80) cc_final: 0.6923 (ttp80) REVERT: B 77 ASP cc_start: 0.6513 (m-30) cc_final: 0.5950 (t0) REVERT: B 147 GLN cc_start: 0.6446 (mt0) cc_final: 0.6111 (mt0) REVERT: B 215 GLU cc_start: 0.7910 (tt0) cc_final: 0.7218 (tm-30) REVERT: B 226 GLU cc_start: 0.8375 (mm-30) cc_final: 0.7938 (tt0) REVERT: C 8 LYS cc_start: 0.8638 (mttt) cc_final: 0.8314 (mttp) REVERT: C 17 LYS cc_start: 0.8107 (mptt) cc_final: 0.7403 (mmmt) REVERT: C 47 TYR cc_start: 0.3803 (m-80) cc_final: 0.2152 (m-80) REVERT: C 158 ASP cc_start: 0.8093 (t0) cc_final: 0.7700 (t0) REVERT: C 163 LYS cc_start: 0.7701 (ptmm) cc_final: 0.7263 (ptmt) REVERT: C 200 ARG cc_start: 0.8456 (mmm160) cc_final: 0.8083 (mmm160) REVERT: C 325 LEU cc_start: 0.9219 (pp) cc_final: 0.8796 (tp) REVERT: C 349 GLU cc_start: 0.7252 (mp0) cc_final: 0.6997 (mt-10) REVERT: C 419 ILE cc_start: 0.8293 (pt) cc_final: 0.7536 (mt) REVERT: C 492 MET cc_start: 0.7618 (ptp) cc_final: 0.7074 (pmm) REVERT: C 510 GLN cc_start: 0.8800 (mt0) cc_final: 0.8310 (mt0) REVERT: C 546 GLU cc_start: 0.7031 (pm20) cc_final: 0.6044 (tp30) REVERT: C 549 ASP cc_start: 0.8477 (t0) cc_final: 0.7726 (m-30) REVERT: C 588 GLU cc_start: 0.8007 (tt0) cc_final: 0.7471 (tt0) REVERT: C 628 HIS cc_start: 0.7721 (m90) cc_final: 0.7413 (m90) REVERT: C 645 PHE cc_start: 0.8376 (m-10) cc_final: 0.8081 (m-10) REVERT: C 694 ARG cc_start: 0.7423 (tpp80) cc_final: 0.6452 (ttp80) REVERT: C 768 MET cc_start: 0.7202 (mtp) cc_final: 0.6679 (mtm) REVERT: C 779 ARG cc_start: 0.8118 (ttt-90) cc_final: 0.7549 (ttp-110) REVERT: C 811 ASN cc_start: 0.8590 (p0) cc_final: 0.8091 (p0) REVERT: C 813 GLU cc_start: 0.8448 (tp30) cc_final: 0.7526 (tt0) REVERT: C 848 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7389 (mp0) REVERT: C 901 LEU cc_start: 0.8677 (tp) cc_final: 0.8415 (pp) REVERT: C 930 ASP cc_start: 0.8388 (t0) cc_final: 0.7973 (m-30) REVERT: C 949 GLU cc_start: 0.8976 (tt0) cc_final: 0.8708 (mt-10) REVERT: C 964 LEU cc_start: 0.7107 (tp) cc_final: 0.6790 (tp) REVERT: C 1018 TYR cc_start: 0.7133 (t80) cc_final: 0.6860 (t80) REVERT: C 1107 MET cc_start: 0.7255 (mtm) cc_final: 0.6659 (mtt) REVERT: C 1119 MET cc_start: 0.8297 (tpp) cc_final: 0.7956 (tpp) REVERT: C 1126 ASP cc_start: 0.8588 (t70) cc_final: 0.8011 (t70) REVERT: C 1134 GLN cc_start: 0.8529 (tt0) cc_final: 0.8230 (pp30) REVERT: C 1174 GLU cc_start: 0.8455 (tt0) cc_final: 0.7922 (tp30) REVERT: C 1194 GLU cc_start: 0.7748 (mp0) cc_final: 0.7338 (mp0) REVERT: C 1211 ARG cc_start: 0.7993 (ptp-170) cc_final: 0.7225 (ptm-80) REVERT: C 1230 MET cc_start: 0.7862 (ttp) cc_final: 0.7546 (ttt) REVERT: C 1291 LEU cc_start: 0.7794 (tp) cc_final: 0.7303 (tp) REVERT: C 1295 SER cc_start: 0.9572 (t) cc_final: 0.8838 (p) REVERT: C 1296 ASP cc_start: 0.8415 (t70) cc_final: 0.7975 (m-30) REVERT: C 1322 SER cc_start: 0.8591 (p) cc_final: 0.8217 (p) REVERT: C 1329 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7924 (tm-30) REVERT: D 180 MET cc_start: 0.7154 (ttp) cc_final: 0.6943 (ttm) REVERT: D 321 LYS cc_start: 0.8049 (mmpt) cc_final: 0.7505 (mttm) REVERT: D 414 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8406 (tm-30) REVERT: D 485 MET cc_start: 0.8909 (tpp) cc_final: 0.8704 (tpt) REVERT: D 497 GLU cc_start: 0.8536 (tt0) cc_final: 0.8206 (mt-10) REVERT: D 596 LEU cc_start: 0.8923 (mt) cc_final: 0.8643 (mt) REVERT: D 684 ASP cc_start: 0.7723 (m-30) cc_final: 0.7523 (m-30) REVERT: D 805 GLN cc_start: 0.8236 (tp-100) cc_final: 0.7713 (tp40) REVERT: D 821 MET cc_start: 0.8411 (ttm) cc_final: 0.8196 (ttp) REVERT: D 979 ASN cc_start: 0.7694 (m-40) cc_final: 0.7307 (p0) REVERT: D 1151 LYS cc_start: 0.8408 (tptp) cc_final: 0.7592 (mtmt) REVERT: D 1186 TYR cc_start: 0.7774 (t80) cc_final: 0.7447 (t80) REVERT: D 1215 GLU cc_start: 0.6687 (tt0) cc_final: 0.6396 (tp30) REVERT: D 1250 ASP cc_start: 0.8282 (m-30) cc_final: 0.7392 (p0) REVERT: D 1273 ASP cc_start: 0.8347 (m-30) cc_final: 0.7467 (t0) REVERT: D 1305 ASP cc_start: 0.7985 (m-30) cc_final: 0.7714 (m-30) REVERT: E 8 ASP cc_start: 0.8470 (m-30) cc_final: 0.7508 (t0) REVERT: E 15 ASN cc_start: 0.8175 (t0) cc_final: 0.7783 (t0) REVERT: E 41 GLU cc_start: 0.7107 (pm20) cc_final: 0.6493 (pt0) REVERT: E 62 GLN cc_start: 0.7819 (tp-100) cc_final: 0.7492 (tm-30) REVERT: E 66 VAL cc_start: 0.7944 (t) cc_final: 0.7697 (t) REVERT: E 70 GLN cc_start: 0.8371 (tt0) cc_final: 0.7994 (tt0) REVERT: F 261 LEU cc_start: 0.8017 (pp) cc_final: 0.7240 (tp) REVERT: F 266 PHE cc_start: 0.8044 (m-80) cc_final: 0.7638 (m-80) REVERT: F 365 MET cc_start: 0.8668 (ttp) cc_final: 0.7988 (tmm) REVERT: F 366 SER cc_start: 0.8460 (m) cc_final: 0.8010 (p) REVERT: F 405 ILE cc_start: 0.8561 (tp) cc_final: 0.8281 (tp) REVERT: P 21 GLU cc_start: 0.8612 (tp30) cc_final: 0.8313 (tp30) REVERT: P 48 GLU cc_start: 0.6610 (tp30) cc_final: 0.6095 (tm-30) REVERT: P 77 ASP cc_start: 0.6826 (t0) cc_final: 0.6486 (t0) REVERT: P 120 LYS cc_start: 0.5566 (mptt) cc_final: 0.5330 (mptt) REVERT: Q 33 GLU cc_start: 0.7089 (mp0) cc_final: 0.6825 (mp0) outliers start: 1 outliers final: 0 residues processed: 510 average time/residue: 0.4135 time to fit residues: 344.8055 Evaluate side-chains 421 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 421 time to evaluate : 3.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 227 optimal weight: 0.1980 chunk 365 optimal weight: 3.9990 chunk 223 optimal weight: 9.9990 chunk 173 optimal weight: 7.9990 chunk 254 optimal weight: 3.9990 chunk 383 optimal weight: 4.9990 chunk 353 optimal weight: 10.0000 chunk 305 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 235 optimal weight: 6.9990 chunk 187 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 314 ASN C 808 ASN ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1146 GLN D 45 ASN D 458 ASN Q 90 HIS Q 95 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.5973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33449 Z= 0.218 Angle : 0.643 11.943 45786 Z= 0.335 Chirality : 0.043 0.165 5201 Planarity : 0.004 0.072 5447 Dihedral : 18.352 178.276 5824 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.84 % Favored : 93.08 % Rotamer: Outliers : 0.06 % Allowed : 0.28 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.13), residues: 3741 helix: 0.69 (0.13), residues: 1499 sheet: -0.70 (0.25), residues: 407 loop : -1.96 (0.14), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 115 HIS 0.007 0.001 HIS Q 95 PHE 0.023 0.001 PHE C 828 TYR 0.018 0.001 TYR C1018 ARG 0.006 0.000 ARG E 26 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 527 time to evaluate : 3.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7353 (tt0) cc_final: 0.6985 (tt0) REVERT: A 51 MET cc_start: 0.8881 (mmm) cc_final: 0.8603 (mmm) REVERT: A 57 THR cc_start: 0.7312 (m) cc_final: 0.7007 (m) REVERT: A 62 ASP cc_start: 0.8443 (t70) cc_final: 0.7988 (p0) REVERT: A 68 TYR cc_start: 0.7517 (m-80) cc_final: 0.6925 (m-80) REVERT: A 181 GLU cc_start: 0.8158 (tp30) cc_final: 0.7764 (tm-30) REVERT: A 206 GLU cc_start: 0.8308 (tp30) cc_final: 0.7744 (tm-30) REVERT: A 212 ASP cc_start: 0.8148 (m-30) cc_final: 0.7940 (m-30) REVERT: B 10 LYS cc_start: 0.9136 (mtmm) cc_final: 0.8665 (mtpt) REVERT: B 49 SER cc_start: 0.8627 (t) cc_final: 0.8316 (m) REVERT: B 77 ASP cc_start: 0.6525 (m-30) cc_final: 0.5963 (t0) REVERT: B 147 GLN cc_start: 0.6372 (mt0) cc_final: 0.6024 (mt0) REVERT: B 215 GLU cc_start: 0.7896 (tt0) cc_final: 0.7421 (tm-30) REVERT: B 226 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7957 (tt0) REVERT: C 5 TYR cc_start: 0.5663 (t80) cc_final: 0.5212 (t80) REVERT: C 8 LYS cc_start: 0.8631 (mttt) cc_final: 0.8198 (mttp) REVERT: C 17 LYS cc_start: 0.8060 (mptt) cc_final: 0.7377 (mmmt) REVERT: C 47 TYR cc_start: 0.3674 (m-80) cc_final: 0.2135 (m-80) REVERT: C 158 ASP cc_start: 0.8215 (t0) cc_final: 0.7814 (t70) REVERT: C 163 LYS cc_start: 0.7616 (ptmm) cc_final: 0.7392 (ptmt) REVERT: C 200 ARG cc_start: 0.8429 (mmm160) cc_final: 0.8057 (mmm160) REVERT: C 325 LEU cc_start: 0.9123 (pp) cc_final: 0.8725 (tp) REVERT: C 337 PHE cc_start: 0.5754 (t80) cc_final: 0.5520 (t80) REVERT: C 419 ILE cc_start: 0.8220 (pt) cc_final: 0.7490 (mt) REVERT: C 510 GLN cc_start: 0.8737 (mt0) cc_final: 0.8310 (mt0) REVERT: C 516 ASP cc_start: 0.7436 (p0) cc_final: 0.7228 (p0) REVERT: C 546 GLU cc_start: 0.7141 (pm20) cc_final: 0.6149 (tp30) REVERT: C 549 ASP cc_start: 0.8461 (t0) cc_final: 0.7711 (m-30) REVERT: C 588 GLU cc_start: 0.7746 (tt0) cc_final: 0.7295 (tt0) REVERT: C 606 LEU cc_start: 0.7950 (mm) cc_final: 0.7680 (mp) REVERT: C 628 HIS cc_start: 0.7727 (m90) cc_final: 0.7423 (m90) REVERT: C 645 PHE cc_start: 0.8356 (m-10) cc_final: 0.8048 (m-10) REVERT: C 694 ARG cc_start: 0.7388 (tpp80) cc_final: 0.6656 (ttp-110) REVERT: C 768 MET cc_start: 0.7201 (mtp) cc_final: 0.6672 (mtm) REVERT: C 775 GLU cc_start: 0.8126 (tt0) cc_final: 0.7608 (tp30) REVERT: C 779 ARG cc_start: 0.8123 (ttt-90) cc_final: 0.7558 (ttp-110) REVERT: C 811 ASN cc_start: 0.8575 (p0) cc_final: 0.8058 (p0) REVERT: C 848 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7379 (mp0) REVERT: C 930 ASP cc_start: 0.8349 (t0) cc_final: 0.7949 (m-30) REVERT: C 949 GLU cc_start: 0.9050 (tt0) cc_final: 0.8757 (mt-10) REVERT: C 1018 TYR cc_start: 0.7177 (t80) cc_final: 0.6894 (t80) REVERT: C 1080 ASN cc_start: 0.8300 (t0) cc_final: 0.7765 (t0) REVERT: C 1107 MET cc_start: 0.7217 (mtm) cc_final: 0.6712 (mtt) REVERT: C 1119 MET cc_start: 0.8231 (tpp) cc_final: 0.7932 (tpp) REVERT: C 1122 LYS cc_start: 0.7927 (tptp) cc_final: 0.7663 (tppt) REVERT: C 1126 ASP cc_start: 0.8576 (t70) cc_final: 0.7984 (t70) REVERT: C 1134 GLN cc_start: 0.8510 (tt0) cc_final: 0.8246 (pp30) REVERT: C 1174 GLU cc_start: 0.8418 (tt0) cc_final: 0.7958 (tp30) REVERT: C 1194 GLU cc_start: 0.7744 (mp0) cc_final: 0.7343 (mp0) REVERT: C 1211 ARG cc_start: 0.7982 (ptp-170) cc_final: 0.7253 (ptm-80) REVERT: C 1291 LEU cc_start: 0.7773 (tp) cc_final: 0.7281 (tp) REVERT: C 1295 SER cc_start: 0.9557 (t) cc_final: 0.9073 (p) REVERT: C 1296 ASP cc_start: 0.8356 (t70) cc_final: 0.7837 (m-30) REVERT: C 1322 SER cc_start: 0.8469 (p) cc_final: 0.8105 (p) REVERT: C 1329 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7898 (tm-30) REVERT: D 207 GLU cc_start: 0.7475 (tp30) cc_final: 0.6836 (mm-30) REVERT: D 321 LYS cc_start: 0.8099 (mmpt) cc_final: 0.7578 (mttm) REVERT: D 387 LEU cc_start: 0.7456 (tp) cc_final: 0.7222 (mm) REVERT: D 414 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8439 (tm-30) REVERT: D 497 GLU cc_start: 0.8540 (tt0) cc_final: 0.8209 (mt-10) REVERT: D 596 LEU cc_start: 0.8931 (mt) cc_final: 0.8696 (mt) REVERT: D 720 ASN cc_start: 0.7547 (t0) cc_final: 0.6891 (t0) REVERT: D 805 GLN cc_start: 0.8140 (tp-100) cc_final: 0.7635 (tp40) REVERT: D 821 MET cc_start: 0.8401 (ttm) cc_final: 0.8140 (ttp) REVERT: D 979 ASN cc_start: 0.7717 (m-40) cc_final: 0.7358 (p0) REVERT: D 1151 LYS cc_start: 0.8317 (tptp) cc_final: 0.7555 (mtmt) REVERT: D 1186 TYR cc_start: 0.7673 (t80) cc_final: 0.7334 (t80) REVERT: D 1215 GLU cc_start: 0.6560 (tt0) cc_final: 0.6317 (tp30) REVERT: D 1250 ASP cc_start: 0.8224 (m-30) cc_final: 0.7418 (p0) REVERT: D 1273 ASP cc_start: 0.8016 (m-30) cc_final: 0.7185 (t0) REVERT: D 1305 ASP cc_start: 0.8005 (m-30) cc_final: 0.7698 (m-30) REVERT: E 8 ASP cc_start: 0.8471 (m-30) cc_final: 0.7607 (t0) REVERT: E 15 ASN cc_start: 0.8150 (t0) cc_final: 0.7766 (t0) REVERT: E 26 ARG cc_start: 0.8486 (tpp80) cc_final: 0.8273 (tpt90) REVERT: E 41 GLU cc_start: 0.7016 (pm20) cc_final: 0.6285 (pt0) REVERT: E 53 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7247 (mt-10) REVERT: E 62 GLN cc_start: 0.7654 (tp-100) cc_final: 0.7348 (tm-30) REVERT: F 261 LEU cc_start: 0.7889 (pp) cc_final: 0.7087 (tp) REVERT: F 266 PHE cc_start: 0.8014 (m-80) cc_final: 0.7606 (m-80) REVERT: F 365 MET cc_start: 0.8564 (ttp) cc_final: 0.7873 (tmm) REVERT: F 405 ILE cc_start: 0.8299 (tp) cc_final: 0.8096 (tp) REVERT: F 409 ASN cc_start: 0.8021 (m-40) cc_final: 0.7790 (m-40) REVERT: P 21 GLU cc_start: 0.8621 (tp30) cc_final: 0.8250 (tp30) REVERT: P 33 GLU cc_start: 0.7947 (pm20) cc_final: 0.7730 (pm20) REVERT: P 48 GLU cc_start: 0.6655 (tp30) cc_final: 0.6257 (tm-30) REVERT: P 53 MET cc_start: 0.4362 (mmp) cc_final: 0.3906 (tpt) REVERT: P 77 ASP cc_start: 0.6904 (t0) cc_final: 0.6563 (t0) REVERT: P 120 LYS cc_start: 0.5587 (mptt) cc_final: 0.5345 (mptt) REVERT: Q 27 VAL cc_start: 0.7228 (t) cc_final: 0.6804 (m) REVERT: Q 33 GLU cc_start: 0.7135 (mp0) cc_final: 0.6881 (mp0) outliers start: 2 outliers final: 1 residues processed: 527 average time/residue: 0.4155 time to fit residues: 362.5475 Evaluate side-chains 438 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 437 time to evaluate : 3.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 242 optimal weight: 0.8980 chunk 325 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 chunk 281 optimal weight: 7.9990 chunk 45 optimal weight: 0.0770 chunk 84 optimal weight: 5.9990 chunk 305 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 314 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.4740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 147 GLN C 808 ASN ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 90 HIS Q 95 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.151330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.125293 restraints weight = 61700.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.124974 restraints weight = 74213.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.125479 restraints weight = 74278.822| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.6105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33449 Z= 0.176 Angle : 0.618 11.956 45786 Z= 0.320 Chirality : 0.042 0.171 5201 Planarity : 0.004 0.069 5447 Dihedral : 18.244 179.022 5824 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.88 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.14), residues: 3741 helix: 0.90 (0.14), residues: 1498 sheet: -0.58 (0.25), residues: 404 loop : -1.87 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP Q 19 HIS 0.006 0.001 HIS Q 95 PHE 0.022 0.001 PHE F 266 TYR 0.018 0.001 TYR Q 100 ARG 0.005 0.000 ARG C 272 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7379.88 seconds wall clock time: 133 minutes 10.62 seconds (7990.62 seconds total)