Starting phenix.real_space_refine on Fri Jul 26 10:36:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t7s_41093/07_2024/8t7s_41093_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t7s_41093/07_2024/8t7s_41093.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t7s_41093/07_2024/8t7s_41093.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t7s_41093/07_2024/8t7s_41093.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t7s_41093/07_2024/8t7s_41093_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t7s_41093/07_2024/8t7s_41093_neut.cif" } resolution = 3.01 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= 0.004 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8998 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 239 5.49 5 Mg 5 5.21 5 S 39 5.16 5 C 15010 2.51 5 N 4380 2.21 5 O 5321 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1162": "OE1" <-> "OE2" Residue "A GLU 1205": "OE1" <-> "OE2" Residue "A GLU 1207": "OE1" <-> "OE2" Residue "G ASP 23": "OD1" <-> "OD2" Residue "G LEU 419": "CD1" <-> "CD2" Residue "G GLU 470": "OE1" <-> "OE2" Residue "G PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 746": "OE1" <-> "OE2" Residue "G GLU 1207": "OE1" <-> "OE2" Residue "G PHE 1235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1243": "OE1" <-> "OE2" Residue "G ASP 1288": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 24994 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 10774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1312, 10774 Classifications: {'peptide': 1312} Link IDs: {'PTRANS': 34, 'TRANS': 1277} Chain breaks: 5 Chain: "B" Number of atoms: 2103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2103 Classifications: {'RNA': 98} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p_pur': 51, 'rna3p_pyr': 34} Link IDs: {'rna2p': 12, 'rna3p': 85} Chain breaks: 1 Chain: "C" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 433 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "G" Number of atoms: 9139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1157, 9139 Classifications: {'peptide': 1157} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 31, 'TRANS': 1125} Chain breaks: 5 Unresolved non-hydrogen bonds: 348 Unresolved non-hydrogen angles: 391 Unresolved non-hydrogen dihedrals: 309 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 7, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 160 Chain: "H" Number of atoms: 1887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1887 Classifications: {'RNA': 88} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 44, 'rna3p_pyr': 30} Link IDs: {'rna2p': 13, 'rna3p': 74} Chain: "c" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 302 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "D" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 349 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 12.53, per 1000 atoms: 0.50 Number of scatterers: 24994 At special positions: 0 Unit cell: (104.49, 125.55, 207.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 39 16.00 P 239 15.00 Mg 5 11.99 O 5321 8.00 N 4380 7.00 C 15010 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: 11.00 Conformation dependent library (CDL) restraints added in 3.4 seconds 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4704 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 17 sheets defined 55.3% alpha, 8.4% beta 80 base pairs and 136 stacking pairs defined. Time for finding SS restraints: 9.22 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 3.751A pdb=" N ALA A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.760A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 183 through 195 removed outlier: 3.679A pdb=" N GLN A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.982A pdb=" N GLU A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 242 removed outlier: 4.605A pdb=" N ASN A 240 " --> pdb=" O GLY A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 271 through 276 removed outlier: 3.850A pdb=" N ASP A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 306 Processing helix chain 'A' and resid 315 through 343 removed outlier: 3.581A pdb=" N ALA A 337 " --> pdb=" O THR A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 removed outlier: 3.644A pdb=" N ILE A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 383 Proline residue: A 378 - end of helix removed outlier: 3.867A pdb=" N LYS A 382 " --> pdb=" O PRO A 378 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET A 383 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 395 removed outlier: 3.544A pdb=" N ARG A 395 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.902A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.170A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.601A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 removed outlier: 3.728A pdb=" N ILE A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 444 " --> pdb=" O ILE A 440 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR A 445 " --> pdb=" O GLU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 483 through 494 removed outlier: 3.652A pdb=" N ILE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 541 through 553 Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 591 through 601 Processing helix chain 'A' and resid 603 through 608 removed outlier: 3.580A pdb=" N LEU A 607 " --> pdb=" O ASP A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 644 through 652 Processing helix chain 'A' and resid 663 through 669 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 699 Processing helix chain 'A' and resid 703 through 712 Processing helix chain 'A' and resid 719 through 727 Processing helix chain 'A' and resid 733 through 751 removed outlier: 3.600A pdb=" N THR A 740 " --> pdb=" O GLY A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 776 Processing helix chain 'A' and resid 779 through 792 removed outlier: 3.749A pdb=" N ARG A 783 " --> pdb=" O GLU A 779 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 784 " --> pdb=" O ARG A 780 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 787 " --> pdb=" O ARG A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 799 Processing helix chain 'A' and resid 804 through 807 Processing helix chain 'A' and resid 808 through 817 Processing helix chain 'A' and resid 851 through 853 No H-bonds generated for 'chain 'A' and resid 851 through 853' Processing helix chain 'A' and resid 860 through 865 Processing helix chain 'A' and resid 872 through 889 removed outlier: 5.569A pdb=" N ASN A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N TYR A 882 " --> pdb=" O LYS A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 901 Processing helix chain 'A' and resid 902 through 906 Processing helix chain 'A' and resid 918 through 940 removed outlier: 3.735A pdb=" N VAL A 922 " --> pdb=" O LYS A 918 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 970 Processing helix chain 'A' and resid 980 through 1001 removed outlier: 4.491A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1008 Processing helix chain 'A' and resid 1030 through 1042 Processing helix chain 'A' and resid 1043 through 1047 Processing helix chain 'A' and resid 1077 through 1088 removed outlier: 3.682A pdb=" N ALA A1081 " --> pdb=" O GLY A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 removed outlier: 3.612A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1185 removed outlier: 3.644A pdb=" N PHE A1181 " --> pdb=" O ASN A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1195 Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1240 Processing helix chain 'A' and resid 1248 through 1261 Processing helix chain 'A' and resid 1264 through 1281 removed outlier: 3.604A pdb=" N GLU A1268 " --> pdb=" O HIS A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1298 Processing helix chain 'A' and resid 1301 through 1317 removed outlier: 5.071A pdb=" N HIS A1311 " --> pdb=" O GLU A1307 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE A1313 " --> pdb=" O ILE A1309 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N THR A1314 " --> pdb=" O ILE A1310 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU A1315 " --> pdb=" O HIS A1311 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR A1316 " --> pdb=" O LEU A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1344 removed outlier: 3.543A pdb=" N LEU A1343 " --> pdb=" O LYS A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing helix chain 'G' and resid 59 through 94 removed outlier: 4.934A pdb=" N ASN G 88 " --> pdb=" O GLU G 84 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N GLU G 89 " --> pdb=" O ILE G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 103 Processing helix chain 'G' and resid 104 through 106 No H-bonds generated for 'chain 'G' and resid 104 through 106' Processing helix chain 'G' and resid 121 through 132 Processing helix chain 'G' and resid 134 through 145 removed outlier: 3.731A pdb=" N LEU G 138 " --> pdb=" O THR G 134 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER G 145 " --> pdb=" O LYS G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 163 Processing helix chain 'G' and resid 180 through 196 Processing helix chain 'G' and resid 202 through 206 removed outlier: 3.934A pdb=" N GLY G 205 " --> pdb=" O ASN G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 227 Processing helix chain 'G' and resid 236 through 246 Processing helix chain 'G' and resid 252 through 257 Processing helix chain 'G' and resid 270 through 283 Processing helix chain 'G' and resid 286 through 306 Processing helix chain 'G' and resid 315 through 343 Processing helix chain 'G' and resid 346 through 352 Processing helix chain 'G' and resid 358 through 364 Processing helix chain 'G' and resid 368 through 381 Proline residue: G 378 - end of helix Processing helix chain 'G' and resid 386 through 395 Processing helix chain 'G' and resid 404 through 410 removed outlier: 3.958A pdb=" N GLY G 408 " --> pdb=" O PHE G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 411 through 427 removed outlier: 4.081A pdb=" N HIS G 415 " --> pdb=" O PRO G 411 " (cutoff:3.500A) Processing helix chain 'G' and resid 430 through 436 removed outlier: 3.524A pdb=" N LYS G 434 " --> pdb=" O TYR G 430 " (cutoff:3.500A) Processing helix chain 'G' and resid 436 through 446 Processing helix chain 'G' and resid 477 through 482 Processing helix chain 'G' and resid 483 through 496 Processing helix chain 'G' and resid 512 through 525 Processing helix chain 'G' and resid 544 through 552 Processing helix chain 'G' and resid 560 through 568 Processing helix chain 'G' and resid 591 through 602 Processing helix chain 'G' and resid 603 through 607 removed outlier: 3.568A pdb=" N PHE G 606 " --> pdb=" O ASP G 603 " (cutoff:3.500A) Processing helix chain 'G' and resid 609 through 611 No H-bonds generated for 'chain 'G' and resid 609 through 611' Processing helix chain 'G' and resid 612 through 626 removed outlier: 3.645A pdb=" N LEU G 616 " --> pdb=" O ASN G 612 " (cutoff:3.500A) Processing helix chain 'G' and resid 628 through 637 Processing helix chain 'G' and resid 638 through 640 No H-bonds generated for 'chain 'G' and resid 638 through 640' Processing helix chain 'G' and resid 644 through 654 Processing helix chain 'G' and resid 663 through 668 Processing helix chain 'G' and resid 678 through 685 Processing helix chain 'G' and resid 692 through 699 Processing helix chain 'G' and resid 703 through 712 Processing helix chain 'G' and resid 719 through 725 Processing helix chain 'G' and resid 730 through 750 Processing helix chain 'G' and resid 751 through 754 Processing helix chain 'G' and resid 909 through 922 Processing helix chain 'G' and resid 925 through 940 removed outlier: 3.802A pdb=" N LYS G 929 " --> pdb=" O ARG G 925 " (cutoff:3.500A) Processing helix chain 'G' and resid 959 through 970 removed outlier: 3.649A pdb=" N VAL G 963 " --> pdb=" O LYS G 959 " (cutoff:3.500A) Processing helix chain 'G' and resid 980 through 1001 removed outlier: 4.433A pdb=" N ALA G 984 " --> pdb=" O ASN G 980 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS G 999 " --> pdb=" O THR G 995 " (cutoff:3.500A) Processing helix chain 'G' and resid 1002 through 1007 removed outlier: 3.570A pdb=" N GLU G1005 " --> pdb=" O PRO G1002 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER G1006 " --> pdb=" O LYS G1003 " (cutoff:3.500A) Processing helix chain 'G' and resid 1041 through 1047 removed outlier: 4.107A pdb=" N PHE G1045 " --> pdb=" O ILE G1042 " (cutoff:3.500A) Processing helix chain 'G' and resid 1078 through 1089 Processing helix chain 'G' and resid 1127 through 1132 Processing helix chain 'G' and resid 1168 through 1177 removed outlier: 4.572A pdb=" N SER G1172 " --> pdb=" O ILE G1168 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N SER G1173 " --> pdb=" O MET G1169 " (cutoff:3.500A) Processing helix chain 'G' and resid 1177 through 1185 Processing helix chain 'G' and resid 1191 through 1195 Processing helix chain 'G' and resid 1229 through 1241 Processing helix chain 'G' and resid 1253 through 1261 removed outlier: 3.563A pdb=" N VAL G1259 " --> pdb=" O LYS G1255 " (cutoff:3.500A) Processing helix chain 'G' and resid 1263 through 1280 removed outlier: 4.049A pdb=" N ASP G1267 " --> pdb=" O LYS G1263 " (cutoff:3.500A) Processing helix chain 'G' and resid 1283 through 1298 Processing helix chain 'G' and resid 1301 through 1313 removed outlier: 3.583A pdb=" N HIS G1311 " --> pdb=" O GLU G1307 " (cutoff:3.500A) Processing helix chain 'G' and resid 1314 through 1316 No H-bonds generated for 'chain 'G' and resid 1314 through 1316' Processing helix chain 'G' and resid 1341 through 1344 Processing helix chain 'G' and resid 1363 through 1365 No H-bonds generated for 'chain 'G' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 959 removed outlier: 6.183A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU A 958 " --> pdb=" O ILE A 759 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE A 761 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASN A 758 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ILE A 11 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 10.167A pdb=" N GLU A1357 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LYS A 33 " --> pdb=" O GLU A1357 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N ARG A1359 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLN A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA4, first strand: chain 'A' and resid 836 through 840 Processing sheet with id=AA5, first strand: chain 'A' and resid 1049 through 1051 Processing sheet with id=AA6, first strand: chain 'A' and resid 1063 through 1065 removed outlier: 6.605A pdb=" N GLU A1064 " --> pdb=" O VAL A1073 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AA8, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.521A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1324 through 1326 Processing sheet with id=AB1, first strand: chain 'G' and resid 954 through 957 removed outlier: 6.281A pdb=" N ILE G 759 " --> pdb=" O ILE G 956 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASN G 758 " --> pdb=" O TYR G 5 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 42 through 44 removed outlier: 9.469A pdb=" N GLU G1357 " --> pdb=" O LYS G 31 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LYS G 33 " --> pdb=" O GLU G1357 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ARG G1359 " --> pdb=" O LYS G 33 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N LEU G 35 " --> pdb=" O ARG G1359 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ASP G1361 " --> pdb=" O LEU G 35 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU G1203 " --> pdb=" O ILE G1348 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLN G1219 " --> pdb=" O ALA G1215 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 942 through 943 removed outlier: 3.921A pdb=" N LYS G 942 " --> pdb=" O ILE G 950 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 1049 through 1051 Processing sheet with id=AB5, first strand: chain 'G' and resid 1063 through 1065 Processing sheet with id=AB6, first strand: chain 'G' and resid 1120 through 1121 Processing sheet with id=AB7, first strand: chain 'G' and resid 1156 through 1167 Processing sheet with id=AB8, first strand: chain 'G' and resid 1324 through 1326 943 hydrogen bonds defined for protein. 2700 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 198 hydrogen bonds 384 hydrogen bond angles 0 basepair planarities 80 basepair parallelities 136 stacking parallelities Total time for adding SS restraints: 13.47 Time building geometry restraints manager: 11.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.43: 11751 1.43 - 1.75: 14133 1.75 - 2.06: 67 2.06 - 2.38: 0 2.38 - 2.69: 1 Bond restraints: 25952 Sorted by residual: bond pdb=" O3' G B 4 " pdb=" P C B 5 " ideal model delta sigma weight residual 1.607 2.694 -1.087 1.50e-02 4.44e+03 5.25e+03 bond pdb=" C3' G B 4 " pdb=" O3' G B 4 " ideal model delta sigma weight residual 1.417 1.634 -0.217 1.50e-02 4.44e+03 2.10e+02 bond pdb=" C1' G B 4 " pdb=" N9 G B 4 " ideal model delta sigma weight residual 1.475 1.617 -0.142 1.50e-02 4.44e+03 8.91e+01 bond pdb=" CE1 PHE G 643 " pdb=" CZ PHE G 643 " ideal model delta sigma weight residual 1.382 1.118 0.264 3.00e-02 1.11e+03 7.76e+01 bond pdb=" C3' G B 4 " pdb=" C2' G B 4 " ideal model delta sigma weight residual 1.523 1.650 -0.127 1.50e-02 4.44e+03 7.20e+01 ... (remaining 25947 not shown) Histogram of bond angle deviations from ideal: 66.36 - 85.98: 15 85.98 - 105.59: 1656 105.59 - 125.21: 33183 125.21 - 144.83: 1267 144.83 - 164.45: 5 Bond angle restraints: 36126 Sorted by residual: angle pdb=" C3' G B 4 " pdb=" O3' G B 4 " pdb=" P C B 5 " ideal model delta sigma weight residual 120.20 69.33 50.87 1.50e+00 4.44e-01 1.15e+03 angle pdb=" O3' G B 4 " pdb=" P C B 5 " pdb=" O5' C B 5 " ideal model delta sigma weight residual 104.00 152.66 -48.66 1.50e+00 4.44e-01 1.05e+03 angle pdb=" C3' G B 4 " pdb=" C2' G B 4 " pdb=" C1' G B 4 " ideal model delta sigma weight residual 101.30 119.66 -18.36 1.00e+00 1.00e+00 3.37e+02 angle pdb=" CB LEU G 616 " pdb=" CG LEU G 616 " pdb=" CD1 LEU G 616 " ideal model delta sigma weight residual 110.70 164.45 -53.75 3.00e+00 1.11e-01 3.21e+02 angle pdb=" CD1 LEU G 246 " pdb=" CG LEU G 246 " pdb=" CD2 LEU G 246 " ideal model delta sigma weight residual 110.80 71.56 39.24 2.20e+00 2.07e-01 3.18e+02 ... (remaining 36121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.67: 14821 33.67 - 67.34: 854 67.34 - 101.01: 85 101.01 - 134.68: 1 134.68 - 168.35: 5 Dihedral angle restraints: 15766 sinusoidal: 8508 harmonic: 7258 Sorted by residual: dihedral pdb=" CD ARG G 424 " pdb=" NE ARG G 424 " pdb=" CZ ARG G 424 " pdb=" NH1 ARG G 424 " ideal model delta sinusoidal sigma weight residual 0.00 89.57 -89.57 1 1.00e+01 1.00e-02 9.53e+01 dihedral pdb=" O4' U B 59 " pdb=" C1' U B 59 " pdb=" N1 U B 59 " pdb=" C2 U B 59 " ideal model delta sinusoidal sigma weight residual 200.00 32.41 167.59 1 1.50e+01 4.44e-03 8.43e+01 dihedral pdb=" CA ASP G 144 " pdb=" C ASP G 144 " pdb=" N SER G 145 " pdb=" CA SER G 145 " ideal model delta harmonic sigma weight residual -180.00 -137.31 -42.69 0 5.00e+00 4.00e-02 7.29e+01 ... (remaining 15763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.601: 4169 0.601 - 1.202: 10 1.202 - 1.802: 4 1.802 - 2.403: 1 2.403 - 3.004: 3 Chirality restraints: 4187 Sorted by residual: chirality pdb=" CG LEU G 419 " pdb=" CB LEU G 419 " pdb=" CD1 LEU G 419 " pdb=" CD2 LEU G 419 " both_signs ideal model delta sigma weight residual False -2.59 0.41 -3.00 2.00e-01 2.50e+01 2.26e+02 chirality pdb=" CB THR G1069 " pdb=" CA THR G1069 " pdb=" OG1 THR G1069 " pdb=" CG2 THR G1069 " both_signs ideal model delta sigma weight residual False 2.55 -0.37 2.92 2.00e-01 2.50e+01 2.14e+02 chirality pdb=" CB THR G1358 " pdb=" CA THR G1358 " pdb=" OG1 THR G1358 " pdb=" CG2 THR G1358 " both_signs ideal model delta sigma weight residual False 2.55 -0.09 2.64 2.00e-01 2.50e+01 1.74e+02 ... (remaining 4184 not shown) Planarity restraints: 3739 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE G 643 " 0.013 2.00e-02 2.50e+03 1.52e-01 4.02e+02 pdb=" CG PHE G 643 " -0.150 2.00e-02 2.50e+03 pdb=" CD1 PHE G 643 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 PHE G 643 " 0.123 2.00e-02 2.50e+03 pdb=" CE1 PHE G 643 " 0.262 2.00e-02 2.50e+03 pdb=" CE2 PHE G 643 " 0.022 2.00e-02 2.50e+03 pdb=" CZ PHE G 643 " -0.229 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 4 " -0.128 2.00e-02 2.50e+03 1.13e-01 3.81e+02 pdb=" N9 G B 4 " -0.078 2.00e-02 2.50e+03 pdb=" C8 G B 4 " 0.335 2.00e-02 2.50e+03 pdb=" N7 G B 4 " -0.057 2.00e-02 2.50e+03 pdb=" C5 G B 4 " -0.009 2.00e-02 2.50e+03 pdb=" C6 G B 4 " -0.017 2.00e-02 2.50e+03 pdb=" O6 G B 4 " -0.089 2.00e-02 2.50e+03 pdb=" N1 G B 4 " -0.013 2.00e-02 2.50e+03 pdb=" C2 G B 4 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G B 4 " 0.074 2.00e-02 2.50e+03 pdb=" N3 G B 4 " 0.002 2.00e-02 2.50e+03 pdb=" C4 G B 4 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU G 746 " 0.081 2.00e-02 2.50e+03 1.48e-01 2.18e+02 pdb=" CD GLU G 746 " -0.255 2.00e-02 2.50e+03 pdb=" OE1 GLU G 746 " 0.075 2.00e-02 2.50e+03 pdb=" OE2 GLU G 746 " 0.099 2.00e-02 2.50e+03 ... (remaining 3736 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 281 2.60 - 3.18: 20823 3.18 - 3.75: 43569 3.75 - 4.33: 59935 4.33 - 4.90: 90628 Nonbonded interactions: 215236 Sorted by model distance: nonbonded pdb=" O6 DG c 35 " pdb="MG MG c 101 " model vdw 2.028 2.170 nonbonded pdb=" OD1 ASN A 863 " pdb="MG MG A1403 " model vdw 2.035 2.170 nonbonded pdb=" OP2 DT c 23 " pdb="MG MG A1403 " model vdw 2.048 2.170 nonbonded pdb=" OD1 ASP A 10 " pdb="MG MG A1401 " model vdw 2.061 2.170 nonbonded pdb=" OD1 ASP A 839 " pdb="MG MG A1403 " model vdw 2.071 2.170 ... (remaining 215231 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 3 through 4 and (name N or name CA or name C or name O or \ name CB )) or resid 5 through 30 or (resid 31 and (name N or name CA or name C \ or name O or name CB )) or resid 32 through 139 or (resid 140 and (name N or nam \ e CA or name C or name O or name CB )) or resid 141 through 147 or (resid 148 th \ rough 149 and (name N or name CA or name C or name O or name CB )) or resid 150 \ through 176 or (resid 177 and (name N or name CA or name C or name O or name CB \ )) or resid 178 through 179 or (resid 180 and (name N or name CA or name C or na \ me O or name CB )) or resid 181 or (resid 182 through 183 and (name N or name CA \ or name C or name O or name CB )) or resid 184 through 215 or (resid 216 and (n \ ame N or name CA or name C or name O or name CB )) or resid 217 through 220 or ( \ resid 221 and (name N or name CA or name C or name O or name CB )) or resid 222 \ through 228 or (resid 234 and (name N or name CA or name C or name O or name CB \ )) or resid 235 through 252 or (resid 253 and (name N or name CA or name C or na \ me O or name CB )) or resid 254 through 259 or (resid 260 and (name N or name CA \ or name C or name O or name CB )) or resid 261 through 267 or (resid 268 and (n \ ame N or name CA or name C or name O or name CB )) or resid 269 through 310 or ( \ resid 311 through 312 and (name N or name CA or name C or name O or name CB )) o \ r resid 313 or (resid 314 through 315 and (name N or name CA or name C or name O \ or name CB )) or resid 316 through 322 or (resid 323 and (name N or name CA or \ name C or name O or name CB )) or resid 324 through 339 or (resid 340 and (name \ N or name CA or name C or name O or name CB )) or resid 341 through 345 or (resi \ d 346 and (name N or name CA or name C or name O or name CB )) or resid 347 or ( \ resid 348 through 349 and (name N or name CA or name C or name O or name CB )) o \ r resid 350 through 353 or (resid 354 and (name N or name CA or name C or name O \ or name CB )) or resid 355 through 363 or (resid 364 and (name N or name CA or \ name C or name O or name CB )) or resid 365 through 373 or (resid 374 and (name \ N or name CA or name C or name O or name CB )) or resid 375 through 376 or (resi \ d 377 and (name N or name CA or name C or name O or name CB )) or resid 378 thro \ ugh 380 or (resid 381 through 382 and (name N or name CA or name C or name O or \ name CB )) or resid 383 or (resid 384 and (name N or name CA or name C or name O \ or name CB )) or resid 385 through 386 or (resid 387 through 388 and (name N or \ name CA or name C or name O or name CB )) or resid 389 through 391 or (resid 39 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 393 through \ 394 or (resid 395 and (name N or name CA or name C or name O or name CB )) or re \ sid 396 through 424 or (resid 425 and (name N or name CA or name C or name O or \ name CB )) or resid 426 through 433 or (resid 434 and (name N or name CA or name \ C or name O or name CB )) or resid 435 through 436 or (resid 437 and (name N or \ name CA or name C or name O or name CB )) or resid 438 or (resid 439 and (name \ N or name CA or name C or name O or name CB )) or resid 440 through 467 or (resi \ d 468 and (name N or name CA or name C or name O or name CB )) or resid 469 thro \ ugh 499 or (resid 500 and (name N or name CA or name C or name O or name CB )) o \ r resid 501 through 525 or (resid 543 and (name N or name CA or name C or name O \ or name CB )) or resid 544 through 545 or (resid 546 through 547 and (name N or \ name CA or name C or name O or name CB )) or resid 548 through 557 or (resid 55 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 559 through \ 571 or resid 586 through 609 or (resid 610 and (name N or name CA or name C or n \ ame O or name CB )) or resid 611 through 636 or (resid 637 and (name N or name C \ A or name C or name O or name CB )) or resid 638 through 645 or (resid 646 and ( \ name N or name CA or name C or name O or name CB )) or resid 647 through 648 or \ (resid 649 and (name N or name CA or name C or name O or name CB )) or resid 650 \ through 651 or (resid 652 through 653 and (name N or name CA or name C or name \ O or name CB )) or resid 654 or (resid 655 and (name N or name CA or name C or n \ ame O or name CB )) or resid 656 through 660 or (resid 661 and (name N or name C \ A or name C or name O or name CB )) or resid 662 through 664 or (resid 665 and ( \ name N or name CA or name C or name O or name CB )) or resid 666 through 672 or \ (resid 673 and (name N or name CA or name C or name O or name CB )) or resid 674 \ through 687 or (resid 688 through 689 and (name N or name CA or name C or name \ O or name CB )) or resid 690 through 697 or (resid 698 and (name N or name CA or \ name C or name O or name CB )) or resid 699 through 721 or (resid 722 and (name \ N or name CA or name C or name O or name CB )) or resid 723 through 764 or (res \ id 765 through 766 and (name N or name CA or name C or name O or name CB )) or r \ esid 907 through 910 or (resid 911 and (name N or name CA or name C or name O or \ name CB )) or resid 912 through 928 or (resid 929 and (name N or name CA or nam \ e C or name O or name CB )) or resid 930 through 960 or (resid 961 and (name N o \ r name CA or name C or name O or name CB )) or resid 962 through 1004 or (resid \ 1005 and (name N or name CA or name C or name O or name CB )) or resid 1006 thro \ ugh 1010 or resid 1039 through 1057 or (resid 1058 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1059 through 1067 or (resid 1068 and (name \ N or name CA or name C or name O or name CB )) or resid 1069 through 1070 or (re \ sid 1071 and (name N or name CA or name C or name O or name CB )) or resid 1072 \ through 1077 or (resid 1078 and (name N or name CA or name C or name O or name C \ B )) or resid 1079 through 1112 or (resid 1113 and (name N or name CA or name C \ or name O or name CB )) or resid 1114 through 1116 or (resid 1117 through 1118 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1119 through 11 \ 29 or (resid 1130 and (name N or name CA or name C or name O or name CB )) or re \ sid 1131 through 1150 or (resid 1151 and (name N or name CA or name C or name O \ or name CB )) or resid 1152 or (resid 1153 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1154 through 1157 or (resid 1158 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1159 through 1179 or (resid 1180 \ and (name N or name CA or name C or name O or name CB )) or resid 1181 through \ 1243 or resid 1252 through 1255 or (resid 1256 and (name N or name CA or name C \ or name O or name CB )) or resid 1257 through 1299 or (resid 1300 and (name N or \ name CA or name C or name O or name CB )) or resid 1301 through 1302 or (resid \ 1303 through 1304 and (name N or name CA or name C or name O or name CB )) or re \ sid 1305 through 1324 or (resid 1325 and (name N or name CA or name C or name O \ or name CB )) or resid 1326 through 1339 or (resid 1340 and (name N or name CA o \ r name C or name O or name CB )) or resid 1341 through 1366)) selection = (chain 'G' and (resid 3 through 195 or resid 208 through 228 or resid 234 throug \ h 278 or resid 292 through 712 or resid 718 through 1366)) } ncs_group { reference = (chain 'B' and resid 11 through 98) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 4.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.020 Extract box with map and model: 0.960 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 77.110 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 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 : 0.013 1.087 25952 Z= 0.870 Angle : 2.021 53.749 36126 Z= 1.027 Chirality : 0.140 3.004 4187 Planarity : 0.020 0.443 3739 Dihedral : 19.057 168.348 11062 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.11 % Favored : 96.85 % Rotamer: Outliers : 0.89 % Allowed : 10.89 % Favored : 88.22 % Cbeta Deviations : 0.98 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.84 (0.15), residues: 2445 helix: -1.56 (0.13), residues: 1200 sheet: -0.24 (0.36), residues: 194 loop : -0.77 (0.18), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.007 TRP G 18 HIS 0.154 0.012 HIS G 641 PHE 0.262 0.010 PHE G 643 TYR 0.096 0.008 TYR G 192 ARG 0.115 0.006 ARG G 586 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 171 time to evaluate : 2.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 694 MET cc_start: 0.8328 (mmm) cc_final: 0.5527 (ptt) REVERT: A 832 ARG cc_start: 0.7151 (mtt180) cc_final: 0.6768 (mtt90) REVERT: A 856 VAL cc_start: 0.7936 (t) cc_final: 0.7675 (m) REVERT: A 1090 PRO cc_start: 0.7274 (Cg_endo) cc_final: 0.6906 (Cg_exo) REVERT: A 1303 ARG cc_start: 0.8182 (ttm170) cc_final: 0.7891 (ttm170) outliers start: 19 outliers final: 6 residues processed: 185 average time/residue: 0.3716 time to fit residues: 108.8485 Evaluate side-chains 149 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 143 time to evaluate : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 709 GLN Chi-restraints excluded: chain A residue 723 HIS Chi-restraints excluded: chain A residue 1117 ASP Chi-restraints excluded: chain G residue 419 LEU Chi-restraints excluded: chain G residue 623 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 225 optimal weight: 0.0070 chunk 202 optimal weight: 7.9990 chunk 112 optimal weight: 0.7980 chunk 69 optimal weight: 8.9990 chunk 136 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 209 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 242 optimal weight: 1.9990 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 ASN ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 GLN A 831 ASN A 844 GLN A1252 ASN G 412 HIS ** G 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 609 ASN G 612 ASN ** G 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 25952 Z= 0.253 Angle : 0.656 11.848 36126 Z= 0.346 Chirality : 0.042 0.259 4187 Planarity : 0.005 0.060 3739 Dihedral : 19.583 171.996 6082 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.54 % Allowed : 10.66 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.60 (0.16), residues: 2445 helix: -0.14 (0.14), residues: 1199 sheet: -0.82 (0.33), residues: 217 loop : -0.40 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G1136 HIS 0.011 0.001 HIS G 511 PHE 0.020 0.002 PHE G 643 TYR 0.023 0.002 TYR A1242 ARG 0.010 0.001 ARG A1303 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 165 time to evaluate : 2.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8117 (mp) REVERT: A 508 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.9029 (mt) REVERT: A 648 MET cc_start: 0.7470 (tpp) cc_final: 0.7096 (tpp) REVERT: A 694 MET cc_start: 0.8312 (mmm) cc_final: 0.5669 (ptt) REVERT: A 1303 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7636 (ttt90) REVERT: G 16 VAL cc_start: 0.1639 (t) cc_final: 0.1184 (p) REVERT: G 343 LEU cc_start: 0.2826 (OUTLIER) cc_final: 0.1763 (tt) outliers start: 33 outliers final: 13 residues processed: 189 average time/residue: 0.4547 time to fit residues: 131.3931 Evaluate side-chains 144 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 2.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1303 ARG Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain G residue 419 LEU Chi-restraints excluded: chain G residue 1072 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 134 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 201 optimal weight: 1.9990 chunk 165 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 242 optimal weight: 3.9990 chunk 262 optimal weight: 6.9990 chunk 216 optimal weight: 4.9990 chunk 240 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 194 optimal weight: 30.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 436 ASN A 588 ASN A 595 HIS A 776 ASN A 971 GLN A 982 HIS A1252 ASN ** A1264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 920 GLN ** G 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1262 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 25952 Z= 0.537 Angle : 0.773 13.505 36126 Z= 0.404 Chirality : 0.048 0.216 4187 Planarity : 0.005 0.055 3739 Dihedral : 19.697 166.168 6071 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.90 % Allowed : 10.52 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.16), residues: 2445 helix: -0.03 (0.14), residues: 1199 sheet: -1.06 (0.35), residues: 182 loop : -0.44 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A1136 HIS 0.013 0.002 HIS A 329 PHE 0.024 0.003 PHE A1038 TYR 0.026 0.002 TYR A 430 ARG 0.009 0.001 ARG G 139 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 160 time to evaluate : 2.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7682 (pm20) REVERT: A 122 ILE cc_start: 0.9252 (OUTLIER) cc_final: 0.8949 (tp) REVERT: A 341 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8167 (tm-30) REVERT: A 608 ASP cc_start: 0.8176 (m-30) cc_final: 0.7745 (t0) REVERT: A 648 MET cc_start: 0.7787 (tpp) cc_final: 0.7581 (tpp) REVERT: A 694 MET cc_start: 0.8281 (mmm) cc_final: 0.6183 (ptt) REVERT: A 1136 TRP cc_start: 0.8763 (OUTLIER) cc_final: 0.8247 (m100) REVERT: A 1261 GLN cc_start: 0.8928 (tt0) cc_final: 0.8646 (tt0) REVERT: G 192 TYR cc_start: 0.0189 (t80) cc_final: -0.0048 (t80) REVERT: G 654 ARG cc_start: 0.0015 (tpt170) cc_final: -0.0546 (tpp-160) REVERT: G 966 PHE cc_start: -0.4463 (t80) cc_final: -0.4718 (t80) REVERT: G 970 PHE cc_start: -0.1479 (m-10) cc_final: -0.1865 (m-10) outliers start: 62 outliers final: 32 residues processed: 207 average time/residue: 0.4392 time to fit residues: 138.6793 Evaluate side-chains 153 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 117 time to evaluate : 2.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1136 TRP Chi-restraints excluded: chain A residue 1265 TYR Chi-restraints excluded: chain A residue 1332 ASP Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 419 LEU Chi-restraints excluded: chain G residue 428 ASP Chi-restraints excluded: chain G residue 724 ILE Chi-restraints excluded: chain G residue 928 THR Chi-restraints excluded: chain G residue 972 PHE Chi-restraints excluded: chain G residue 1069 THR Chi-restraints excluded: chain G residue 1072 ILE Chi-restraints excluded: chain G residue 1073 VAL Chi-restraints excluded: chain G residue 1213 MET Chi-restraints excluded: chain G residue 1358 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 239 optimal weight: 0.9980 chunk 182 optimal weight: 0.6980 chunk 126 optimal weight: 0.9990 chunk 26 optimal weight: 20.0000 chunk 115 optimal weight: 0.9990 chunk 163 optimal weight: 0.9990 chunk 243 optimal weight: 0.8980 chunk 258 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 231 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 971 GLN G 77 ASN ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25952 Z= 0.182 Angle : 0.566 15.094 36126 Z= 0.295 Chirality : 0.038 0.221 4187 Planarity : 0.003 0.043 3739 Dihedral : 19.638 168.784 6071 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.29 % Allowed : 11.55 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.17), residues: 2445 helix: 0.51 (0.15), residues: 1194 sheet: -1.09 (0.33), residues: 209 loop : -0.15 (0.19), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G1136 HIS 0.005 0.001 HIS A 116 PHE 0.037 0.001 PHE G1008 TYR 0.030 0.001 TYR G1294 ARG 0.005 0.000 ARG A 884 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 141 time to evaluate : 2.475 Fit side-chains revert: symmetry clash REVERT: A 114 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7642 (pm20) REVERT: A 122 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8920 (tp) REVERT: A 341 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8161 (tm-30) REVERT: A 457 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7591 (mtm110) REVERT: A 668 ASN cc_start: 0.7998 (p0) cc_final: 0.7797 (t0) REVERT: A 694 MET cc_start: 0.8300 (mmm) cc_final: 0.6107 (ptt) REVERT: A 1043 MET cc_start: 0.8578 (mmp) cc_final: 0.8195 (mmp) REVERT: A 1261 GLN cc_start: 0.8893 (tt0) cc_final: 0.8561 (tt0) REVERT: G 343 LEU cc_start: 0.2463 (OUTLIER) cc_final: 0.2259 (tt) REVERT: G 1047 LYS cc_start: 0.4288 (mmtm) cc_final: 0.0640 (mmtt) outliers start: 49 outliers final: 20 residues processed: 178 average time/residue: 0.4610 time to fit residues: 125.6848 Evaluate side-chains 143 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 118 time to evaluate : 2.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 709 GLN Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 890 LYS Chi-restraints excluded: chain A residue 918 LYS Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1039 TYR Chi-restraints excluded: chain A residue 1328 ASP Chi-restraints excluded: chain A residue 1332 ASP Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain G residue 419 LEU Chi-restraints excluded: chain G residue 928 THR Chi-restraints excluded: chain G residue 972 PHE Chi-restraints excluded: chain G residue 1213 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 214 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 192 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 220 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 chunk 231 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 983 HIS ** A1264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 25952 Z= 0.321 Angle : 0.584 12.239 36126 Z= 0.306 Chirality : 0.040 0.229 4187 Planarity : 0.004 0.046 3739 Dihedral : 19.507 170.637 6071 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.34 % Allowed : 12.53 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.17), residues: 2445 helix: 0.66 (0.15), residues: 1203 sheet: -1.11 (0.34), residues: 209 loop : -0.08 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G1136 HIS 0.006 0.001 HIS G 160 PHE 0.021 0.002 PHE G1008 TYR 0.038 0.002 TYR G1294 ARG 0.007 0.001 ARG A 884 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 132 time to evaluate : 2.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7569 (pm20) REVERT: A 341 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8217 (tm-30) REVERT: A 694 MET cc_start: 0.8376 (mmm) cc_final: 0.6194 (ptt) REVERT: A 1188 LYS cc_start: 0.8877 (mmtp) cc_final: 0.8544 (mppt) REVERT: A 1261 GLN cc_start: 0.8938 (tt0) cc_final: 0.8605 (tt0) outliers start: 50 outliers final: 30 residues processed: 173 average time/residue: 0.4365 time to fit residues: 114.6527 Evaluate side-chains 153 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 121 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 890 LYS Chi-restraints excluded: chain A residue 918 LYS Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1039 TYR Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1328 ASP Chi-restraints excluded: chain A residue 1332 ASP Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 419 LEU Chi-restraints excluded: chain G residue 428 ASP Chi-restraints excluded: chain G residue 450 TYR Chi-restraints excluded: chain G residue 928 THR Chi-restraints excluded: chain G residue 972 PHE Chi-restraints excluded: chain G residue 1213 MET Chi-restraints excluded: chain G residue 1225 GLU Chi-restraints excluded: chain G residue 1287 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 86 optimal weight: 8.9990 chunk 232 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 151 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 258 optimal weight: 4.9990 chunk 214 optimal weight: 1.9990 chunk 119 optimal weight: 0.0670 chunk 21 optimal weight: 30.0000 chunk 85 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 overall best weight: 2.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** A1264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 25952 Z= 0.331 Angle : 0.592 10.730 36126 Z= 0.310 Chirality : 0.041 0.233 4187 Planarity : 0.004 0.049 3739 Dihedral : 19.505 173.993 6071 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.66 % Allowed : 12.53 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.17), residues: 2445 helix: 0.61 (0.15), residues: 1212 sheet: -1.21 (0.33), residues: 213 loop : -0.11 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G1136 HIS 0.005 0.001 HIS A 329 PHE 0.016 0.002 PHE G 446 TYR 0.037 0.002 TYR G1294 ARG 0.007 0.001 ARG A 884 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 145 time to evaluate : 2.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7522 (pm20) REVERT: A 122 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8935 (tp) REVERT: A 341 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8189 (tm-30) REVERT: A 694 MET cc_start: 0.8444 (mmm) cc_final: 0.6205 (ptt) REVERT: A 763 MET cc_start: 0.8540 (mmm) cc_final: 0.7997 (mmm) REVERT: A 834 SER cc_start: 0.8656 (m) cc_final: 0.8176 (p) REVERT: A 1261 GLN cc_start: 0.8949 (tt0) cc_final: 0.8638 (tt0) outliers start: 57 outliers final: 37 residues processed: 191 average time/residue: 0.4297 time to fit residues: 123.4999 Evaluate side-chains 161 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 121 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 890 LYS Chi-restraints excluded: chain A residue 918 LYS Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1265 TYR Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1328 ASP Chi-restraints excluded: chain A residue 1332 ASP Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 412 HIS Chi-restraints excluded: chain G residue 419 LEU Chi-restraints excluded: chain G residue 428 ASP Chi-restraints excluded: chain G residue 476 TRP Chi-restraints excluded: chain G residue 928 THR Chi-restraints excluded: chain G residue 1073 VAL Chi-restraints excluded: chain G residue 1213 MET Chi-restraints excluded: chain G residue 1225 GLU Chi-restraints excluded: chain G residue 1287 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 249 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 188 optimal weight: 7.9990 chunk 146 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 257 optimal weight: 4.9990 chunk 161 optimal weight: 0.4980 chunk 156 optimal weight: 0.0970 chunk 118 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS A1264 HIS ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 971 GLN ** G 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.5082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 25952 Z= 0.189 Angle : 0.536 10.095 36126 Z= 0.280 Chirality : 0.038 0.238 4187 Planarity : 0.003 0.047 3739 Dihedral : 19.416 174.612 6071 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.10 % Allowed : 13.18 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.17), residues: 2445 helix: 0.87 (0.15), residues: 1199 sheet: -1.02 (0.34), residues: 203 loop : 0.01 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G1136 HIS 0.006 0.001 HIS G 160 PHE 0.022 0.001 PHE G1008 TYR 0.026 0.001 TYR G1294 ARG 0.008 0.000 ARG G 220 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 143 time to evaluate : 2.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 THR cc_start: 0.9075 (m) cc_final: 0.8869 (p) REVERT: A 114 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7557 (pm20) REVERT: A 122 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8938 (tp) REVERT: A 341 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8132 (tm-30) REVERT: A 465 MET cc_start: 0.8860 (ppp) cc_final: 0.8529 (ttp) REVERT: A 694 MET cc_start: 0.8513 (mmm) cc_final: 0.6186 (ptt) REVERT: A 763 MET cc_start: 0.8484 (mmm) cc_final: 0.7996 (mmm) REVERT: A 834 SER cc_start: 0.8545 (m) cc_final: 0.8086 (p) REVERT: A 1261 GLN cc_start: 0.8922 (tt0) cc_final: 0.8618 (tt0) outliers start: 45 outliers final: 27 residues processed: 181 average time/residue: 0.4324 time to fit residues: 118.5317 Evaluate side-chains 150 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 120 time to evaluate : 2.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 890 LYS Chi-restraints excluded: chain A residue 918 LYS Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1328 ASP Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 419 LEU Chi-restraints excluded: chain G residue 450 TYR Chi-restraints excluded: chain G residue 928 THR Chi-restraints excluded: chain G residue 1073 VAL Chi-restraints excluded: chain G residue 1213 MET Chi-restraints excluded: chain G residue 1225 GLU Chi-restraints excluded: chain G residue 1287 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 159 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 163 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 23 optimal weight: 30.0000 chunk 202 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.5388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 25952 Z= 0.484 Angle : 0.662 11.510 36126 Z= 0.344 Chirality : 0.044 0.241 4187 Planarity : 0.004 0.050 3739 Dihedral : 19.449 178.788 6071 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.20 % Allowed : 13.23 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.17), residues: 2445 helix: 0.67 (0.15), residues: 1204 sheet: -1.16 (0.34), residues: 197 loop : -0.11 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 659 HIS 0.009 0.002 HIS G 328 PHE 0.019 0.002 PHE G 966 TYR 0.030 0.002 TYR G1294 ARG 0.009 0.001 ARG G 139 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 124 time to evaluate : 2.504 Fit side-chains revert: symmetry clash REVERT: A 114 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7518 (pm20) REVERT: A 122 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8930 (tp) REVERT: A 341 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8157 (tm-30) REVERT: A 694 MET cc_start: 0.8458 (mmm) cc_final: 0.6234 (ptt) REVERT: A 763 MET cc_start: 0.8611 (mmm) cc_final: 0.8083 (mmm) REVERT: A 834 SER cc_start: 0.8701 (m) cc_final: 0.8234 (p) REVERT: A 1208 ASN cc_start: 0.8583 (OUTLIER) cc_final: 0.8170 (t0) REVERT: A 1261 GLN cc_start: 0.8974 (tt0) cc_final: 0.8697 (tt0) REVERT: A 1322 ARG cc_start: 0.7494 (ttt180) cc_final: 0.7288 (ttt90) outliers start: 47 outliers final: 32 residues processed: 165 average time/residue: 0.4277 time to fit residues: 108.1387 Evaluate side-chains 145 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 109 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 890 LYS Chi-restraints excluded: chain A residue 918 LYS Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1208 ASN Chi-restraints excluded: chain A residue 1265 TYR Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1328 ASP Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 428 ASP Chi-restraints excluded: chain G residue 476 TRP Chi-restraints excluded: chain G residue 718 ASP Chi-restraints excluded: chain G residue 928 THR Chi-restraints excluded: chain G residue 1073 VAL Chi-restraints excluded: chain G residue 1213 MET Chi-restraints excluded: chain G residue 1225 GLU Chi-restraints excluded: chain G residue 1287 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 234 optimal weight: 2.9990 chunk 246 optimal weight: 4.9990 chunk 224 optimal weight: 0.8980 chunk 239 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 188 optimal weight: 0.4980 chunk 73 optimal weight: 6.9990 chunk 216 optimal weight: 10.0000 chunk 226 optimal weight: 1.9990 chunk 238 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 ASN G 224 ASN ** G 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.5414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25952 Z= 0.188 Angle : 0.554 11.618 36126 Z= 0.288 Chirality : 0.038 0.241 4187 Planarity : 0.003 0.047 3739 Dihedral : 19.439 175.168 6069 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.54 % Allowed : 13.70 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.17), residues: 2445 helix: 0.91 (0.15), residues: 1204 sheet: -1.10 (0.33), residues: 220 loop : 0.04 (0.20), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 18 HIS 0.005 0.001 HIS A 595 PHE 0.023 0.001 PHE G1008 TYR 0.021 0.001 TYR G 155 ARG 0.008 0.000 ARG G 220 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 128 time to evaluate : 2.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7524 (pm20) REVERT: A 122 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8929 (tp) REVERT: A 341 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7921 (tm-30) REVERT: A 557 ARG cc_start: 0.8589 (ttm110) cc_final: 0.8302 (tpp-160) REVERT: A 694 MET cc_start: 0.8509 (mmm) cc_final: 0.6162 (ptt) REVERT: A 763 MET cc_start: 0.8455 (mmm) cc_final: 0.7969 (mmm) REVERT: A 834 SER cc_start: 0.8580 (m) cc_final: 0.8112 (p) REVERT: A 1004 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8390 (mp) REVERT: A 1208 ASN cc_start: 0.8518 (OUTLIER) cc_final: 0.8160 (t0) REVERT: A 1261 GLN cc_start: 0.8939 (tt0) cc_final: 0.8656 (tt0) outliers start: 33 outliers final: 22 residues processed: 154 average time/residue: 0.4040 time to fit residues: 95.5476 Evaluate side-chains 143 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 116 time to evaluate : 4.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 890 LYS Chi-restraints excluded: chain A residue 918 LYS Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1208 ASN Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1328 ASP Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 428 ASP Chi-restraints excluded: chain G residue 564 LEU Chi-restraints excluded: chain G residue 928 THR Chi-restraints excluded: chain G residue 1213 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 157 optimal weight: 3.9990 chunk 253 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 176 optimal weight: 4.9990 chunk 266 optimal weight: 4.9990 chunk 244 optimal weight: 0.9990 chunk 211 optimal weight: 0.7980 chunk 21 optimal weight: 30.0000 chunk 163 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** G 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.5595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 25952 Z= 0.426 Angle : 0.631 10.517 36126 Z= 0.328 Chirality : 0.043 0.252 4187 Planarity : 0.004 0.049 3739 Dihedral : 19.438 178.261 6069 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.54 % Allowed : 14.17 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.17), residues: 2445 helix: 0.83 (0.15), residues: 1201 sheet: -1.16 (0.34), residues: 197 loop : -0.08 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 476 HIS 0.007 0.001 HIS G 328 PHE 0.020 0.002 PHE G 966 TYR 0.021 0.002 TYR G1294 ARG 0.013 0.001 ARG G 220 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 116 time to evaluate : 2.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7483 (pm20) REVERT: A 122 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8933 (tp) REVERT: A 341 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.7928 (tm-30) REVERT: A 557 ARG cc_start: 0.8610 (ttm110) cc_final: 0.8312 (tpp-160) REVERT: A 694 MET cc_start: 0.8470 (mmm) cc_final: 0.6222 (ptt) REVERT: A 763 MET cc_start: 0.8583 (mmm) cc_final: 0.8094 (mmm) REVERT: A 834 SER cc_start: 0.8661 (m) cc_final: 0.8191 (p) REVERT: A 1004 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8529 (mp) REVERT: A 1208 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.8181 (t0) REVERT: A 1261 GLN cc_start: 0.8964 (tt0) cc_final: 0.8707 (tt0) outliers start: 33 outliers final: 26 residues processed: 144 average time/residue: 0.4254 time to fit residues: 94.6157 Evaluate side-chains 140 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 109 time to evaluate : 2.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 890 LYS Chi-restraints excluded: chain A residue 918 LYS Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1208 ASN Chi-restraints excluded: chain A residue 1265 TYR Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1328 ASP Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 428 ASP Chi-restraints excluded: chain G residue 476 TRP Chi-restraints excluded: chain G residue 564 LEU Chi-restraints excluded: chain G residue 928 THR Chi-restraints excluded: chain G residue 1213 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 168 optimal weight: 5.9990 chunk 225 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 195 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 212 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.087586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.062900 restraints weight = 71369.932| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.57 r_work: 0.3019 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.5647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 25952 Z= 0.219 Angle : 0.555 11.355 36126 Z= 0.288 Chirality : 0.039 0.249 4187 Planarity : 0.003 0.047 3739 Dihedral : 19.401 174.931 6069 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.59 % Allowed : 14.26 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.17), residues: 2445 helix: 0.97 (0.15), residues: 1206 sheet: -1.03 (0.33), residues: 214 loop : 0.05 (0.20), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 476 HIS 0.005 0.001 HIS G 160 PHE 0.023 0.001 PHE G 290 TYR 0.018 0.001 TYR G 271 ARG 0.010 0.000 ARG G 220 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4634.01 seconds wall clock time: 84 minutes 39.62 seconds (5079.62 seconds total)