Starting phenix.real_space_refine on Tue Feb 20 04:13:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2w_29683/02_2024/8g2w_29683.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2w_29683/02_2024/8g2w_29683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2w_29683/02_2024/8g2w_29683.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2w_29683/02_2024/8g2w_29683.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2w_29683/02_2024/8g2w_29683.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2w_29683/02_2024/8g2w_29683.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 94 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16495 2.51 5 N 4755 2.21 5 O 5378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ASP 120": "OD1" <-> "OD2" Residue "G TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 62": "OD1" <-> "OD2" Residue "H GLU 204": "OE1" <-> "OE2" Residue "H ASP 212": "OD1" <-> "OD2" Residue "I PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 187": "OE1" <-> "OE2" Residue "I GLU 231": "OE1" <-> "OE2" Residue "I GLU 249": "OE1" <-> "OE2" Residue "I GLU 264": "OE1" <-> "OE2" Residue "I ASP 342": "OD1" <-> "OD2" Residue "I PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 696": "OD1" <-> "OD2" Residue "I ASP 781": "OD1" <-> "OD2" Residue "I GLU 849": "OE1" <-> "OE2" Residue "I GLU 867": "OE1" <-> "OE2" Residue "I GLU 947": "OE1" <-> "OE2" Residue "I GLU 963": "OE1" <-> "OE2" Residue "I ASP 1004": "OD1" <-> "OD2" Residue "I GLU 1089": "OE1" <-> "OE2" Residue "I GLU 1167": "OE1" <-> "OE2" Residue "I GLU 1289": "OE1" <-> "OE2" Residue "I GLU 1316": "OE1" <-> "OE2" Residue "I GLU 1338": "OE1" <-> "OE2" Residue "I GLU 1340": "OE1" <-> "OE2" Residue "J ASP 54": "OD1" <-> "OD2" Residue "J GLU 86": "OE1" <-> "OE2" Residue "J GLU 136": "OE1" <-> "OE2" Residue "J GLU 148": "OE1" <-> "OE2" Residue "J GLU 204": "OE1" <-> "OE2" Residue "J GLU 207": "OE1" <-> "OE2" Residue "J GLU 211": "OE1" <-> "OE2" Residue "J GLU 301": "OE1" <-> "OE2" Residue "J GLU 562": "OE1" <-> "OE2" Residue "J GLU 666": "OE1" <-> "OE2" Residue "J GLU 677": "OE1" <-> "OE2" Residue "J GLU 714": "OE1" <-> "OE2" Residue "J GLU 846": "OE1" <-> "OE2" Residue "J GLU 1052": "OE1" <-> "OE2" Residue "J ASP 1073": "OD1" <-> "OD2" Residue "J PHE 1319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 8": "OD1" <-> "OD2" Residue "K GLU 79": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26829 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 388 Inner-chain residues flagged as termini: ['pdbres=" DG A 25 "'] Classifications: {'DNA': 19} Modifications used: {'5*END': 2} Link IDs: {'rna3p': 18} Chain: "B" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 631 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "G" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1708 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 1 Chain: "H" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1693 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 8, 'TRANS': 210} Chain breaks: 1 Chain: "I" Number of atoms: 10381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10381 Classifications: {'peptide': 1316} Link IDs: {'PTRANS': 55, 'TRANS': 1260} Chain breaks: 1 Chain: "J" Number of atoms: 10403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10403 Classifications: {'peptide': 1337} Link IDs: {'PTRANS': 55, 'TRANS': 1281} Chain breaks: 2 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 997 Classifications: {'RNA': 47} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 20, 'rna3p_pyr': 16} Link IDs: {'rna2p': 11, 'rna3p': 35} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.92, per 1000 atoms: 0.56 Number of scatterers: 26829 At special positions: 0 Unit cell: (135, 157, 161, 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 106 16.00 P 94 15.00 Mg 1 11.99 O 5378 8.00 N 4755 7.00 C 16495 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: 12.21 Conformation dependent library (CDL) restraints added in 4.6 seconds 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5856 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 41 sheets defined 39.4% alpha, 15.6% beta 32 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 9.87 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 Processing helix chain 'G' and resid 77 through 88 Processing helix chain 'G' and resid 212 through 232 removed outlier: 3.607A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.642A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 88 Processing helix chain 'H' and resid 212 through 228 Processing helix chain 'H' and resid 228 through 233 removed outlier: 3.545A pdb=" N VAL H 232 " --> pdb=" O LEU H 228 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP H 233 " --> pdb=" O GLU H 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 228 through 233' Processing helix chain 'I' and resid 4 through 10 Processing helix chain 'I' and resid 28 through 40 Processing helix chain 'I' and resid 48 through 56 Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 4.202A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 removed outlier: 4.028A pdb=" N LEU I 246 " --> pdb=" O VAL I 242 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG I 247 " --> pdb=" O PRO I 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 242 through 247' Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 295 removed outlier: 3.833A pdb=" N ILE I 292 " --> pdb=" O PRO I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 329 Processing helix chain 'I' and resid 345 through 354 removed outlier: 3.578A pdb=" N GLU I 349 " --> pdb=" O PRO I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 482 Processing helix chain 'I' and resid 494 through 508 removed outlier: 4.597A pdb=" N ILE I 498 " --> pdb=" O ASN I 494 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 529 Processing helix chain 'I' and resid 544 through 549 removed outlier: 3.550A pdb=" N ARG I 548 " --> pdb=" O GLY I 544 " (cutoff:3.500A) Processing helix chain 'I' and resid 551 through 555 Processing helix chain 'I' and resid 608 through 614 removed outlier: 3.743A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR I 614 " --> pdb=" O GLU I 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 614' Processing helix chain 'I' and resid 662 through 667 removed outlier: 3.553A pdb=" N LEU I 667 " --> pdb=" O VAL I 663 " (cutoff:3.500A) Processing helix chain 'I' and resid 675 through 688 removed outlier: 3.758A pdb=" N ARG I 687 " --> pdb=" O ALA I 683 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN I 688 " --> pdb=" O ASN I 684 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 858 through 865 removed outlier: 3.775A pdb=" N LYS I 864 " --> pdb=" O ALA I 860 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU I 865 " --> pdb=" O ALA I 861 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 977 Processing helix chain 'I' and resid 985 through 992 removed outlier: 3.611A pdb=" N ASP I 990 " --> pdb=" O ALA I 986 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS I 991 " --> pdb=" O GLU I 987 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU I 992 " --> pdb=" O LYS I 988 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 3.866A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 Processing helix chain 'I' and resid 1137 through 1151 Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.536A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1177 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1243 removed outlier: 3.615A pdb=" N LYS I1242 " --> pdb=" O LEU I1238 " (cutoff:3.500A) Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1284 through 1292 Processing helix chain 'I' and resid 1297 through 1311 Processing helix chain 'I' and resid 1320 through 1333 Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 95 through 101 removed outlier: 3.762A pdb=" N ARG J 99 " --> pdb=" O THR J 95 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU J 100 " --> pdb=" O LYS J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 119 removed outlier: 3.554A pdb=" N SER J 119 " --> pdb=" O TRP J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 162 through 172 Processing helix chain 'J' and resid 181 through 192 Processing helix chain 'J' and resid 193 through 208 Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 255 through 259 Processing helix chain 'J' and resid 264 through 286 removed outlier: 3.830A pdb=" N LEU J 268 " --> pdb=" O ASP J 264 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 318 through 322 removed outlier: 3.535A pdb=" N LYS J 321 " --> pdb=" O GLY J 318 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG J 322 " --> pdb=" O SER J 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 318 through 322' Processing helix chain 'J' and resid 326 through 332 Processing helix chain 'J' and resid 336 through 342 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 389 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 418 removed outlier: 3.720A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU J 418 " --> pdb=" O GLU J 414 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 450 through 458 removed outlier: 4.037A pdb=" N ALA J 455 " --> pdb=" O PRO J 451 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA J 456 " --> pdb=" O LEU J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 540 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.881A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 589 through 594 removed outlier: 3.851A pdb=" N GLN J 594 " --> pdb=" O SER J 590 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 612 Processing helix chain 'J' and resid 613 through 636 Processing helix chain 'J' and resid 647 through 670 removed outlier: 4.426A pdb=" N HIS J 651 " --> pdb=" O PRO J 647 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU J 652 " --> pdb=" O GLU J 648 " (cutoff:3.500A) Processing helix chain 'J' and resid 674 through 703 Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 741 Processing helix chain 'J' and resid 768 through 804 removed outlier: 3.612A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 895 through 900 Processing helix chain 'J' and resid 914 through 925 removed outlier: 3.619A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 929 Processing helix chain 'J' and resid 1068 through 1074 removed outlier: 4.355A pdb=" N LEU J1074 " --> pdb=" O GLY J1070 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1147 removed outlier: 3.599A pdb=" N VAL J1141 " --> pdb=" O GLY J1137 " (cutoff:3.500A) Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 4.036A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 3.981A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE J1256 " --> pdb=" O HIS J1252 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1326 removed outlier: 3.735A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1354 Processing helix chain 'J' and resid 1361 through 1373 removed outlier: 4.074A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 33 Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 80 removed outlier: 3.514A pdb=" N GLU K 79 " --> pdb=" O GLN K 75 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 13 through 17 removed outlier: 4.005A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'G' and resid 115 through 116 removed outlier: 3.830A pdb=" N THR G 101 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AA5, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.556A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 15 through 18 removed outlier: 4.611A pdb=" N ASP H 15 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR H 27 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU H 198 " --> pdb=" O ALA H 189 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA H 189 " --> pdb=" O LEU H 198 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LYS H 200 " --> pdb=" O VAL H 187 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL H 187 " --> pdb=" O LYS H 200 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL H 202 " --> pdb=" O TYR H 185 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TYR H 185 " --> pdb=" O VAL H 202 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLU H 204 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE H 183 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 99 through 105 removed outlier: 3.699A pdb=" N LEU H 102 " --> pdb=" O MET H 142 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AA9, first strand: chain 'H' and resid 108 through 111 removed outlier: 3.967A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.359A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 66 through 75 removed outlier: 3.757A pdb=" N VAL I 71 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'I' and resid 451 through 454 removed outlier: 6.414A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 154 through 158 Processing sheet with id=AB7, first strand: chain 'I' and resid 227 through 231 Processing sheet with id=AB8, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AB9, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.703A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 301 through 302 removed outlier: 6.917A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.541A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.612A pdb=" N ASP I 654 " --> pdb=" O ALA I 617 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE I 616 " --> pdb=" O ARG I 637 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 716 through 717 removed outlier: 7.128A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 750 through 752 removed outlier: 6.916A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN I 725 " --> pdb=" O VAL I 733 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 3.580A pdb=" N VAL I1225 " --> pdb=" O ILE I1210 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL I 818 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE I1079 " --> pdb=" O VAL I 818 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.717A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.717A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.991A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 1087 through 1088 Processing sheet with id=AD3, first strand: chain 'I' and resid 1335 through 1338 Processing sheet with id=AD4, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.626A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 10.517A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 10.056A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 143 through 145 Processing sheet with id=AD6, first strand: chain 'J' and resid 350 through 356 removed outlier: 7.412A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER J 353 " --> pdb=" O MET J 466 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 547 through 556 Processing sheet with id=AD8, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AD9, first strand: chain 'J' and resid 949 through 951 removed outlier: 3.953A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 957 through 961 removed outlier: 3.505A pdb=" N GLU J 981 " --> pdb=" O SER J 961 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 1024 through 1025 removed outlier: 3.506A pdb=" N ILE J1124 " --> pdb=" O MET J1025 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE J1106 " --> pdb=" O ARG J1123 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 1034 through 1038 Processing sheet with id=AE4, first strand: chain 'J' and resid 1186 through 1190 removed outlier: 4.325A pdb=" N TYR J1186 " --> pdb=" O ILE J1177 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE J1177 " --> pdb=" O TYR J1186 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 1279 through 1281 1072 hydrogen bonds defined for protein. 3063 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 158 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 12.58 Time building geometry restraints manager: 12.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7333 1.33 - 1.45: 4479 1.45 - 1.57: 15249 1.57 - 1.69: 187 1.69 - 1.81: 184 Bond restraints: 27432 Sorted by residual: bond pdb=" C ALA J 459 " pdb=" N ASP J 460 " ideal model delta sigma weight residual 1.330 1.434 -0.104 1.60e-02 3.91e+03 4.24e+01 bond pdb=" O3' DC B 3 " pdb=" P DT B 4 " ideal model delta sigma weight residual 1.607 1.667 -0.060 1.50e-02 4.44e+03 1.63e+01 bond pdb=" O3' DC B 17 " pdb=" P DG B 18 " ideal model delta sigma weight residual 1.607 1.664 -0.057 1.50e-02 4.44e+03 1.47e+01 bond pdb=" N GLN I1257 " pdb=" CA GLN I1257 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.04e-02 9.25e+03 1.27e+01 bond pdb=" N LEU J 252 " pdb=" CA LEU J 252 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.29e-02 6.01e+03 1.10e+01 ... (remaining 27427 not shown) Histogram of bond angle deviations from ideal: 98.58 - 105.66: 975 105.66 - 112.74: 15076 112.74 - 119.82: 8690 119.82 - 126.90: 12298 126.90 - 133.98: 448 Bond angle restraints: 37487 Sorted by residual: angle pdb=" N ASP J 806 " pdb=" CA ASP J 806 " pdb=" C ASP J 806 " ideal model delta sigma weight residual 112.59 105.37 7.22 1.22e+00 6.72e-01 3.50e+01 angle pdb=" O ALA J 459 " pdb=" C ALA J 459 " pdb=" N ASP J 460 " ideal model delta sigma weight residual 123.29 130.19 -6.90 1.18e+00 7.18e-01 3.42e+01 angle pdb=" O3' DG B 22 " pdb=" C3' DG B 22 " pdb=" C2' DG B 22 " ideal model delta sigma weight residual 111.50 120.18 -8.68 1.50e+00 4.44e-01 3.35e+01 angle pdb=" N ALA I1263 " pdb=" CA ALA I1263 " pdb=" C ALA I1263 " ideal model delta sigma weight residual 111.28 105.52 5.76 1.09e+00 8.42e-01 2.79e+01 angle pdb=" N VAL J 803 " pdb=" CA VAL J 803 " pdb=" C VAL J 803 " ideal model delta sigma weight residual 111.09 104.77 6.32 1.25e+00 6.40e-01 2.56e+01 ... (remaining 37482 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 16119 35.88 - 71.76: 573 71.76 - 107.64: 52 107.64 - 143.52: 5 143.52 - 179.40: 2 Dihedral angle restraints: 16751 sinusoidal: 7648 harmonic: 9103 Sorted by residual: dihedral pdb=" O4' U R 15 " pdb=" C1' U R 15 " pdb=" N1 U R 15 " pdb=" C2 U R 15 " ideal model delta sinusoidal sigma weight residual 200.00 59.10 140.90 1 1.50e+01 4.44e-03 7.58e+01 dihedral pdb=" O4' C R 17 " pdb=" C1' C R 17 " pdb=" N1 C R 17 " pdb=" C2 C R 17 " ideal model delta sinusoidal sigma weight residual 200.00 64.11 135.89 1 1.50e+01 4.44e-03 7.33e+01 dihedral pdb=" CA PHE I 57 " pdb=" C PHE I 57 " pdb=" N PRO I 58 " pdb=" CA PRO I 58 " ideal model delta harmonic sigma weight residual 180.00 157.80 22.20 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 16748 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3634 0.055 - 0.110: 582 0.110 - 0.165: 84 0.165 - 0.220: 12 0.220 - 0.275: 5 Chirality restraints: 4317 Sorted by residual: chirality pdb=" CA GLN I1257 " pdb=" N GLN I1257 " pdb=" C GLN I1257 " pdb=" CB GLN I1257 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C3' DG B 22 " pdb=" C4' DG B 22 " pdb=" O3' DG B 22 " pdb=" C2' DG B 22 " both_signs ideal model delta sigma weight residual False -2.66 -2.40 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" P G R 38 " pdb=" OP1 G R 38 " pdb=" OP2 G R 38 " pdb=" O5' G R 38 " both_signs ideal model delta sigma weight residual True 2.41 -2.64 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 4314 not shown) Planarity restraints: 4558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP J 460 " 0.015 2.00e-02 2.50e+03 3.13e-02 9.77e+00 pdb=" C ASP J 460 " -0.054 2.00e-02 2.50e+03 pdb=" O ASP J 460 " 0.021 2.00e-02 2.50e+03 pdb=" N PHE J 461 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA J 804 " 0.014 2.00e-02 2.50e+03 2.85e-02 8.10e+00 pdb=" C ALA J 804 " -0.049 2.00e-02 2.50e+03 pdb=" O ALA J 804 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN J 805 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS J 749 " 0.037 5.00e-02 4.00e+02 5.54e-02 4.90e+00 pdb=" N PRO J 750 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO J 750 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO J 750 " 0.031 5.00e-02 4.00e+02 ... (remaining 4555 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 338 2.61 - 3.18: 24245 3.18 - 3.76: 44515 3.76 - 4.33: 60715 4.33 - 4.90: 97090 Nonbonded interactions: 226903 Sorted by model distance: nonbonded pdb=" CB ALA J 108 " pdb=" CD2 LEU J 279 " model vdw 2.039 3.880 nonbonded pdb=" O ASP J 462 " pdb=" OD1 ASP J 462 " model vdw 2.085 3.040 nonbonded pdb=" CB TYR I1251 " pdb=" OE1 GLN I1257 " model vdw 2.096 3.440 nonbonded pdb=" OG1 THR H 22 " pdb=" O THR H 207 " model vdw 2.101 2.440 nonbonded pdb=" OG SER I 391 " pdb=" OD1 ASP I 393 " model vdw 2.108 2.440 ... (remaining 226898 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 'G' and (resid 8 through 158 or resid 170 through 234)) selection = (chain 'H' and resid 8 through 234) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.290 Check model and map are aligned: 0.420 Set scattering table: 0.260 Process input model: 81.670 Find NCS groups from input model: 0.970 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: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 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 : 0.004 0.104 27432 Z= 0.237 Angle : 0.633 9.959 37487 Z= 0.376 Chirality : 0.043 0.275 4317 Planarity : 0.004 0.055 4558 Dihedral : 17.336 179.396 10895 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.38 % Favored : 97.59 % Rotamer: Outliers : 0.11 % Allowed : 0.37 % Favored : 99.52 % 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: 1.34 (0.15), residues: 3152 helix: 1.84 (0.15), residues: 1105 sheet: 1.00 (0.25), residues: 425 loop : 0.28 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 183 HIS 0.007 0.001 HIS J1366 PHE 0.018 0.001 PHE J 461 TYR 0.015 0.001 TYR J 631 ARG 0.004 0.000 ARG I 779 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 704 time to evaluate : 3.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 156 SER cc_start: 0.9373 (p) cc_final: 0.9022 (t) REVERT: G 185 TYR cc_start: 0.8934 (p90) cc_final: 0.8626 (p90) REVERT: H 32 GLU cc_start: 0.7298 (tp30) cc_final: 0.6701 (mm-30) REVERT: H 131 CYS cc_start: 0.7348 (p) cc_final: 0.5776 (p) REVERT: H 185 TYR cc_start: 0.8631 (p90) cc_final: 0.8386 (p90) REVERT: I 142 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7764 (mt-10) REVERT: I 454 ARG cc_start: 0.8873 (ttm170) cc_final: 0.8657 (ttp80) REVERT: I 516 ASP cc_start: 0.6817 (p0) cc_final: 0.6216 (p0) REVERT: I 768 MET cc_start: 0.7169 (ttt) cc_final: 0.6911 (ttt) REVERT: I 785 ASP cc_start: 0.6463 (m-30) cc_final: 0.6046 (p0) REVERT: I 788 SER cc_start: 0.9129 (m) cc_final: 0.8740 (p) REVERT: I 1066 MET cc_start: 0.8375 (tpp) cc_final: 0.8047 (tpp) REVERT: I 1085 MET cc_start: 0.9055 (mmm) cc_final: 0.8728 (mmm) REVERT: I 1117 LEU cc_start: 0.9401 (tp) cc_final: 0.9178 (tp) REVERT: J 96 LYS cc_start: 0.8373 (ttmt) cc_final: 0.8043 (mtpt) REVERT: J 97 VAL cc_start: 0.7773 (t) cc_final: 0.7065 (t) REVERT: J 100 GLU cc_start: 0.8109 (mp0) cc_final: 0.7613 (mp0) REVERT: J 197 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7947 (mt-10) REVERT: J 249 LEU cc_start: 0.9212 (mt) cc_final: 0.9003 (mt) REVERT: J 301 GLU cc_start: 0.8624 (tp30) cc_final: 0.8249 (tm-30) REVERT: J 342 LEU cc_start: 0.9463 (mp) cc_final: 0.9246 (mp) REVERT: J 398 LYS cc_start: 0.8366 (mttt) cc_final: 0.8049 (mttp) REVERT: J 429 LEU cc_start: 0.9123 (mt) cc_final: 0.8894 (mp) REVERT: J 445 LYS cc_start: 0.8385 (mttt) cc_final: 0.8023 (mttt) REVERT: J 470 VAL cc_start: 0.9227 (t) cc_final: 0.9007 (t) REVERT: J 484 MET cc_start: 0.8682 (mmm) cc_final: 0.8308 (mmm) REVERT: J 723 TYR cc_start: 0.8745 (t80) cc_final: 0.8517 (t80) REVERT: J 835 LEU cc_start: 0.8506 (tp) cc_final: 0.8288 (tp) REVERT: J 836 ARG cc_start: 0.8067 (tmm160) cc_final: 0.7452 (ttp80) REVERT: J 1123 ARG cc_start: 0.8480 (mtt180) cc_final: 0.8085 (mtp85) REVERT: J 1189 MET cc_start: 0.7331 (tpt) cc_final: 0.6995 (mmt) REVERT: J 1208 ASP cc_start: 0.7443 (m-30) cc_final: 0.7170 (m-30) REVERT: J 1250 ASP cc_start: 0.8517 (m-30) cc_final: 0.8291 (m-30) REVERT: J 1254 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7815 (mt-10) REVERT: K 55 GLU cc_start: 0.8468 (tt0) cc_final: 0.8124 (tt0) outliers start: 3 outliers final: 0 residues processed: 706 average time/residue: 0.4614 time to fit residues: 486.5293 Evaluate side-chains 341 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 341 time to evaluate : 3.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 271 optimal weight: 8.9990 chunk 244 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 164 optimal weight: 0.9990 chunk 130 optimal weight: 8.9990 chunk 252 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 187 optimal weight: 6.9990 chunk 292 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 23 HIS H 194 GLN I 36 GLN I 46 GLN ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 613 ASN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 684 ASN ** I 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1209 GLN I1244 HIS ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1264 GLN ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1195 GLN J1235 ASN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27432 Z= 0.275 Angle : 0.625 12.933 37487 Z= 0.327 Chirality : 0.042 0.265 4317 Planarity : 0.004 0.052 4558 Dihedral : 15.881 177.394 4692 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.70 % Allowed : 13.29 % Favored : 84.01 % 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: 1.14 (0.14), residues: 3152 helix: 1.63 (0.15), residues: 1139 sheet: 0.98 (0.26), residues: 398 loop : 0.16 (0.15), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 580 HIS 0.012 0.001 HIS I 165 PHE 0.017 0.002 PHE J 377 TYR 0.028 0.002 TYR I1229 ARG 0.005 0.001 ARG J 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 380 time to evaluate : 3.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 32 GLU cc_start: 0.7333 (tp30) cc_final: 0.7000 (mm-30) REVERT: H 37 HIS cc_start: 0.8009 (OUTLIER) cc_final: 0.7411 (t-90) REVERT: H 185 TYR cc_start: 0.8861 (p90) cc_final: 0.8361 (p90) REVERT: I 116 ASP cc_start: 0.6525 (p0) cc_final: 0.6297 (t0) REVERT: I 142 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7552 (mt-10) REVERT: I 414 ILE cc_start: 0.9170 (mm) cc_final: 0.8646 (tp) REVERT: I 422 LYS cc_start: 0.7357 (mptt) cc_final: 0.6974 (mptt) REVERT: I 516 ASP cc_start: 0.7210 (p0) cc_final: 0.6254 (p0) REVERT: I 768 MET cc_start: 0.7245 (ttt) cc_final: 0.6861 (ttt) REVERT: I 788 SER cc_start: 0.9047 (m) cc_final: 0.8716 (p) REVERT: I 1085 MET cc_start: 0.9057 (mmm) cc_final: 0.8652 (mmm) REVERT: I 1229 TYR cc_start: 0.8898 (m-10) cc_final: 0.8667 (m-10) REVERT: I 1273 MET cc_start: 0.8473 (mtp) cc_final: 0.8066 (mtt) REVERT: I 1281 TYR cc_start: 0.8503 (m-10) cc_final: 0.8261 (m-10) REVERT: J 96 LYS cc_start: 0.8241 (ttmt) cc_final: 0.7911 (mtpt) REVERT: J 97 VAL cc_start: 0.7719 (t) cc_final: 0.7057 (t) REVERT: J 100 GLU cc_start: 0.8149 (mp0) cc_final: 0.7641 (mp0) REVERT: J 137 ARG cc_start: 0.8459 (mtp-110) cc_final: 0.7992 (ptp90) REVERT: J 418 GLU cc_start: 0.7220 (mm-30) cc_final: 0.7016 (mm-30) REVERT: J 466 MET cc_start: 0.7923 (mtm) cc_final: 0.7695 (mtt) REVERT: J 504 GLN cc_start: 0.7483 (mp10) cc_final: 0.7138 (mp10) REVERT: J 656 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7615 (mt-10) REVERT: J 697 MET cc_start: 0.8191 (ttp) cc_final: 0.7625 (tmm) REVERT: J 723 TYR cc_start: 0.8833 (t80) cc_final: 0.8617 (t80) REVERT: J 835 LEU cc_start: 0.8355 (tp) cc_final: 0.8126 (tp) REVERT: J 1025 MET cc_start: 0.8472 (mpp) cc_final: 0.8245 (mpp) REVERT: J 1123 ARG cc_start: 0.8327 (mtt180) cc_final: 0.7958 (mtp180) REVERT: J 1254 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7871 (mt-10) REVERT: K 11 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8183 (mp0) REVERT: K 43 ASN cc_start: 0.8811 (t0) cc_final: 0.8529 (t0) outliers start: 73 outliers final: 52 residues processed: 426 average time/residue: 0.3847 time to fit residues: 259.4064 Evaluate side-chains 371 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 317 time to evaluate : 3.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 423 ASP Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 531 SER Chi-restraints excluded: chain I residue 611 GLU Chi-restraints excluded: chain I residue 692 THR Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1303 LYS Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 370 LYS Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 516 ASP Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 978 ARG Chi-restraints excluded: chain J residue 1328 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain K residue 62 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 162 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 chunk 243 optimal weight: 6.9990 chunk 199 optimal weight: 4.9990 chunk 80 optimal weight: 20.0000 chunk 292 optimal weight: 5.9990 chunk 316 optimal weight: 3.9990 chunk 260 optimal weight: 0.9980 chunk 290 optimal weight: 9.9990 chunk 99 optimal weight: 0.8980 chunk 235 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 HIS I 450 ASN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 628 HIS I 766 ASN ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1244 HIS ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 186 GLN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27432 Z= 0.183 Angle : 0.579 13.273 37487 Z= 0.300 Chirality : 0.041 0.177 4317 Planarity : 0.004 0.049 4558 Dihedral : 15.834 177.229 4692 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.22 % Allowed : 15.07 % Favored : 81.71 % 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: 0.99 (0.14), residues: 3152 helix: 1.56 (0.15), residues: 1141 sheet: 0.73 (0.26), residues: 390 loop : 0.06 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 580 HIS 0.012 0.001 HIS I 165 PHE 0.025 0.001 PHE I1025 TYR 0.026 0.001 TYR H 177 ARG 0.006 0.000 ARG J 978 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 372 time to evaluate : 2.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 185 TYR cc_start: 0.8718 (p90) cc_final: 0.8429 (p90) REVERT: H 37 HIS cc_start: 0.7943 (OUTLIER) cc_final: 0.7538 (t-90) REVERT: H 185 TYR cc_start: 0.8826 (p90) cc_final: 0.8386 (p90) REVERT: I 142 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7533 (mt-10) REVERT: I 193 ASN cc_start: 0.8183 (m-40) cc_final: 0.7706 (t0) REVERT: I 253 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.7542 (t80) REVERT: I 422 LYS cc_start: 0.7339 (mptt) cc_final: 0.6615 (mptt) REVERT: I 516 ASP cc_start: 0.7102 (p0) cc_final: 0.6263 (p0) REVERT: I 788 SER cc_start: 0.8951 (m) cc_final: 0.8651 (p) REVERT: I 1085 MET cc_start: 0.9025 (mmm) cc_final: 0.8601 (mmm) REVERT: I 1273 MET cc_start: 0.8452 (mtp) cc_final: 0.8046 (mtt) REVERT: J 96 LYS cc_start: 0.8308 (ttmt) cc_final: 0.7919 (mtpt) REVERT: J 97 VAL cc_start: 0.7644 (t) cc_final: 0.7066 (t) REVERT: J 100 GLU cc_start: 0.8148 (mp0) cc_final: 0.7599 (mp0) REVERT: J 130 MET cc_start: 0.8574 (ttm) cc_final: 0.8369 (tmm) REVERT: J 137 ARG cc_start: 0.8477 (mtp-110) cc_final: 0.8029 (ptp90) REVERT: J 249 LEU cc_start: 0.9152 (mt) cc_final: 0.8730 (mt) REVERT: J 504 GLN cc_start: 0.7421 (mp10) cc_final: 0.7131 (mp10) REVERT: J 656 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7596 (mt-10) REVERT: J 697 MET cc_start: 0.8230 (ttp) cc_final: 0.7995 (ttp) REVERT: J 1123 ARG cc_start: 0.8365 (mtt180) cc_final: 0.8002 (mtp-110) REVERT: J 1254 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7780 (mt-10) REVERT: K 43 ASN cc_start: 0.8926 (t0) cc_final: 0.8601 (t0) outliers start: 87 outliers final: 53 residues processed: 428 average time/residue: 0.3875 time to fit residues: 265.0554 Evaluate side-chains 359 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 304 time to evaluate : 3.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain I residue 423 ASP Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 531 SER Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 611 GLU Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1303 LYS Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 370 LYS Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 516 ASP Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 994 SER Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 62 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 289 optimal weight: 9.9990 chunk 220 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 196 optimal weight: 5.9990 chunk 293 optimal weight: 9.9990 chunk 311 optimal weight: 0.9980 chunk 153 optimal weight: 0.7980 chunk 278 optimal weight: 20.0000 chunk 83 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 HIS ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1209 GLN ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27432 Z= 0.195 Angle : 0.568 13.369 37487 Z= 0.294 Chirality : 0.041 0.218 4317 Planarity : 0.004 0.054 4558 Dihedral : 15.810 176.341 4692 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.44 % Allowed : 16.96 % Favored : 79.60 % 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: 0.96 (0.15), residues: 3152 helix: 1.55 (0.15), residues: 1144 sheet: 0.66 (0.26), residues: 400 loop : 0.05 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 580 HIS 0.013 0.001 HIS I 165 PHE 0.030 0.001 PHE G 35 TYR 0.028 0.002 TYR H 177 ARG 0.009 0.000 ARG K 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 336 time to evaluate : 2.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 142 MET cc_start: 0.8581 (mtt) cc_final: 0.8263 (mtt) REVERT: G 185 TYR cc_start: 0.8733 (p90) cc_final: 0.8482 (p90) REVERT: H 37 HIS cc_start: 0.8024 (OUTLIER) cc_final: 0.7646 (t-90) REVERT: H 185 TYR cc_start: 0.8846 (p90) cc_final: 0.8447 (p90) REVERT: I 142 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7522 (mt-10) REVERT: I 213 LEU cc_start: 0.8676 (mt) cc_final: 0.8211 (mt) REVERT: I 422 LYS cc_start: 0.7462 (mptt) cc_final: 0.6105 (mptt) REVERT: I 516 ASP cc_start: 0.7145 (p0) cc_final: 0.6297 (p0) REVERT: I 788 SER cc_start: 0.8964 (m) cc_final: 0.8701 (p) REVERT: I 1085 MET cc_start: 0.9012 (mmm) cc_final: 0.8609 (mmm) REVERT: I 1273 MET cc_start: 0.8577 (mtp) cc_final: 0.8349 (mtp) REVERT: I 1339 LEU cc_start: 0.8458 (mt) cc_final: 0.8183 (mt) REVERT: J 96 LYS cc_start: 0.8316 (ttmt) cc_final: 0.7983 (mtpt) REVERT: J 97 VAL cc_start: 0.7642 (t) cc_final: 0.7289 (t) REVERT: J 100 GLU cc_start: 0.8140 (mp0) cc_final: 0.7630 (mp0) REVERT: J 137 ARG cc_start: 0.8460 (mtp-110) cc_final: 0.8005 (ptp90) REVERT: J 398 LYS cc_start: 0.8220 (mttt) cc_final: 0.7923 (mtmm) REVERT: J 495 ASN cc_start: 0.7858 (OUTLIER) cc_final: 0.7575 (p0) REVERT: J 504 GLN cc_start: 0.7472 (mp10) cc_final: 0.7255 (mp10) REVERT: J 656 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7580 (mt-10) REVERT: J 697 MET cc_start: 0.8342 (ttp) cc_final: 0.8039 (tmm) REVERT: J 1123 ARG cc_start: 0.8343 (mtt180) cc_final: 0.8017 (mtp-110) REVERT: J 1254 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7764 (mt-10) REVERT: K 11 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8141 (mp0) REVERT: K 42 GLU cc_start: 0.8362 (mp0) cc_final: 0.8149 (pm20) REVERT: K 43 ASN cc_start: 0.8918 (t0) cc_final: 0.8591 (t0) outliers start: 93 outliers final: 59 residues processed: 398 average time/residue: 0.3769 time to fit residues: 240.7622 Evaluate side-chains 367 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 305 time to evaluate : 3.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 166 SER Chi-restraints excluded: chain I residue 423 ASP Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 531 SER Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 611 GLU Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1303 LYS Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 370 LYS Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 495 ASN Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 994 SER Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain K residue 62 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 259 optimal weight: 0.4980 chunk 176 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 231 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 265 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 158 optimal weight: 9.9990 chunk 279 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 HIS I 490 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 808 ASN ** I 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1195 GLN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27432 Z= 0.224 Angle : 0.578 13.055 37487 Z= 0.297 Chirality : 0.041 0.229 4317 Planarity : 0.004 0.049 4558 Dihedral : 15.833 176.159 4692 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.67 % Allowed : 17.51 % Favored : 78.82 % 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: 0.89 (0.15), residues: 3152 helix: 1.52 (0.15), residues: 1138 sheet: 0.53 (0.26), residues: 405 loop : 0.01 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I1276 HIS 0.013 0.001 HIS I 165 PHE 0.028 0.001 PHE I1025 TYR 0.028 0.002 TYR H 177 ARG 0.011 0.000 ARG J1330 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 318 time to evaluate : 3.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 185 TYR cc_start: 0.8763 (p90) cc_final: 0.8485 (p90) REVERT: H 37 HIS cc_start: 0.8046 (OUTLIER) cc_final: 0.7655 (t-90) REVERT: H 104 LYS cc_start: 0.7436 (mmmt) cc_final: 0.7005 (tttt) REVERT: H 185 TYR cc_start: 0.8901 (p90) cc_final: 0.8548 (p90) REVERT: I 142 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7469 (mt-10) REVERT: I 213 LEU cc_start: 0.8750 (mt) cc_final: 0.8219 (mt) REVERT: I 422 LYS cc_start: 0.7444 (mptt) cc_final: 0.6199 (mptt) REVERT: I 516 ASP cc_start: 0.7144 (p0) cc_final: 0.6305 (p0) REVERT: I 562 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8214 (tm-30) REVERT: I 788 SER cc_start: 0.9127 (m) cc_final: 0.8825 (p) REVERT: I 1085 MET cc_start: 0.9022 (mmm) cc_final: 0.8550 (mmm) REVERT: I 1244 HIS cc_start: 0.6770 (OUTLIER) cc_final: 0.5582 (t70) REVERT: I 1273 MET cc_start: 0.8633 (mtp) cc_final: 0.8387 (mtp) REVERT: I 1339 LEU cc_start: 0.8588 (mt) cc_final: 0.8327 (mt) REVERT: J 96 LYS cc_start: 0.8303 (ttmt) cc_final: 0.7971 (mtpt) REVERT: J 97 VAL cc_start: 0.7602 (t) cc_final: 0.7314 (t) REVERT: J 100 GLU cc_start: 0.8164 (mp0) cc_final: 0.7607 (mp0) REVERT: J 137 ARG cc_start: 0.8455 (mtp-110) cc_final: 0.8002 (ptp90) REVERT: J 330 MET cc_start: 0.7590 (OUTLIER) cc_final: 0.7107 (ptm) REVERT: J 375 GLU cc_start: 0.7822 (mp0) cc_final: 0.7403 (mp0) REVERT: J 656 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7617 (mt-10) REVERT: J 697 MET cc_start: 0.8249 (ttp) cc_final: 0.7845 (tmm) REVERT: J 1123 ARG cc_start: 0.8380 (mtt180) cc_final: 0.8051 (mtp-110) REVERT: J 1254 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7825 (mt-10) REVERT: K 43 ASN cc_start: 0.8877 (t0) cc_final: 0.8607 (t0) REVERT: K 52 ARG cc_start: 0.8176 (mtm-85) cc_final: 0.7949 (ttp-110) outliers start: 99 outliers final: 73 residues processed: 388 average time/residue: 0.3783 time to fit residues: 235.8039 Evaluate side-chains 376 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 300 time to evaluate : 3.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 229 GLU Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 193 ASN Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 423 ASP Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 486 THR Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 611 GLU Chi-restraints excluded: chain I residue 692 THR Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 330 MET Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 370 LYS Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 516 ASP Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 994 SER Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1089 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 62 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 104 optimal weight: 3.9990 chunk 280 optimal weight: 0.0010 chunk 61 optimal weight: 5.9990 chunk 182 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 311 optimal weight: 9.9990 chunk 258 optimal weight: 9.9990 chunk 144 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 163 optimal weight: 10.0000 overall best weight: 2.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 HIS I 238 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 932 GLN ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 477 GLN ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1366 HIS K 15 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 27432 Z= 0.303 Angle : 0.611 12.399 37487 Z= 0.316 Chirality : 0.042 0.196 4317 Planarity : 0.004 0.047 4558 Dihedral : 15.915 175.390 4692 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.48 % Allowed : 18.29 % Favored : 77.23 % 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: 0.76 (0.15), residues: 3152 helix: 1.42 (0.15), residues: 1137 sheet: 0.42 (0.26), residues: 383 loop : -0.05 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 580 HIS 0.012 0.001 HIS I 165 PHE 0.032 0.002 PHE I1025 TYR 0.025 0.002 TYR H 177 ARG 0.020 0.001 ARG K 3 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 304 time to evaluate : 2.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 137 ASN cc_start: 0.8941 (t0) cc_final: 0.8454 (t0) REVERT: G 142 MET cc_start: 0.8521 (mtt) cc_final: 0.8288 (mtt) REVERT: H 185 TYR cc_start: 0.9001 (p90) cc_final: 0.8786 (p90) REVERT: I 213 LEU cc_start: 0.8865 (mt) cc_final: 0.8653 (mt) REVERT: I 422 LYS cc_start: 0.7449 (mptt) cc_final: 0.6326 (mptt) REVERT: I 516 ASP cc_start: 0.7281 (p0) cc_final: 0.6304 (p0) REVERT: I 562 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8217 (tm-30) REVERT: I 788 SER cc_start: 0.9215 (m) cc_final: 0.8888 (p) REVERT: I 1085 MET cc_start: 0.9039 (mmm) cc_final: 0.8465 (mmm) REVERT: I 1244 HIS cc_start: 0.6910 (OUTLIER) cc_final: 0.5646 (t70) REVERT: I 1273 MET cc_start: 0.8691 (mtp) cc_final: 0.8269 (mtt) REVERT: J 96 LYS cc_start: 0.8428 (ttmt) cc_final: 0.8121 (mtpt) REVERT: J 97 VAL cc_start: 0.7747 (t) cc_final: 0.7440 (t) REVERT: J 100 GLU cc_start: 0.8183 (mp0) cc_final: 0.7664 (mp0) REVERT: J 180 MET cc_start: 0.7282 (tpp) cc_final: 0.6698 (tpt) REVERT: J 330 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7239 (ptm) REVERT: J 352 ARG cc_start: 0.8049 (ttm-80) cc_final: 0.7615 (ttm-80) REVERT: J 356 THR cc_start: 0.8726 (m) cc_final: 0.8503 (m) REVERT: J 642 ASP cc_start: 0.8379 (m-30) cc_final: 0.8166 (m-30) REVERT: J 697 MET cc_start: 0.8436 (ttp) cc_final: 0.7932 (tmm) REVERT: J 1123 ARG cc_start: 0.8374 (mtt180) cc_final: 0.8080 (mtp180) REVERT: J 1254 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7939 (mt-10) REVERT: J 1370 MET cc_start: 0.7664 (mmp) cc_final: 0.7092 (mmt) REVERT: K 7 GLN cc_start: 0.8472 (tp40) cc_final: 0.7931 (tp40) REVERT: K 11 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8327 (pm20) outliers start: 121 outliers final: 91 residues processed: 392 average time/residue: 0.4101 time to fit residues: 259.5143 Evaluate side-chains 379 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 285 time to evaluate : 3.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 152 TYR Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 165 HIS Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 423 ASP Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 486 THR Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 611 GLU Chi-restraints excluded: chain I residue 692 THR Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 871 VAL Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 330 MET Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 370 LYS Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 495 ASN Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 516 ASP Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 994 SER Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1089 LEU Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1328 THR Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 62 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 300 optimal weight: 0.0570 chunk 35 optimal weight: 0.0980 chunk 177 optimal weight: 0.8980 chunk 227 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 chunk 262 optimal weight: 8.9990 chunk 173 optimal weight: 2.9990 chunk 310 optimal weight: 0.0980 chunk 194 optimal weight: 3.9990 chunk 189 optimal weight: 8.9990 chunk 143 optimal weight: 8.9990 overall best weight: 0.4300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 150 HIS ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 27432 Z= 0.162 Angle : 0.572 13.367 37487 Z= 0.293 Chirality : 0.041 0.179 4317 Planarity : 0.004 0.049 4558 Dihedral : 15.909 173.697 4692 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.15 % Allowed : 19.81 % Favored : 77.05 % 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: 0.75 (0.15), residues: 3152 helix: 1.44 (0.15), residues: 1134 sheet: 0.45 (0.27), residues: 380 loop : -0.08 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 580 HIS 0.017 0.001 HIS I 165 PHE 0.031 0.001 PHE I1025 TYR 0.032 0.001 TYR G 185 ARG 0.008 0.000 ARG K 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 332 time to evaluate : 3.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 137 ASN cc_start: 0.8896 (t0) cc_final: 0.8394 (t0) REVERT: G 142 MET cc_start: 0.8545 (mtt) cc_final: 0.8285 (mtt) REVERT: H 37 HIS cc_start: 0.7999 (OUTLIER) cc_final: 0.7660 (t-90) REVERT: H 104 LYS cc_start: 0.7171 (mmmt) cc_final: 0.6948 (tttt) REVERT: H 185 TYR cc_start: 0.8906 (p90) cc_final: 0.8604 (p90) REVERT: I 414 ILE cc_start: 0.9096 (mm) cc_final: 0.8745 (tp) REVERT: I 422 LYS cc_start: 0.7411 (mptt) cc_final: 0.6330 (mptt) REVERT: I 516 ASP cc_start: 0.7265 (OUTLIER) cc_final: 0.6334 (p0) REVERT: I 562 GLU cc_start: 0.8359 (tm-30) cc_final: 0.8143 (tm-30) REVERT: I 788 SER cc_start: 0.9166 (m) cc_final: 0.8832 (p) REVERT: I 1034 ARG cc_start: 0.8086 (mpt90) cc_final: 0.7845 (mpt90) REVERT: I 1085 MET cc_start: 0.8999 (mmm) cc_final: 0.8474 (mmm) REVERT: I 1244 HIS cc_start: 0.6831 (OUTLIER) cc_final: 0.5501 (t70) REVERT: I 1273 MET cc_start: 0.8520 (mtp) cc_final: 0.8142 (mtp) REVERT: I 1339 LEU cc_start: 0.8701 (mt) cc_final: 0.8308 (mt) REVERT: J 96 LYS cc_start: 0.8315 (ttmt) cc_final: 0.8092 (mtmt) REVERT: J 97 VAL cc_start: 0.7616 (t) cc_final: 0.7355 (t) REVERT: J 100 GLU cc_start: 0.8222 (mp0) cc_final: 0.7742 (mp0) REVERT: J 137 ARG cc_start: 0.8389 (mtp-110) cc_final: 0.7984 (ptp90) REVERT: J 180 MET cc_start: 0.7253 (tpp) cc_final: 0.6605 (tpt) REVERT: J 352 ARG cc_start: 0.7738 (ttm-80) cc_final: 0.7399 (ttm-80) REVERT: J 375 GLU cc_start: 0.7760 (mp0) cc_final: 0.7358 (mp0) REVERT: J 382 TYR cc_start: 0.9109 (m-80) cc_final: 0.8908 (m-80) REVERT: J 398 LYS cc_start: 0.8330 (mptt) cc_final: 0.8039 (mppt) REVERT: J 697 MET cc_start: 0.8411 (ttp) cc_final: 0.7713 (tmm) REVERT: J 1123 ARG cc_start: 0.8362 (mtt180) cc_final: 0.8073 (mtp180) REVERT: J 1155 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8618 (mp) REVERT: J 1254 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7704 (mt-10) REVERT: K 7 GLN cc_start: 0.8349 (tp40) cc_final: 0.7754 (tp40) REVERT: K 69 ARG cc_start: 0.8696 (mtp-110) cc_final: 0.8422 (ttm110) outliers start: 85 outliers final: 65 residues processed: 391 average time/residue: 0.3800 time to fit residues: 235.7098 Evaluate side-chains 364 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 295 time to evaluate : 3.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 229 GLU Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 423 ASP Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 486 THR Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 1040 ASP Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 370 LYS Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 495 ASN Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 516 ASP Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1089 LEU Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 62 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 192 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 197 optimal weight: 0.8980 chunk 211 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 243 optimal weight: 0.8980 chunk 282 optimal weight: 20.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 165 HIS ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27432 Z= 0.190 Angle : 0.571 12.735 37487 Z= 0.291 Chirality : 0.041 0.180 4317 Planarity : 0.004 0.048 4558 Dihedral : 15.904 174.100 4692 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.30 % Allowed : 20.21 % Favored : 76.49 % 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: 0.75 (0.15), residues: 3152 helix: 1.44 (0.15), residues: 1135 sheet: 0.46 (0.27), residues: 380 loop : -0.09 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP J 115 HIS 0.013 0.001 HIS I 165 PHE 0.033 0.001 PHE I1025 TYR 0.027 0.001 TYR G 185 ARG 0.011 0.000 ARG J1372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 313 time to evaluate : 3.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 137 ASN cc_start: 0.8892 (t0) cc_final: 0.8395 (t0) REVERT: H 37 HIS cc_start: 0.8008 (OUTLIER) cc_final: 0.7668 (t-90) REVERT: H 104 LYS cc_start: 0.7280 (mmmt) cc_final: 0.7018 (tttt) REVERT: H 185 TYR cc_start: 0.8930 (p90) cc_final: 0.8599 (p90) REVERT: I 414 ILE cc_start: 0.9100 (mm) cc_final: 0.8719 (tp) REVERT: I 422 LYS cc_start: 0.7643 (mptt) cc_final: 0.7141 (mptt) REVERT: I 516 ASP cc_start: 0.7315 (p0) cc_final: 0.6511 (p0) REVERT: I 524 ILE cc_start: 0.9102 (tp) cc_final: 0.8840 (tp) REVERT: I 562 GLU cc_start: 0.8330 (tm-30) cc_final: 0.8086 (tm-30) REVERT: I 788 SER cc_start: 0.9208 (m) cc_final: 0.8879 (p) REVERT: I 825 GLU cc_start: 0.7905 (pt0) cc_final: 0.7695 (pt0) REVERT: I 1085 MET cc_start: 0.8988 (mmm) cc_final: 0.8557 (mmm) REVERT: I 1243 MET cc_start: 0.6967 (ttm) cc_final: 0.6746 (mtp) REVERT: I 1244 HIS cc_start: 0.6774 (OUTLIER) cc_final: 0.5373 (t70) REVERT: I 1273 MET cc_start: 0.8622 (mtp) cc_final: 0.8194 (mtt) REVERT: I 1339 LEU cc_start: 0.8754 (mt) cc_final: 0.8363 (mt) REVERT: J 96 LYS cc_start: 0.8382 (ttmt) cc_final: 0.8140 (mtmt) REVERT: J 97 VAL cc_start: 0.7606 (t) cc_final: 0.7340 (t) REVERT: J 100 GLU cc_start: 0.8172 (mp0) cc_final: 0.7723 (mp0) REVERT: J 115 TRP cc_start: 0.8563 (m-10) cc_final: 0.8311 (m-10) REVERT: J 130 MET cc_start: 0.7864 (ptm) cc_final: 0.7610 (ppp) REVERT: J 137 ARG cc_start: 0.8365 (mtp-110) cc_final: 0.7965 (ptp90) REVERT: J 180 MET cc_start: 0.7259 (tpp) cc_final: 0.6611 (tpt) REVERT: J 352 ARG cc_start: 0.7826 (ttm-80) cc_final: 0.7451 (ttm-80) REVERT: J 375 GLU cc_start: 0.7840 (mp0) cc_final: 0.7474 (mp0) REVERT: J 382 TYR cc_start: 0.9107 (m-80) cc_final: 0.8894 (m-80) REVERT: J 398 LYS cc_start: 0.8370 (mptt) cc_final: 0.8123 (mppt) REVERT: J 697 MET cc_start: 0.8425 (ttp) cc_final: 0.7756 (tmm) REVERT: J 796 LEU cc_start: 0.9510 (tp) cc_final: 0.9246 (tp) REVERT: J 821 MET cc_start: 0.8750 (tpp) cc_final: 0.8502 (tpp) REVERT: J 1123 ARG cc_start: 0.8322 (mtt180) cc_final: 0.8053 (mtp180) REVERT: J 1254 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7736 (mt-10) REVERT: J 1370 MET cc_start: 0.7776 (mmp) cc_final: 0.7089 (mmt) outliers start: 89 outliers final: 68 residues processed: 372 average time/residue: 0.4173 time to fit residues: 249.3993 Evaluate side-chains 370 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 300 time to evaluate : 3.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 229 GLU Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 165 HIS Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 423 ASP Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 486 THR Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 1040 ASP Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 370 LYS Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 495 ASN Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 516 ASP Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1089 LEU Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain K residue 62 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 297 optimal weight: 3.9990 chunk 271 optimal weight: 10.0000 chunk 289 optimal weight: 0.0370 chunk 174 optimal weight: 0.9990 chunk 125 optimal weight: 0.0870 chunk 227 optimal weight: 0.6980 chunk 88 optimal weight: 7.9990 chunk 261 optimal weight: 4.9990 chunk 273 optimal weight: 8.9990 chunk 288 optimal weight: 0.8980 chunk 189 optimal weight: 7.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27432 Z= 0.163 Angle : 0.573 12.672 37487 Z= 0.291 Chirality : 0.040 0.178 4317 Planarity : 0.004 0.048 4558 Dihedral : 15.899 173.924 4692 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.96 % Allowed : 20.55 % Favored : 76.49 % 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: 0.71 (0.15), residues: 3152 helix: 1.40 (0.15), residues: 1141 sheet: 0.52 (0.27), residues: 377 loop : -0.13 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP I1276 HIS 0.054 0.001 HIS I 165 PHE 0.030 0.001 PHE I1025 TYR 0.028 0.001 TYR G 185 ARG 0.010 0.000 ARG K 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 325 time to evaluate : 3.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 137 ASN cc_start: 0.8876 (t0) cc_final: 0.8373 (t0) REVERT: H 37 HIS cc_start: 0.7928 (OUTLIER) cc_final: 0.7654 (t-90) REVERT: H 104 LYS cc_start: 0.7202 (mmmt) cc_final: 0.7002 (tttt) REVERT: H 185 TYR cc_start: 0.8904 (p90) cc_final: 0.8564 (p90) REVERT: I 422 LYS cc_start: 0.7652 (mptt) cc_final: 0.7029 (mptt) REVERT: I 516 ASP cc_start: 0.7284 (p0) cc_final: 0.6645 (p0) REVERT: I 524 ILE cc_start: 0.9083 (tp) cc_final: 0.8753 (tp) REVERT: I 562 GLU cc_start: 0.8341 (tm-30) cc_final: 0.8111 (tm-30) REVERT: I 788 SER cc_start: 0.9199 (m) cc_final: 0.8850 (p) REVERT: I 825 GLU cc_start: 0.7874 (pt0) cc_final: 0.7671 (pt0) REVERT: I 1085 MET cc_start: 0.8988 (mmm) cc_final: 0.8531 (mmm) REVERT: I 1243 MET cc_start: 0.6896 (ttm) cc_final: 0.6664 (mtp) REVERT: I 1244 HIS cc_start: 0.6812 (OUTLIER) cc_final: 0.5413 (t70) REVERT: I 1339 LEU cc_start: 0.8696 (mt) cc_final: 0.8289 (mt) REVERT: J 96 LYS cc_start: 0.8336 (ttmt) cc_final: 0.8101 (mtmt) REVERT: J 97 VAL cc_start: 0.7578 (t) cc_final: 0.7339 (t) REVERT: J 100 GLU cc_start: 0.8274 (mp0) cc_final: 0.7784 (mp0) REVERT: J 115 TRP cc_start: 0.8481 (m-10) cc_final: 0.8268 (m-10) REVERT: J 137 ARG cc_start: 0.8377 (mtp-110) cc_final: 0.8007 (ptp90) REVERT: J 180 MET cc_start: 0.7230 (tpp) cc_final: 0.6585 (tpt) REVERT: J 330 MET cc_start: 0.7560 (ptm) cc_final: 0.7246 (ptm) REVERT: J 375 GLU cc_start: 0.7872 (mp0) cc_final: 0.7528 (mp0) REVERT: J 382 TYR cc_start: 0.9084 (m-10) cc_final: 0.8884 (m-80) REVERT: J 398 LYS cc_start: 0.8360 (mptt) cc_final: 0.8101 (mppt) REVERT: J 796 LEU cc_start: 0.9518 (tp) cc_final: 0.9221 (tp) REVERT: J 1123 ARG cc_start: 0.8324 (mtt180) cc_final: 0.8038 (mmm160) REVERT: J 1155 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8624 (mp) REVERT: J 1254 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7648 (mt-10) REVERT: J 1370 MET cc_start: 0.7819 (mmp) cc_final: 0.7127 (mmt) REVERT: K 41 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8200 (pp20) REVERT: K 69 ARG cc_start: 0.8785 (mtp-110) cc_final: 0.8435 (ttm110) REVERT: K 74 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7295 (tp30) outliers start: 80 outliers final: 62 residues processed: 382 average time/residue: 0.3866 time to fit residues: 238.2583 Evaluate side-chains 372 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 305 time to evaluate : 3.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 229 GLU Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 423 ASP Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 486 THR Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 1040 ASP Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 495 ASN Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 516 ASP Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1089 LEU Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain K residue 62 GLN Chi-restraints excluded: chain K residue 74 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 305 optimal weight: 2.9990 chunk 186 optimal weight: 7.9990 chunk 145 optimal weight: 7.9990 chunk 212 optimal weight: 0.9980 chunk 320 optimal weight: 40.0000 chunk 295 optimal weight: 0.0570 chunk 255 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 197 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 202 optimal weight: 1.9990 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 824 GLN ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1366 HIS K 15 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27432 Z= 0.208 Angle : 0.582 12.197 37487 Z= 0.298 Chirality : 0.041 0.200 4317 Planarity : 0.004 0.049 4558 Dihedral : 15.924 174.301 4692 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.96 % Allowed : 20.84 % Favored : 76.19 % 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: 0.71 (0.15), residues: 3152 helix: 1.42 (0.15), residues: 1141 sheet: 0.51 (0.27), residues: 380 loop : -0.15 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP I1276 HIS 0.004 0.001 HIS J1366 PHE 0.037 0.001 PHE G 35 TYR 0.025 0.001 TYR G 185 ARG 0.011 0.000 ARG K 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 309 time to evaluate : 3.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 137 ASN cc_start: 0.8868 (t0) cc_final: 0.8400 (t0) REVERT: H 37 HIS cc_start: 0.8010 (OUTLIER) cc_final: 0.7667 (t-90) REVERT: H 104 LYS cc_start: 0.7231 (mmmt) cc_final: 0.6983 (tttt) REVERT: H 185 TYR cc_start: 0.8955 (p90) cc_final: 0.8629 (p90) REVERT: I 213 LEU cc_start: 0.8808 (mt) cc_final: 0.8606 (mp) REVERT: I 422 LYS cc_start: 0.7618 (mptt) cc_final: 0.6894 (mptt) REVERT: I 515 MET cc_start: 0.7678 (tpp) cc_final: 0.7425 (tpp) REVERT: I 516 ASP cc_start: 0.7509 (p0) cc_final: 0.6494 (p0) REVERT: I 562 GLU cc_start: 0.8350 (tm-30) cc_final: 0.8105 (tm-30) REVERT: I 788 SER cc_start: 0.9251 (m) cc_final: 0.8910 (p) REVERT: I 1085 MET cc_start: 0.9018 (mmm) cc_final: 0.8553 (mmm) REVERT: I 1244 HIS cc_start: 0.6875 (OUTLIER) cc_final: 0.5415 (t70) REVERT: I 1329 GLU cc_start: 0.7490 (mt-10) cc_final: 0.6852 (mt-10) REVERT: I 1339 LEU cc_start: 0.8785 (mt) cc_final: 0.8385 (mt) REVERT: J 96 LYS cc_start: 0.8370 (ttmt) cc_final: 0.8127 (mtmt) REVERT: J 97 VAL cc_start: 0.7597 (t) cc_final: 0.7347 (t) REVERT: J 100 GLU cc_start: 0.8219 (mp0) cc_final: 0.7739 (mp0) REVERT: J 115 TRP cc_start: 0.8593 (m-10) cc_final: 0.8313 (m-10) REVERT: J 137 ARG cc_start: 0.8324 (mtp-110) cc_final: 0.7999 (ptp90) REVERT: J 180 MET cc_start: 0.7171 (tpp) cc_final: 0.6524 (tpt) REVERT: J 330 MET cc_start: 0.7607 (ptm) cc_final: 0.7243 (ptm) REVERT: J 382 TYR cc_start: 0.9089 (m-10) cc_final: 0.8872 (m-80) REVERT: J 398 LYS cc_start: 0.8374 (mptt) cc_final: 0.8101 (mppt) REVERT: J 1123 ARG cc_start: 0.8346 (mtt180) cc_final: 0.8053 (mmm160) REVERT: J 1155 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8663 (mp) REVERT: J 1254 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7808 (mt-10) REVERT: J 1370 MET cc_start: 0.7863 (mmp) cc_final: 0.7170 (mmt) REVERT: K 69 ARG cc_start: 0.8838 (mtp-110) cc_final: 0.8447 (ttm110) REVERT: K 74 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7268 (tp30) outliers start: 80 outliers final: 67 residues processed: 365 average time/residue: 0.3804 time to fit residues: 224.4920 Evaluate side-chains 366 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 295 time to evaluate : 3.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 229 GLU Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 315 MET Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 423 ASP Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 486 THR Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 871 VAL Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 1040 ASP Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 495 ASN Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 516 ASP Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1089 LEU Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 62 GLN Chi-restraints excluded: chain K residue 74 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 272 optimal weight: 7.9990 chunk 78 optimal weight: 20.0000 chunk 235 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 255 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 262 optimal weight: 0.6980 chunk 32 optimal weight: 20.0000 chunk 47 optimal weight: 0.8980 chunk 224 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 510 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 824 GLN ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1366 HIS K 15 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.109470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.082868 restraints weight = 71300.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.085295 restraints weight = 36082.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.086895 restraints weight = 23165.367| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27432 Z= 0.228 Angle : 0.605 13.648 37487 Z= 0.309 Chirality : 0.041 0.190 4317 Planarity : 0.004 0.052 4558 Dihedral : 15.959 174.260 4692 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.89 % Allowed : 21.29 % Favored : 75.82 % 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: 0.69 (0.15), residues: 3152 helix: 1.42 (0.15), residues: 1136 sheet: 0.52 (0.27), residues: 375 loop : -0.19 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP I1276 HIS 0.004 0.001 HIS I 447 PHE 0.029 0.001 PHE I1025 TYR 0.024 0.001 TYR G 185 ARG 0.015 0.000 ARG J 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5804.84 seconds wall clock time: 106 minutes 7.98 seconds (6367.98 seconds total)