Starting phenix.real_space_refine on Thu May 29 01:08:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8to1_41433/05_2025/8to1_41433.cif Found real_map, /net/cci-nas-00/data/ceres_data/8to1_41433/05_2025/8to1_41433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8to1_41433/05_2025/8to1_41433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8to1_41433/05_2025/8to1_41433.map" model { file = "/net/cci-nas-00/data/ceres_data/8to1_41433/05_2025/8to1_41433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8to1_41433/05_2025/8to1_41433.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.081 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 70 5.49 5 Mg 1 5.21 5 S 131 5.16 5 C 19491 2.51 5 N 5544 2.21 5 O 6147 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 31386 Number of models: 1 Model: "" Number of chains: 12 Chain: "G" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1773 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 222} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "H" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1669 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "I" Number of atoms: 10514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10514 Classifications: {'peptide': 1337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1280} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "J" Number of atoms: 10395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1338, 10395 Classifications: {'peptide': 1338} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1281} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "L" Number of atoms: 4334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4334 Classifications: {'peptide': 551} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 16, 'TRANS': 534} Chain breaks: 3 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 6, 'GLU:plan': 11, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 103 Chain: "M" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 572 Classifications: {'peptide': 73} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 68} Chain: "O" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 736 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "P" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 701 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "I" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Unusual residues: {'4QM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'4QM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14405 SG CYS J 70 104.243 69.520 74.407 1.00 95.41 S ATOM 14419 SG CYS J 72 102.281 66.441 72.773 1.00107.85 S ATOM 14527 SG CYS J 85 105.407 67.726 71.902 1.00 99.57 S ATOM 14551 SG CYS J 88 102.644 69.923 71.579 1.00104.03 S ATOM 20239 SG CYS J 814 133.357 120.061 110.536 1.00 48.56 S ATOM 20804 SG CYS J 888 129.878 119.176 109.198 1.00 39.24 S ATOM 20855 SG CYS J 895 131.058 117.636 112.350 1.00 42.48 S ATOM 20876 SG CYS J 898 130.328 120.812 112.454 1.00 45.34 S Time building chain proxies: 19.50, per 1000 atoms: 0.62 Number of scatterers: 31386 At special positions: 0 Unit cell: (155.296, 193.276, 195.808, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 131 16.00 P 70 15.00 Mg 1 11.99 O 6147 8.00 N 5544 7.00 C 19491 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 - 3.00 Amino acid : True - 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: 8.56 Conformation dependent library (CDL) restraints added in 3.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " Number of angles added : 12 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7102 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 50 sheets defined 43.1% alpha, 13.7% beta 34 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 12.58 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.561A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.823A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 159 Processing helix chain 'G' and resid 212 through 233 removed outlier: 3.663A pdb=" N GLU G 226 " --> pdb=" O THR G 222 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP G 233 " --> pdb=" O GLU G 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.598A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 87 Processing helix chain 'H' and resid 111 through 115 Processing helix chain 'H' and resid 212 through 226 removed outlier: 3.629A pdb=" N ILE H 223 " --> pdb=" O ARG H 219 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 39 removed outlier: 3.844A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE I 35 " --> pdb=" O GLN I 31 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN I 36 " --> pdb=" O LEU I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.822A 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 270 through 280 Processing helix chain 'I' and resid 288 through 294 removed outlier: 4.215A pdb=" N GLY I 294 " --> pdb=" O TYR I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 328 Processing helix chain 'I' and resid 346 through 353 removed outlier: 3.501A pdb=" N THR I 350 " --> pdb=" O TYR I 346 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 389 removed outlier: 3.772A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 407 Processing helix chain 'I' and resid 421 through 437 Processing helix chain 'I' and resid 455 through 480 Processing helix chain 'I' and resid 494 through 508 removed outlier: 4.477A pdb=" N ILE I 498 " --> pdb=" O ASN I 494 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA I 501 " --> pdb=" O PRO I 497 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL I 502 " --> pdb=" O ILE I 498 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.537A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 648 through 650 No H-bonds generated for 'chain 'I' and resid 648 through 650' Processing helix chain 'I' and resid 664 through 668 removed outlier: 3.544A pdb=" N LEU I 667 " --> pdb=" O GLY I 664 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 664 through 668' Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 687 Processing helix chain 'I' and resid 704 through 711 Processing helix chain 'I' and resid 738 through 741 removed outlier: 3.740A pdb=" N MET I 741 " --> pdb=" O GLU I 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 738 through 741' Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 896 through 907 removed outlier: 3.769A pdb=" N LEU I 901 " --> pdb=" O PRO I 897 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 979 Processing helix chain 'I' and resid 1006 through 1034 removed outlier: 3.546A pdb=" N GLN I1010 " --> pdb=" O GLU I1006 " (cutoff:3.500A) Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 4.450A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG I1106 " --> pdb=" O GLY I1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1101 through 1106' Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.537A pdb=" N LEU I1113 " --> pdb=" O ILE I1109 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE I1128 " --> pdb=" O ILE I1124 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1149 removed outlier: 3.585A pdb=" N TYR I1149 " --> pdb=" O ILE I1145 " (cutoff:3.500A) Processing helix chain 'I' and resid 1166 through 1176 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1242 Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1283 through 1292 Processing helix chain 'I' and resid 1297 through 1309 removed outlier: 3.950A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS I1303 " --> pdb=" O ASN I1299 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.684A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU I1326 " --> pdb=" O SER I1322 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 58 through 63 removed outlier: 3.750A pdb=" N PHE J 62 " --> pdb=" O CYS J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 Processing helix chain 'J' and resid 113 through 119 Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 170 Processing helix chain 'J' and resid 181 through 192 Processing helix chain 'J' and resid 193 through 207 removed outlier: 3.534A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU J 207 " --> pdb=" O GLU J 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 231 removed outlier: 3.760A pdb=" N GLY J 231 " --> pdb=" O PHE J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 255 through 259 removed outlier: 3.693A pdb=" N GLY J 258 " --> pdb=" O LEU J 255 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG J 259 " --> pdb=" O ASP J 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 255 through 259' Processing helix chain 'J' and resid 263 through 285 removed outlier: 4.256A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 removed outlier: 3.541A pdb=" N VAL J 292 " --> pdb=" O PRO J 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 327 through 331 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 416 removed outlier: 3.853A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (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 452 No H-bonds generated for 'chain 'J' and resid 450 through 452' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 573 through 580 Processing helix chain 'J' and resid 581 through 583 No H-bonds generated for 'chain 'J' and resid 581 through 583' Processing helix chain 'J' and resid 597 through 612 removed outlier: 3.668A pdb=" N ILE J 601 " --> pdb=" O GLY J 597 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER J 602 " --> pdb=" O LYS J 598 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.710A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 702 removed outlier: 3.591A pdb=" N ASN J 680 " --> pdb=" O GLY J 676 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 removed outlier: 3.522A pdb=" N GLN J 739 " --> pdb=" O ALA J 735 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 805 removed outlier: 4.077A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA J 787 " --> pdb=" O LEU J 783 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU J 788 " --> pdb=" O ALA J 784 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 removed outlier: 3.893A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 884 through 888 Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 914 through 925 Processing helix chain 'J' and resid 926 through 928 No H-bonds generated for 'chain 'J' and resid 926 through 928' Processing helix chain 'J' and resid 1068 through 1074 removed outlier: 3.626A pdb=" N LEU J1074 " --> pdb=" O GLY J1070 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1146 Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1226 through 1244 removed outlier: 3.775A pdb=" N TYR J1232 " --> pdb=" O ALA J1228 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR J1241 " --> pdb=" O VAL J1237 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1261 removed outlier: 3.772A pdb=" N ILE J1256 " --> pdb=" O HIS J1252 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 removed outlier: 3.696A pdb=" N ILE J1287 " --> pdb=" O SER J1283 " (cutoff:3.500A) Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1326 removed outlier: 3.981A pdb=" N PHE J1325 " --> pdb=" O SER J1321 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1338 Processing helix chain 'J' and resid 1346 through 1354 removed outlier: 3.564A pdb=" N ASN J1350 " --> pdb=" O GLY J1346 " (cutoff:3.500A) Processing helix chain 'J' and resid 1362 through 1375 removed outlier: 3.511A pdb=" N HIS J1366 " --> pdb=" O GLY J1362 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 15 through 32 Processing helix chain 'K' and resid 45 through 56 removed outlier: 3.781A pdb=" N GLU K 56 " --> pdb=" O ARG K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 74 Processing helix chain 'L' and resid 8 through 20 removed outlier: 3.502A pdb=" N ARG L 15 " --> pdb=" O LEU L 11 " (cutoff:3.500A) Processing helix chain 'L' and resid 23 through 31 Processing helix chain 'L' and resid 38 through 52 removed outlier: 4.058A pdb=" N MET L 51 " --> pdb=" O MET L 47 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 90 removed outlier: 3.606A pdb=" N GLU L 88 " --> pdb=" O LEU L 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 106 Processing helix chain 'L' and resid 114 through 137 removed outlier: 3.620A pdb=" N ASP L 118 " --> pdb=" O GLU L 114 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE L 119 " --> pdb=" O GLY L 115 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR L 137 " --> pdb=" O SER L 133 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 153 removed outlier: 4.001A pdb=" N TYR L 143 " --> pdb=" O GLU L 139 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 162 removed outlier: 3.596A pdb=" N LEU L 161 " --> pdb=" O ARG L 157 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE L 162 " --> pdb=" O LEU L 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 157 through 162' Processing helix chain 'L' and resid 213 through 233 removed outlier: 3.532A pdb=" N ASP L 233 " --> pdb=" O VAL L 229 " (cutoff:3.500A) Processing helix chain 'L' and resid 244 through 258 removed outlier: 3.788A pdb=" N GLN L 258 " --> pdb=" O GLU L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 292 Processing helix chain 'L' and resid 298 through 310 removed outlier: 3.588A pdb=" N PHE L 302 " --> pdb=" O PRO L 298 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR L 307 " --> pdb=" O ILE L 303 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N GLY L 308 " --> pdb=" O THR L 304 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASN L 309 " --> pdb=" O LEU L 305 " (cutoff:3.500A) Processing helix chain 'L' and resid 316 through 320 Processing helix chain 'L' and resid 324 through 330 Processing helix chain 'L' and resid 333 through 352 Processing helix chain 'L' and resid 354 through 386 Processing helix chain 'L' and resid 387 through 393 removed outlier: 3.703A pdb=" N LYS L 393 " --> pdb=" O SER L 389 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 418 Processing helix chain 'L' and resid 426 through 431 Processing helix chain 'L' and resid 431 through 446 removed outlier: 3.806A pdb=" N ARG L 436 " --> pdb=" O THR L 432 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 473 Processing helix chain 'L' and resid 479 through 487 Processing helix chain 'L' and resid 491 through 498 Processing helix chain 'L' and resid 518 through 523 removed outlier: 3.700A pdb=" N ILE L 523 " --> pdb=" O GLY L 520 " (cutoff:3.500A) Processing helix chain 'L' and resid 530 through 550 removed outlier: 4.014A pdb=" N HIS L 545 " --> pdb=" O ARG L 541 " (cutoff:3.500A) Processing helix chain 'L' and resid 552 through 564 Processing helix chain 'L' and resid 572 through 581 removed outlier: 3.520A pdb=" N VAL L 576 " --> pdb=" O THR L 572 " (cutoff:3.500A) Processing helix chain 'L' and resid 584 through 600 Processing helix chain 'L' and resid 604 through 610 Processing helix chain 'M' and resid 256 through 261 Processing helix chain 'M' and resid 263 through 274 Processing helix chain 'M' and resid 277 through 283 removed outlier: 3.835A pdb=" N GLN M 283 " --> pdb=" O GLY M 279 " (cutoff:3.500A) Processing helix chain 'M' and resid 285 through 291 Processing helix chain 'M' and resid 296 through 310 removed outlier: 3.539A pdb=" N ARG M 310 " --> pdb=" O VAL M 306 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 13 through 16 removed outlier: 8.764A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (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: 4.481A pdb=" N THR G 101 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.757A 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: 6.557A pdb=" N GLY G 108 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N HIS G 132 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL G 110 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 14 through 20 removed outlier: 6.494A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLU H 204 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE H 183 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 14 through 20 removed outlier: 6.494A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 52 through 61 removed outlier: 5.606A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ALA H 138 " --> pdb=" O GLY H 106 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY H 106 " --> pdb=" O ALA H 138 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 90 through 91 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: 6.754A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 59 through 60 removed outlier: 7.021A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 4.250A 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 Processing sheet with id=AB6, first strand: chain 'I' and resid 154 through 156 Processing sheet with id=AB7, first strand: chain 'I' and resid 187 through 189 removed outlier: 3.655A pdb=" N ASN I 193 " --> pdb=" O ASP I 189 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 227 through 230 Processing sheet with id=AB9, first strand: chain 'I' and resid 238 through 240 Processing sheet with id=AC1, first strand: chain 'I' and resid 296 through 297 removed outlier: 3.899A pdb=" N MET I 315 " --> pdb=" O VAL I 297 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 301 through 303 removed outlier: 6.875A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.379A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.574A pdb=" N ILE I 616 " --> pdb=" O ARG I 637 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.142A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.243A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC8, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC9, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 6.996A pdb=" N ILE I 816 " --> pdb=" O LYS I1078 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ASN I1080 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL I 818 " --> pdb=" O ASN I1080 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 846 through 847 removed outlier: 6.255A pdb=" N THR I 830 " --> pdb=" O LYS I1057 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS I1057 " --> pdb=" O THR I 830 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N HIS I 832 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ALA I1055 " --> pdb=" O HIS I 832 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLN I 834 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR I1053 " --> pdb=" O GLN I 834 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 849 through 850 Processing sheet with id=AD3, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.891A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 7.840A pdb=" N ALA J 446 " --> pdb=" O PRO J 369 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 1268 through 1270 removed outlier: 3.575A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS J 345 " --> pdb=" O PHE I1270 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 1335 through 1341 removed outlier: 4.053A pdb=" N ALA J 19 " --> pdb=" O GLU I1340 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.603A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.414A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 159 through 160 Processing sheet with id=AD9, first strand: chain 'J' and resid 261 through 262 Processing sheet with id=AE1, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AE2, first strand: chain 'J' and resid 703 through 705 Processing sheet with id=AE3, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AE4, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE5, first strand: chain 'J' and resid 825 through 826 removed outlier: 7.194A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS J 832 " --> pdb=" O VAL J 825 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.626A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 959 through 961 Processing sheet with id=AE8, first strand: chain 'J' and resid 1002 through 1003 removed outlier: 3.765A pdb=" N VAL J1002 " --> pdb=" O ASN J1019 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN J1019 " --> pdb=" O VAL J1002 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'J' and resid 1025 through 1028 removed outlier: 3.544A pdb=" N ALA J1122 " --> pdb=" O VAL J1027 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 1034 through 1035 Processing sheet with id=AF2, first strand: chain 'J' and resid 1046 through 1048 Processing sheet with id=AF3, first strand: chain 'J' and resid 1161 through 1162 Processing sheet with id=AF4, first strand: chain 'J' and resid 1172 through 1175 removed outlier: 3.590A pdb=" N LEU J1175 " --> pdb=" O GLU J1188 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU J1188 " --> pdb=" O LEU J1175 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.645A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1300 hydrogen bonds defined for protein. 3693 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 86 hydrogen bonds 172 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 16.66 Time building geometry restraints manager: 9.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5315 1.31 - 1.44: 7823 1.44 - 1.57: 18465 1.57 - 1.70: 153 1.70 - 1.82: 239 Bond restraints: 31995 Sorted by residual: bond pdb=" C PRO H 52 " pdb=" N GLY H 53 " ideal model delta sigma weight residual 1.327 1.589 -0.262 1.15e-02 7.56e+03 5.19e+02 bond pdb=" C PHE L 427 " pdb=" N SER L 428 " ideal model delta sigma weight residual 1.332 1.607 -0.275 1.40e-02 5.10e+03 3.84e+02 bond pdb=" C SER H 178 " pdb=" N PRO H 179 " ideal model delta sigma weight residual 1.336 1.542 -0.206 1.23e-02 6.61e+03 2.82e+02 bond pdb=" C19 4QM L 701 " pdb=" C3 4QM L 701 " ideal model delta sigma weight residual 1.532 1.825 -0.293 2.00e-02 2.50e+03 2.14e+02 bond pdb=" C19 4QM I1401 " pdb=" C3 4QM I1401 " ideal model delta sigma weight residual 1.532 1.823 -0.291 2.00e-02 2.50e+03 2.12e+02 ... (remaining 31990 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.39: 43246 4.39 - 8.77: 271 8.77 - 13.16: 17 13.16 - 17.55: 4 17.55 - 21.93: 2 Bond angle restraints: 43540 Sorted by residual: angle pdb=" O PHE L 427 " pdb=" C PHE L 427 " pdb=" N SER L 428 " ideal model delta sigma weight residual 122.09 144.02 -21.93 1.04e+00 9.25e-01 4.45e+02 angle pdb=" CA PHE L 427 " pdb=" C PHE L 427 " pdb=" N SER L 428 " ideal model delta sigma weight residual 116.97 97.76 19.21 1.20e+00 6.94e-01 2.56e+02 angle pdb=" N THR I1037 " pdb=" CA THR I1037 " pdb=" C THR I1037 " ideal model delta sigma weight residual 112.59 100.14 12.45 1.22e+00 6.72e-01 1.04e+02 angle pdb=" C3' DA P 54 " pdb=" O3' DA P 54 " pdb=" P DA P 55 " ideal model delta sigma weight residual 120.20 133.79 -13.59 1.50e+00 4.44e-01 8.21e+01 angle pdb=" C PHE L 427 " pdb=" N SER L 428 " pdb=" CA SER L 428 " ideal model delta sigma weight residual 121.54 104.94 16.60 1.91e+00 2.74e-01 7.56e+01 ... (remaining 43535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.38: 19182 35.38 - 70.77: 553 70.77 - 106.15: 16 106.15 - 141.53: 7 141.53 - 176.91: 2 Dihedral angle restraints: 19760 sinusoidal: 8756 harmonic: 11004 Sorted by residual: dihedral pdb=" C TYR L 425 " pdb=" N TYR L 425 " pdb=" CA TYR L 425 " pdb=" CB TYR L 425 " ideal model delta harmonic sigma weight residual -122.60 -108.89 -13.71 0 2.50e+00 1.60e-01 3.01e+01 dihedral pdb=" CA TRP I 807 " pdb=" C TRP I 807 " pdb=" N ASN I 808 " pdb=" CA ASN I 808 " ideal model delta harmonic sigma weight residual 180.00 153.40 26.60 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" C ARG I1246 " pdb=" N ARG I1246 " pdb=" CA ARG I1246 " pdb=" CB ARG I1246 " ideal model delta harmonic sigma weight residual -122.60 -110.75 -11.85 0 2.50e+00 1.60e-01 2.25e+01 ... (remaining 19757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 4834 0.157 - 0.315: 169 0.315 - 0.472: 10 0.472 - 0.629: 8 0.629 - 0.787: 2 Chirality restraints: 5023 Sorted by residual: chirality pdb=" P DA P 54 " pdb=" OP1 DA P 54 " pdb=" OP2 DA P 54 " pdb=" O5' DA P 54 " both_signs ideal model delta sigma weight residual True 2.35 -3.13 -0.79 2.00e-01 2.50e+01 1.55e+01 chirality pdb=" P DA P 55 " pdb=" OP1 DA P 55 " pdb=" OP2 DA P 55 " pdb=" O5' DA P 55 " both_signs ideal model delta sigma weight residual True 2.35 -3.13 -0.78 2.00e-01 2.50e+01 1.52e+01 chirality pdb=" P DT O 51 " pdb=" OP1 DT O 51 " pdb=" OP2 DT O 51 " pdb=" O5' DT O 51 " both_signs ideal model delta sigma weight residual True 2.35 -2.92 -0.57 2.00e-01 2.50e+01 8.21e+00 ... (remaining 5020 not shown) Planarity restraints: 5416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE J1309 " 0.031 2.00e-02 2.50e+03 5.96e-02 3.55e+01 pdb=" C ILE J1309 " -0.103 2.00e-02 2.50e+03 pdb=" O ILE J1309 " 0.037 2.00e-02 2.50e+03 pdb=" N THR J1310 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU I 334 " -0.020 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C GLU I 334 " 0.070 2.00e-02 2.50e+03 pdb=" O GLU I 334 " -0.026 2.00e-02 2.50e+03 pdb=" N THR I 335 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR L 526 " 0.018 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C THR L 526 " -0.062 2.00e-02 2.50e+03 pdb=" O THR L 526 " 0.023 2.00e-02 2.50e+03 pdb=" N THR L 527 " 0.021 2.00e-02 2.50e+03 ... (remaining 5413 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 241 2.53 - 3.12: 24582 3.12 - 3.71: 46329 3.71 - 4.31: 66902 4.31 - 4.90: 112347 Nonbonded interactions: 250401 Sorted by model distance: nonbonded pdb=" OG1 THR I 91 " pdb=" O ILE I 138 " model vdw 1.933 3.040 nonbonded pdb=" OG1 THR L 234 " pdb=" OE1 GLU L 248 " model vdw 2.054 3.040 nonbonded pdb=" O LEU L 386 " pdb=" N ILE L 388 " model vdw 2.076 3.120 nonbonded pdb=" O PHE L 427 " pdb=" N THR L 429 " model vdw 2.083 3.120 nonbonded pdb=" OD1 ASP I 303 " pdb=" OG SER I 328 " model vdw 2.085 3.040 ... (remaining 250396 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'G' and (resid 5 through 61 or (resid 62 and (name N or name CA or name C \ or name O or name CB )) or resid 63 through 158 or resid 171 through 233)) selection = (chain 'H' and (resid 5 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 233)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.780 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: 0.040 Extract box with map and model: 1.410 Check model and map are aligned: 0.240 Set scattering table: 0.330 Process input model: 90.980 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.150 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:12.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.293 32003 Z= 0.633 Angle : 1.103 21.932 43552 Z= 0.768 Chirality : 0.073 0.787 5023 Planarity : 0.005 0.125 5416 Dihedral : 14.802 176.913 12658 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.90 % Allowed : 7.33 % Favored : 91.77 % Rotamer: Outliers : 4.78 % Allowed : 7.53 % Favored : 87.69 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.05 % 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: -1.28 (0.13), residues: 3792 helix: 0.11 (0.14), residues: 1506 sheet: -0.72 (0.25), residues: 398 loop : -1.70 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 807 HIS 0.010 0.002 HIS I 447 PHE 0.032 0.002 PHE I1265 TYR 0.031 0.002 TYR J1365 ARG 0.005 0.001 ARG H 44 Details of bonding type rmsd hydrogen bonds : bond 0.18431 ( 1379) hydrogen bonds : angle 6.89541 ( 3865) metal coordination : bond 0.13819 ( 8) metal coordination : angle 9.32040 ( 12) covalent geometry : bond 0.00976 (31995) covalent geometry : angle 1.09257 (43540) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 589 time to evaluate : 3.333 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 181 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8080 (mm-30) REVERT: H 123 ILE cc_start: 0.8671 (mm) cc_final: 0.8238 (mm) REVERT: H 157 THR cc_start: 0.7939 (m) cc_final: 0.7518 (p) REVERT: I 130 MET cc_start: 0.9322 (ttm) cc_final: 0.8991 (ttp) REVERT: I 694 ARG cc_start: 0.8200 (mtm-85) cc_final: 0.7697 (mtp85) REVERT: I 779 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7572 (ttm170) REVERT: I 820 GLU cc_start: 0.7873 (tp30) cc_final: 0.7561 (mt-10) REVERT: I 899 GLU cc_start: 0.7299 (mt-10) cc_final: 0.6709 (mt-10) REVERT: I 1018 TYR cc_start: 0.1763 (OUTLIER) cc_final: 0.0011 (t80) REVERT: I 1119 MET cc_start: 0.8139 (tpt) cc_final: 0.7738 (ttt) REVERT: I 1141 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7757 (mp) REVERT: I 1227 VAL cc_start: 0.9137 (OUTLIER) cc_final: 0.8771 (t) REVERT: I 1273 MET cc_start: 0.8869 (mtm) cc_final: 0.8613 (mtp) REVERT: I 1299 ASN cc_start: 0.7921 (p0) cc_final: 0.7667 (m110) REVERT: I 1331 ARG cc_start: 0.7809 (ttm170) cc_final: 0.7519 (mtt180) REVERT: J 66 LYS cc_start: 0.7735 (tttp) cc_final: 0.7334 (tptp) REVERT: J 76 LYS cc_start: 0.7436 (ttmt) cc_final: 0.7169 (mttm) REVERT: J 81 ARG cc_start: 0.7711 (ttp-110) cc_final: 0.7387 (ttm-80) REVERT: J 94 GLN cc_start: 0.8008 (mt0) cc_final: 0.7746 (mt0) REVERT: J 133 ARG cc_start: 0.7513 (mmm160) cc_final: 0.7227 (tpt90) REVERT: J 137 ARG cc_start: 0.6916 (mtt90) cc_final: 0.6575 (mtm-85) REVERT: J 147 ILE cc_start: 0.7382 (pt) cc_final: 0.7117 (mp) REVERT: J 259 ARG cc_start: 0.7823 (mtp180) cc_final: 0.7421 (mmp-170) REVERT: J 301 GLU cc_start: 0.7404 (tt0) cc_final: 0.7153 (tt0) REVERT: J 399 LYS cc_start: 0.7526 (mmtp) cc_final: 0.7110 (mppt) REVERT: J 416 ILE cc_start: 0.8283 (mm) cc_final: 0.8041 (pp) REVERT: J 497 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7794 (mm-30) REVERT: J 500 ILE cc_start: 0.7715 (mm) cc_final: 0.7454 (pt) REVERT: J 528 THR cc_start: 0.8698 (m) cc_final: 0.8387 (p) REVERT: J 599 LYS cc_start: 0.7729 (ptmm) cc_final: 0.7475 (mppt) REVERT: J 802 ASP cc_start: 0.8382 (m-30) cc_final: 0.8023 (m-30) REVERT: J 1231 ARG cc_start: 0.7918 (ttp80) cc_final: 0.7614 (ttp-110) REVERT: J 1334 GLU cc_start: 0.7795 (tt0) cc_final: 0.7580 (tm-30) REVERT: L 430 TYR cc_start: 0.7345 (t80) cc_final: 0.6914 (t80) REVERT: L 481 GLU cc_start: 0.8395 (tp30) cc_final: 0.8099 (tp30) REVERT: L 504 PRO cc_start: 0.8537 (OUTLIER) cc_final: 0.8312 (Cg_exo) REVERT: L 508 GLU cc_start: 0.7512 (mp0) cc_final: 0.7191 (tp30) REVERT: L 524 GLU cc_start: 0.8555 (pt0) cc_final: 0.8082 (tm-30) REVERT: L 561 MET cc_start: 0.7204 (OUTLIER) cc_final: 0.6954 (mtp) outliers start: 154 outliers final: 46 residues processed: 701 average time/residue: 1.4053 time to fit residues: 1161.6730 Evaluate side-chains 457 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 404 time to evaluate : 3.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 587 LEU Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 749 ASP Chi-restraints excluded: chain I residue 779 ARG Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 1010 GLN Chi-restraints excluded: chain I residue 1018 TYR Chi-restraints excluded: chain I residue 1081 PRO Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 338 PHE Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 413 ASP Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 1086 ASN Chi-restraints excluded: chain J residue 1095 MET Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 504 PRO Chi-restraints excluded: chain L residue 561 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 325 optimal weight: 0.9990 chunk 291 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 chunk 196 optimal weight: 30.0000 chunk 155 optimal weight: 0.6980 chunk 301 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 183 optimal weight: 5.9990 chunk 224 optimal weight: 1.9990 chunk 349 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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** H 103 ASN I 36 GLN I 150 HIS I 437 ASN I 450 ASN I 526 HIS I 628 HIS I 811 ASN I1256 GLN I1257 GLN J 164 GLN J 365 GLN J 910 ASN J 954 ASN J 979 ASN J1126 GLN J1350 ASN K 43 ASN L 464 ASN L 472 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.216037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.147542 restraints weight = 32637.440| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.90 r_work: 0.3275 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 32003 Z= 0.157 Angle : 0.648 20.059 43552 Z= 0.333 Chirality : 0.044 0.278 5023 Planarity : 0.005 0.052 5416 Dihedral : 14.168 178.931 5318 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.09 % Favored : 94.80 % Rotamer: Outliers : 3.94 % Allowed : 13.80 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.05 % 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: -0.58 (0.14), residues: 3792 helix: 0.88 (0.14), residues: 1543 sheet: -0.66 (0.24), residues: 449 loop : -1.44 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 807 HIS 0.011 0.001 HIS L 600 PHE 0.022 0.002 PHE L 427 TYR 0.019 0.001 TYR G 177 ARG 0.011 0.001 ARG I 470 Details of bonding type rmsd hydrogen bonds : bond 0.04867 ( 1379) hydrogen bonds : angle 4.75707 ( 3865) metal coordination : bond 0.01512 ( 8) metal coordination : angle 8.25947 ( 12) covalent geometry : bond 0.00338 (31995) covalent geometry : angle 0.63361 (43540) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 435 time to evaluate : 3.276 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 181 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8283 (mm-30) REVERT: H 75 GLN cc_start: 0.8002 (tm-30) cc_final: 0.7744 (tm-30) REVERT: H 157 THR cc_start: 0.7970 (m) cc_final: 0.7584 (p) REVERT: I 32 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8950 (mm) REVERT: I 151 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8352 (ttm110) REVERT: I 338 THR cc_start: 0.8295 (OUTLIER) cc_final: 0.8063 (m) REVERT: I 583 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7374 (pt0) REVERT: I 820 GLU cc_start: 0.8583 (tp30) cc_final: 0.8302 (tt0) REVERT: I 899 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7382 (mt-10) REVERT: I 955 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.6874 (tm-30) REVERT: I 1018 TYR cc_start: 0.1583 (OUTLIER) cc_final: -0.0130 (t80) REVERT: I 1034 ARG cc_start: 0.7158 (ttm-80) cc_final: 0.6826 (ttm-80) REVERT: I 1119 MET cc_start: 0.8307 (tpt) cc_final: 0.7865 (ttt) REVERT: I 1126 ASP cc_start: 0.8069 (m-30) cc_final: 0.7773 (m-30) REVERT: I 1162 SER cc_start: 0.8991 (t) cc_final: 0.8774 (p) REVERT: I 1200 LYS cc_start: 0.7679 (ttmm) cc_final: 0.7412 (mtmt) REVERT: I 1227 VAL cc_start: 0.9094 (OUTLIER) cc_final: 0.8758 (t) REVERT: I 1331 ARG cc_start: 0.8040 (ttm170) cc_final: 0.7672 (mtm180) REVERT: J 81 ARG cc_start: 0.7870 (ttp-110) cc_final: 0.7529 (ttt-90) REVERT: J 87 LYS cc_start: 0.7969 (mtpp) cc_final: 0.7698 (tttm) REVERT: J 133 ARG cc_start: 0.7933 (mmm160) cc_final: 0.7710 (tpt170) REVERT: J 137 ARG cc_start: 0.7505 (mtt90) cc_final: 0.7152 (mtm-85) REVERT: J 179 LYS cc_start: 0.7966 (mtpp) cc_final: 0.7628 (mtmt) REVERT: J 183 GLU cc_start: 0.7643 (pt0) cc_final: 0.7413 (pt0) REVERT: J 196 GLN cc_start: 0.7787 (tp40) cc_final: 0.7478 (mm110) REVERT: J 259 ARG cc_start: 0.7990 (mtp180) cc_final: 0.7715 (mmp-170) REVERT: J 281 ARG cc_start: 0.7848 (ttm170) cc_final: 0.7502 (ptp90) REVERT: J 414 GLU cc_start: 0.8299 (tt0) cc_final: 0.7807 (mt-10) REVERT: J 497 GLU cc_start: 0.8475 (mt-10) cc_final: 0.7667 (mm-30) REVERT: J 528 THR cc_start: 0.8864 (m) cc_final: 0.8540 (p) REVERT: J 846 GLU cc_start: 0.7860 (pp20) cc_final: 0.7565 (pm20) REVERT: J 1158 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7488 (tm-30) REVERT: J 1231 ARG cc_start: 0.8072 (ttp80) cc_final: 0.7724 (ttp-110) REVERT: J 1247 LYS cc_start: 0.8446 (mtpp) cc_final: 0.7502 (tptt) REVERT: J 1284 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7751 (ttt-90) REVERT: J 1289 ASN cc_start: 0.7422 (p0) cc_final: 0.7166 (p0) REVERT: J 1334 GLU cc_start: 0.8218 (tt0) cc_final: 0.7972 (tm-30) REVERT: L 105 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.7431 (ptt) REVERT: L 128 ASN cc_start: 0.9340 (t0) cc_final: 0.8912 (t0) REVERT: L 430 TYR cc_start: 0.8348 (t80) cc_final: 0.8043 (t80) REVERT: L 481 GLU cc_start: 0.8325 (tp30) cc_final: 0.8060 (tp30) REVERT: L 508 GLU cc_start: 0.7859 (mp0) cc_final: 0.7062 (tp30) REVERT: L 524 GLU cc_start: 0.8807 (pt0) cc_final: 0.8108 (pt0) REVERT: L 561 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7591 (mtp) REVERT: M 316 MET cc_start: 0.7644 (tpt) cc_final: 0.7170 (pmm) outliers start: 127 outliers final: 48 residues processed: 526 average time/residue: 1.4045 time to fit residues: 871.3107 Evaluate side-chains 436 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 377 time to evaluate : 3.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 452 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 583 GLU Chi-restraints excluded: chain I residue 587 LEU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 749 ASP Chi-restraints excluded: chain I residue 927 THR Chi-restraints excluded: chain I residue 955 GLN Chi-restraints excluded: chain I residue 1013 GLN Chi-restraints excluded: chain I residue 1018 TYR Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 338 PHE Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 413 ASP Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 663 GLU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1095 MET Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1284 ARG Chi-restraints excluded: chain J residue 1341 ARG Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 389 SER Chi-restraints excluded: chain L residue 561 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 330 optimal weight: 20.0000 chunk 228 optimal weight: 0.9990 chunk 224 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 343 optimal weight: 0.9990 chunk 240 optimal weight: 0.3980 chunk 357 optimal weight: 7.9990 chunk 327 optimal weight: 20.0000 chunk 375 optimal weight: 10.0000 chunk 294 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN H 103 ASN I 811 ASN I 955 GLN J 365 GLN J 867 GLN K 31 GLN L 131 GLN L 579 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.213213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.140230 restraints weight = 32501.193| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.85 r_work: 0.3219 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 32003 Z= 0.188 Angle : 0.631 17.755 43552 Z= 0.327 Chirality : 0.045 0.216 5023 Planarity : 0.005 0.059 5416 Dihedral : 13.679 179.713 5276 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.35 % Favored : 94.54 % Rotamer: Outliers : 4.50 % Allowed : 15.13 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.14), residues: 3792 helix: 1.09 (0.13), residues: 1544 sheet: -0.50 (0.24), residues: 421 loop : -1.42 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 807 HIS 0.008 0.001 HIS L 600 PHE 0.018 0.002 PHE I1265 TYR 0.026 0.002 TYR G 177 ARG 0.010 0.001 ARG J1369 Details of bonding type rmsd hydrogen bonds : bond 0.05016 ( 1379) hydrogen bonds : angle 4.45877 ( 3865) metal coordination : bond 0.01075 ( 8) metal coordination : angle 6.42494 ( 12) covalent geometry : bond 0.00457 (31995) covalent geometry : angle 0.62236 (43540) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 392 time to evaluate : 3.466 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 25 LYS cc_start: 0.8651 (mtpp) cc_final: 0.8353 (mttm) REVERT: G 181 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7891 (mt-10) REVERT: H 75 GLN cc_start: 0.8083 (tm-30) cc_final: 0.7770 (tm-30) REVERT: H 157 THR cc_start: 0.7925 (m) cc_final: 0.7555 (p) REVERT: I 32 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8942 (mp) REVERT: I 36 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.8024 (tm-30) REVERT: I 101 ARG cc_start: 0.6529 (ttm110) cc_final: 0.6266 (mtm110) REVERT: I 151 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8477 (ttm110) REVERT: I 315 MET cc_start: 0.7180 (mmm) cc_final: 0.6004 (mtm) REVERT: I 407 ARG cc_start: 0.7777 (ttp80) cc_final: 0.7327 (ptp-170) REVERT: I 516 ASP cc_start: 0.8446 (m-30) cc_final: 0.8071 (t0) REVERT: I 641 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7308 (mp0) REVERT: I 646 SER cc_start: 0.8601 (t) cc_final: 0.8286 (p) REVERT: I 820 GLU cc_start: 0.8586 (tp30) cc_final: 0.8278 (tt0) REVERT: I 899 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7326 (mt-10) REVERT: I 955 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.7154 (tp-100) REVERT: I 1018 TYR cc_start: 0.1568 (OUTLIER) cc_final: -0.0306 (t80) REVERT: I 1034 ARG cc_start: 0.7191 (ttm-80) cc_final: 0.6919 (ttm-80) REVERT: I 1119 MET cc_start: 0.8331 (tpt) cc_final: 0.7865 (ttt) REVERT: I 1219 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8104 (mt-10) REVERT: I 1331 ARG cc_start: 0.8193 (ttm170) cc_final: 0.7685 (mtm180) REVERT: J 81 ARG cc_start: 0.7834 (ttp-110) cc_final: 0.7486 (ttt-90) REVERT: J 118 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.7996 (mtmt) REVERT: J 133 ARG cc_start: 0.7904 (mmm160) cc_final: 0.7700 (tpt170) REVERT: J 179 LYS cc_start: 0.8032 (mtpp) cc_final: 0.7634 (mtmt) REVERT: J 183 GLU cc_start: 0.7574 (pt0) cc_final: 0.7349 (pt0) REVERT: J 259 ARG cc_start: 0.7976 (mtp180) cc_final: 0.7686 (mmp-170) REVERT: J 414 GLU cc_start: 0.8398 (tt0) cc_final: 0.7935 (mt-10) REVERT: J 497 GLU cc_start: 0.8516 (mt-10) cc_final: 0.7816 (mm-30) REVERT: J 528 THR cc_start: 0.8946 (m) cc_final: 0.8590 (p) REVERT: J 831 VAL cc_start: 0.7915 (OUTLIER) cc_final: 0.7562 (t) REVERT: J 839 VAL cc_start: 0.8830 (OUTLIER) cc_final: 0.8376 (m) REVERT: J 846 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7558 (pm20) REVERT: J 1158 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7308 (tm-30) REVERT: J 1231 ARG cc_start: 0.8061 (ttp80) cc_final: 0.7586 (ttm110) REVERT: J 1284 ARG cc_start: 0.8180 (ttt-90) cc_final: 0.7857 (ttt-90) REVERT: L 22 LEU cc_start: 0.8591 (mp) cc_final: 0.7981 (mp) REVERT: L 56 MET cc_start: 0.4631 (mtp) cc_final: 0.4379 (ptm) REVERT: L 105 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.7360 (ptt) REVERT: L 481 GLU cc_start: 0.8187 (tp30) cc_final: 0.7935 (tp30) REVERT: L 508 GLU cc_start: 0.7870 (mp0) cc_final: 0.7034 (tp30) REVERT: L 524 GLU cc_start: 0.8901 (pt0) cc_final: 0.8176 (pt0) REVERT: L 561 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7642 (mtp) REVERT: M 262 LEU cc_start: 0.8523 (pt) cc_final: 0.7720 (pp) REVERT: M 316 MET cc_start: 0.7737 (tpt) cc_final: 0.7286 (pmm) outliers start: 145 outliers final: 66 residues processed: 495 average time/residue: 1.3854 time to fit residues: 810.7617 Evaluate side-chains 439 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 359 time to evaluate : 3.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 423 ASP Chi-restraints excluded: chain I residue 452 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 587 LEU Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 740 GLU Chi-restraints excluded: chain I residue 927 THR Chi-restraints excluded: chain I residue 955 GLN Chi-restraints excluded: chain I residue 1013 GLN Chi-restraints excluded: chain I residue 1018 TYR Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1109 ILE Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 118 LYS Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 338 PHE Chi-restraints excluded: chain J residue 339 ARG Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 846 GLU Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1095 MET Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1341 ARG Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 561 MET Chi-restraints excluded: chain L residue 606 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 216 optimal weight: 0.9980 chunk 185 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 341 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 280 optimal weight: 50.0000 chunk 291 optimal weight: 0.0770 chunk 112 optimal weight: 0.5980 chunk 324 optimal weight: 30.0000 chunk 158 optimal weight: 2.9990 chunk 320 optimal weight: 20.0000 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN I 165 HIS I 450 ASN I 811 ASN J 341 ASN J 777 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.215280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.146735 restraints weight = 32749.583| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.86 r_work: 0.3255 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 32003 Z= 0.122 Angle : 0.558 12.700 43552 Z= 0.290 Chirality : 0.042 0.237 5023 Planarity : 0.004 0.050 5416 Dihedral : 13.462 179.956 5271 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.77 % Favored : 95.17 % Rotamer: Outliers : 3.22 % Allowed : 16.81 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.14), residues: 3792 helix: 1.31 (0.14), residues: 1540 sheet: -0.46 (0.25), residues: 413 loop : -1.31 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 807 HIS 0.008 0.001 HIS L 600 PHE 0.017 0.001 PHE J1319 TYR 0.017 0.001 TYR L 425 ARG 0.009 0.000 ARG J1369 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 1379) hydrogen bonds : angle 4.24171 ( 3865) metal coordination : bond 0.00631 ( 8) metal coordination : angle 4.72187 ( 12) covalent geometry : bond 0.00275 (31995) covalent geometry : angle 0.55218 (43540) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 392 time to evaluate : 3.314 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 57 THR cc_start: 0.9026 (m) cc_final: 0.8767 (p) REVERT: G 181 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7994 (mt-10) REVERT: H 75 GLN cc_start: 0.8130 (tm-30) cc_final: 0.7801 (tm-30) REVERT: H 97 GLU cc_start: 0.8280 (tt0) cc_final: 0.8063 (tt0) REVERT: H 157 THR cc_start: 0.7969 (m) cc_final: 0.7624 (p) REVERT: I 32 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8907 (mm) REVERT: I 36 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7908 (tm-30) REVERT: I 151 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8368 (ttm110) REVERT: I 203 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.7629 (ptmm) REVERT: I 471 VAL cc_start: 0.6748 (OUTLIER) cc_final: 0.6281 (m) REVERT: I 516 ASP cc_start: 0.8451 (m-30) cc_final: 0.8059 (t0) REVERT: I 641 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7225 (mp0) REVERT: I 820 GLU cc_start: 0.8591 (tp30) cc_final: 0.8276 (tt0) REVERT: I 899 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7421 (mt-10) REVERT: I 955 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7588 (tp-100) REVERT: I 1018 TYR cc_start: 0.1502 (OUTLIER) cc_final: -0.0386 (t80) REVERT: I 1034 ARG cc_start: 0.7031 (ttm-80) cc_final: 0.6767 (ttm-80) REVERT: I 1119 MET cc_start: 0.8351 (tpt) cc_final: 0.7887 (ttt) REVERT: I 1136 GLN cc_start: 0.7954 (mt0) cc_final: 0.7659 (mt0) REVERT: I 1219 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8101 (mt-10) REVERT: I 1331 ARG cc_start: 0.8162 (ttm170) cc_final: 0.7637 (mtt180) REVERT: J 81 ARG cc_start: 0.7848 (ttp-110) cc_final: 0.7481 (ttt90) REVERT: J 179 LYS cc_start: 0.8102 (mtpp) cc_final: 0.7727 (mtmt) REVERT: J 183 GLU cc_start: 0.7584 (pt0) cc_final: 0.7383 (pt0) REVERT: J 259 ARG cc_start: 0.7965 (mtp180) cc_final: 0.7645 (mmp-170) REVERT: J 281 ARG cc_start: 0.7808 (ttm170) cc_final: 0.7557 (ttm170) REVERT: J 343 LEU cc_start: 0.6300 (OUTLIER) cc_final: 0.6094 (pt) REVERT: J 414 GLU cc_start: 0.8375 (tt0) cc_final: 0.7922 (mt-10) REVERT: J 497 GLU cc_start: 0.8474 (mt-10) cc_final: 0.7710 (mm-30) REVERT: J 528 THR cc_start: 0.8928 (m) cc_final: 0.8585 (p) REVERT: J 712 GLN cc_start: 0.7043 (mp10) cc_final: 0.6757 (mm-40) REVERT: J 831 VAL cc_start: 0.7884 (p) cc_final: 0.7535 (t) REVERT: J 839 VAL cc_start: 0.8880 (OUTLIER) cc_final: 0.8427 (m) REVERT: J 846 GLU cc_start: 0.7959 (pp20) cc_final: 0.7751 (pm20) REVERT: J 1025 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.6695 (tmm) REVERT: J 1158 GLU cc_start: 0.7494 (tm-30) cc_final: 0.7040 (tm-30) REVERT: J 1247 LYS cc_start: 0.8451 (mtpp) cc_final: 0.7534 (tmtm) REVERT: J 1284 ARG cc_start: 0.8209 (ttt-90) cc_final: 0.7864 (ttt-90) REVERT: L 369 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8289 (tm-30) REVERT: L 379 MET cc_start: 0.8138 (tpt) cc_final: 0.7770 (tpt) REVERT: L 449 THR cc_start: 0.7555 (OUTLIER) cc_final: 0.7327 (p) REVERT: L 481 GLU cc_start: 0.8116 (tp30) cc_final: 0.7907 (tp30) REVERT: L 508 GLU cc_start: 0.7889 (mp0) cc_final: 0.7074 (tp30) REVERT: L 524 GLU cc_start: 0.8894 (pt0) cc_final: 0.8165 (pt0) REVERT: L 561 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7636 (mtp) REVERT: M 316 MET cc_start: 0.7605 (tpt) cc_final: 0.7268 (pmm) outliers start: 104 outliers final: 47 residues processed: 466 average time/residue: 1.4294 time to fit residues: 785.1359 Evaluate side-chains 426 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 364 time to evaluate : 3.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 203 LYS Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 423 ASP Chi-restraints excluded: chain I residue 452 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 587 LEU Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 740 GLU Chi-restraints excluded: chain I residue 927 THR Chi-restraints excluded: chain I residue 955 GLN Chi-restraints excluded: chain I residue 1013 GLN Chi-restraints excluded: chain I residue 1018 TYR Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 338 PHE Chi-restraints excluded: chain J residue 339 ARG Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 413 ASP Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 1025 MET Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1095 MET Chi-restraints excluded: chain J residue 1341 ARG Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 561 MET Chi-restraints excluded: chain L residue 606 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 46 optimal weight: 0.2980 chunk 141 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 303 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 323 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN I 811 ASN I 955 GLN J 157 GLN J 777 HIS K 31 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.213440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.140525 restraints weight = 32505.170| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.93 r_work: 0.3212 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 32003 Z= 0.165 Angle : 0.592 12.586 43552 Z= 0.307 Chirality : 0.043 0.256 5023 Planarity : 0.005 0.057 5416 Dihedral : 13.392 179.834 5263 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.41 % Favored : 94.51 % Rotamer: Outliers : 3.88 % Allowed : 16.81 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.14), residues: 3792 helix: 1.35 (0.14), residues: 1534 sheet: -0.50 (0.24), residues: 430 loop : -1.27 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 807 HIS 0.007 0.001 HIS L 600 PHE 0.017 0.001 PHE J1319 TYR 0.026 0.002 TYR G 177 ARG 0.011 0.000 ARG J1369 Details of bonding type rmsd hydrogen bonds : bond 0.04504 ( 1379) hydrogen bonds : angle 4.20934 ( 3865) metal coordination : bond 0.00787 ( 8) metal coordination : angle 4.49428 ( 12) covalent geometry : bond 0.00399 (31995) covalent geometry : angle 0.58738 (43540) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 371 time to evaluate : 3.503 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 181 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7885 (mt-10) REVERT: G 233 ASP cc_start: 0.7462 (p0) cc_final: 0.7111 (p0) REVERT: H 75 GLN cc_start: 0.8124 (tm-30) cc_final: 0.7775 (tm-30) REVERT: H 97 GLU cc_start: 0.8278 (tt0) cc_final: 0.8030 (tt0) REVERT: H 157 THR cc_start: 0.7949 (m) cc_final: 0.7594 (p) REVERT: I 32 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8966 (mp) REVERT: I 36 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7970 (tm-30) REVERT: I 151 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8417 (ttm110) REVERT: I 315 MET cc_start: 0.7368 (mmm) cc_final: 0.6040 (ptt) REVERT: I 407 ARG cc_start: 0.7789 (ttp80) cc_final: 0.7392 (ptp-170) REVERT: I 413 GLU cc_start: 0.7013 (mp0) cc_final: 0.6628 (pm20) REVERT: I 516 ASP cc_start: 0.8502 (m-30) cc_final: 0.8154 (t70) REVERT: I 641 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7321 (mp0) REVERT: I 646 SER cc_start: 0.8599 (t) cc_final: 0.8274 (p) REVERT: I 820 GLU cc_start: 0.8596 (tp30) cc_final: 0.8261 (tt0) REVERT: I 899 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7478 (mt-10) REVERT: I 1018 TYR cc_start: 0.1574 (OUTLIER) cc_final: -0.0367 (t80) REVERT: I 1119 MET cc_start: 0.8392 (tpt) cc_final: 0.7894 (ttt) REVERT: I 1136 GLN cc_start: 0.7960 (mt0) cc_final: 0.7667 (mm-40) REVERT: I 1154 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7876 (t0) REVERT: I 1219 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8122 (mt-10) REVERT: I 1331 ARG cc_start: 0.8281 (ttm170) cc_final: 0.7722 (mtt180) REVERT: J 81 ARG cc_start: 0.7871 (ttp-110) cc_final: 0.7492 (tpt-90) REVERT: J 183 GLU cc_start: 0.7671 (pt0) cc_final: 0.7433 (pt0) REVERT: J 259 ARG cc_start: 0.7977 (mtp180) cc_final: 0.7650 (mmp-170) REVERT: J 339 ARG cc_start: 0.6310 (OUTLIER) cc_final: 0.5908 (mmt90) REVERT: J 343 LEU cc_start: 0.6386 (OUTLIER) cc_final: 0.6181 (pt) REVERT: J 414 GLU cc_start: 0.8426 (tt0) cc_final: 0.8000 (mt-10) REVERT: J 497 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8288 (mt-10) REVERT: J 528 THR cc_start: 0.8943 (OUTLIER) cc_final: 0.8570 (p) REVERT: J 644 MET cc_start: 0.8811 (mtt) cc_final: 0.8570 (mtt) REVERT: J 712 GLN cc_start: 0.7157 (mp10) cc_final: 0.6831 (mm-40) REVERT: J 751 ASP cc_start: 0.7288 (OUTLIER) cc_final: 0.6971 (m-30) REVERT: J 839 VAL cc_start: 0.8880 (OUTLIER) cc_final: 0.8427 (m) REVERT: J 846 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7913 (pm20) REVERT: J 1025 MET cc_start: 0.7125 (OUTLIER) cc_final: 0.6674 (tmm) REVERT: J 1158 GLU cc_start: 0.7416 (tm-30) cc_final: 0.6952 (tm-30) REVERT: J 1284 ARG cc_start: 0.8241 (ttt-90) cc_final: 0.7869 (ttt-90) REVERT: J 1290 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.6106 (ptp90) REVERT: L 369 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8167 (tm-30) REVERT: L 379 MET cc_start: 0.8200 (tpt) cc_final: 0.7808 (tpt) REVERT: L 481 GLU cc_start: 0.8166 (tp30) cc_final: 0.7917 (tp30) REVERT: L 508 GLU cc_start: 0.7878 (mp0) cc_final: 0.7028 (tp30) REVERT: L 524 GLU cc_start: 0.8929 (pt0) cc_final: 0.8246 (pt0) REVERT: L 561 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.7683 (mtp) REVERT: M 260 LEU cc_start: 0.8765 (mp) cc_final: 0.8466 (tp) REVERT: M 316 MET cc_start: 0.7805 (tpt) cc_final: 0.7316 (pmm) outliers start: 125 outliers final: 65 residues processed: 455 average time/residue: 1.4304 time to fit residues: 769.0854 Evaluate side-chains 437 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 355 time to evaluate : 3.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 423 ASP Chi-restraints excluded: chain I residue 452 ARG Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 587 LEU Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 611 GLU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 740 GLU Chi-restraints excluded: chain I residue 927 THR Chi-restraints excluded: chain I residue 1013 GLN Chi-restraints excluded: chain I residue 1018 TYR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1109 ILE Chi-restraints excluded: chain I residue 1154 ASP Chi-restraints excluded: chain I residue 1162 SER Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 338 PHE Chi-restraints excluded: chain J residue 339 ARG Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 846 GLU Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 1025 MET Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1095 MET Chi-restraints excluded: chain J residue 1290 ARG Chi-restraints excluded: chain J residue 1341 ARG Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 561 MET Chi-restraints excluded: chain L residue 606 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 275 optimal weight: 20.0000 chunk 346 optimal weight: 50.0000 chunk 319 optimal weight: 10.0000 chunk 374 optimal weight: 50.0000 chunk 267 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 360 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 355 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN I 811 ASN J 777 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.213917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.140676 restraints weight = 32594.138| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.88 r_work: 0.3232 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 32003 Z= 0.150 Angle : 0.578 13.582 43552 Z= 0.299 Chirality : 0.043 0.268 5023 Planarity : 0.004 0.054 5416 Dihedral : 13.334 179.788 5262 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.25 % Favored : 94.70 % Rotamer: Outliers : 3.41 % Allowed : 17.80 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.05 % 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: -0.08 (0.14), residues: 3792 helix: 1.39 (0.14), residues: 1536 sheet: -0.39 (0.24), residues: 419 loop : -1.25 (0.14), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 807 HIS 0.008 0.001 HIS J 777 PHE 0.017 0.001 PHE J1319 TYR 0.023 0.001 TYR G 177 ARG 0.012 0.000 ARG J1369 Details of bonding type rmsd hydrogen bonds : bond 0.04254 ( 1379) hydrogen bonds : angle 4.15445 ( 3865) metal coordination : bond 0.00661 ( 8) metal coordination : angle 4.38990 ( 12) covalent geometry : bond 0.00358 (31995) covalent geometry : angle 0.57325 (43540) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 372 time to evaluate : 3.439 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 181 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7899 (mt-10) REVERT: G 233 ASP cc_start: 0.7389 (p0) cc_final: 0.7048 (p0) REVERT: H 75 GLN cc_start: 0.8122 (tm-30) cc_final: 0.7743 (tm-30) REVERT: H 97 GLU cc_start: 0.8307 (tt0) cc_final: 0.8069 (tt0) REVERT: H 157 THR cc_start: 0.7866 (m) cc_final: 0.7499 (p) REVERT: I 32 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8957 (mp) REVERT: I 36 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7904 (tm-30) REVERT: I 151 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8366 (ttm110) REVERT: I 315 MET cc_start: 0.7456 (mmm) cc_final: 0.6155 (ptt) REVERT: I 413 GLU cc_start: 0.6962 (mp0) cc_final: 0.6628 (pm20) REVERT: I 465 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.6309 (tmt170) REVERT: I 471 VAL cc_start: 0.6833 (OUTLIER) cc_final: 0.6480 (m) REVERT: I 516 ASP cc_start: 0.8479 (m-30) cc_final: 0.8112 (t70) REVERT: I 641 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7288 (mp0) REVERT: I 646 SER cc_start: 0.8583 (t) cc_final: 0.8248 (p) REVERT: I 820 GLU cc_start: 0.8576 (tp30) cc_final: 0.8238 (tt0) REVERT: I 899 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7411 (mt-10) REVERT: I 943 LYS cc_start: 0.7720 (mptt) cc_final: 0.7414 (mttp) REVERT: I 955 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7206 (tp-100) REVERT: I 1018 TYR cc_start: 0.1573 (OUTLIER) cc_final: -0.0399 (t80) REVERT: I 1119 MET cc_start: 0.8370 (tpt) cc_final: 0.7852 (ttt) REVERT: I 1141 LEU cc_start: 0.8045 (mt) cc_final: 0.7752 (mm) REVERT: I 1233 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.8904 (mt) REVERT: I 1331 ARG cc_start: 0.8235 (ttm170) cc_final: 0.7672 (mtt180) REVERT: J 81 ARG cc_start: 0.7841 (ttp-110) cc_final: 0.7471 (tpt-90) REVERT: J 139 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7727 (mp) REVERT: J 183 GLU cc_start: 0.7631 (pt0) cc_final: 0.7382 (pt0) REVERT: J 259 ARG cc_start: 0.7901 (mtp180) cc_final: 0.7604 (mmp-170) REVERT: J 339 ARG cc_start: 0.6417 (OUTLIER) cc_final: 0.6049 (mmt90) REVERT: J 414 GLU cc_start: 0.8398 (tt0) cc_final: 0.7961 (mt-10) REVERT: J 497 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7721 (mm-30) REVERT: J 528 THR cc_start: 0.8928 (m) cc_final: 0.8564 (p) REVERT: J 712 GLN cc_start: 0.7157 (mp10) cc_final: 0.6816 (mm-40) REVERT: J 751 ASP cc_start: 0.7309 (OUTLIER) cc_final: 0.6990 (m-30) REVERT: J 839 VAL cc_start: 0.8834 (OUTLIER) cc_final: 0.8400 (m) REVERT: J 846 GLU cc_start: 0.8130 (pp20) cc_final: 0.7916 (pm20) REVERT: J 928 THR cc_start: 0.9164 (t) cc_final: 0.8762 (m) REVERT: J 1025 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6656 (tmm) REVERT: J 1158 GLU cc_start: 0.7370 (tm-30) cc_final: 0.6815 (tm-30) REVERT: J 1284 ARG cc_start: 0.8185 (ttt-90) cc_final: 0.7799 (ttt-90) REVERT: J 1290 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.6105 (ptp90) REVERT: J 1341 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7316 (ttm-80) REVERT: L 369 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8111 (tm-30) REVERT: L 481 GLU cc_start: 0.8152 (tp30) cc_final: 0.7914 (tp30) REVERT: L 508 GLU cc_start: 0.7844 (mp0) cc_final: 0.6986 (tp30) REVERT: L 524 GLU cc_start: 0.8908 (pt0) cc_final: 0.8242 (pt0) REVERT: L 567 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.7814 (mtm) REVERT: M 316 MET cc_start: 0.7813 (tpt) cc_final: 0.7341 (pmm) outliers start: 110 outliers final: 61 residues processed: 447 average time/residue: 1.5339 time to fit residues: 804.6212 Evaluate side-chains 438 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 359 time to evaluate : 3.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 423 ASP Chi-restraints excluded: chain I residue 452 ARG Chi-restraints excluded: chain I residue 465 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 587 LEU Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 611 GLU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 740 GLU Chi-restraints excluded: chain I residue 927 THR Chi-restraints excluded: chain I residue 955 GLN Chi-restraints excluded: chain I residue 1013 GLN Chi-restraints excluded: chain I residue 1018 TYR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1109 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 338 PHE Chi-restraints excluded: chain J residue 339 ARG Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 413 ASP Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 1025 MET Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1095 MET Chi-restraints excluded: chain J residue 1290 ARG Chi-restraints excluded: chain J residue 1341 ARG Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 567 MET Chi-restraints excluded: chain L residue 606 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 58 optimal weight: 2.9990 chunk 299 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 294 optimal weight: 6.9990 chunk 135 optimal weight: 0.0370 chunk 87 optimal weight: 8.9990 chunk 107 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 342 optimal weight: 30.0000 chunk 214 optimal weight: 0.1980 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN I 450 ASN I 811 ASN J 777 HIS K 61 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.214674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.142944 restraints weight = 32690.221| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.85 r_work: 0.3246 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32003 Z= 0.132 Angle : 0.564 12.332 43552 Z= 0.293 Chirality : 0.042 0.278 5023 Planarity : 0.004 0.065 5416 Dihedral : 13.243 179.850 5257 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.12 % Favored : 94.83 % Rotamer: Outliers : 3.47 % Allowed : 18.05 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.05 % 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: -0.01 (0.14), residues: 3792 helix: 1.44 (0.14), residues: 1537 sheet: -0.34 (0.25), residues: 417 loop : -1.21 (0.14), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 807 HIS 0.008 0.001 HIS L 600 PHE 0.017 0.001 PHE J1319 TYR 0.025 0.001 TYR L 430 ARG 0.012 0.000 ARG J1369 Details of bonding type rmsd hydrogen bonds : bond 0.03974 ( 1379) hydrogen bonds : angle 4.06776 ( 3865) metal coordination : bond 0.00507 ( 8) metal coordination : angle 3.69482 ( 12) covalent geometry : bond 0.00307 (31995) covalent geometry : angle 0.56035 (43540) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 378 time to evaluate : 3.360 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 181 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7954 (mt-10) REVERT: G 233 ASP cc_start: 0.7308 (p0) cc_final: 0.6976 (p0) REVERT: H 75 GLN cc_start: 0.8105 (tm-30) cc_final: 0.7713 (tm-30) REVERT: H 97 GLU cc_start: 0.8316 (tt0) cc_final: 0.8035 (tt0) REVERT: H 157 THR cc_start: 0.7859 (m) cc_final: 0.7489 (p) REVERT: I 32 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8963 (mp) REVERT: I 36 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7842 (tm-30) REVERT: I 101 ARG cc_start: 0.6652 (ttm110) cc_final: 0.6408 (mtm110) REVERT: I 126 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8474 (mm-30) REVERT: I 151 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8340 (ttm110) REVERT: I 315 MET cc_start: 0.7480 (mmm) cc_final: 0.6217 (ptt) REVERT: I 427 ASP cc_start: 0.7415 (t0) cc_final: 0.7137 (m-30) REVERT: I 465 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.6341 (tmt170) REVERT: I 516 ASP cc_start: 0.8464 (m-30) cc_final: 0.8090 (t70) REVERT: I 641 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7281 (mp0) REVERT: I 646 SER cc_start: 0.8561 (t) cc_final: 0.8232 (p) REVERT: I 820 GLU cc_start: 0.8590 (tp30) cc_final: 0.8286 (tt0) REVERT: I 899 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7470 (mt-10) REVERT: I 943 LYS cc_start: 0.7759 (mptt) cc_final: 0.7485 (mttp) REVERT: I 955 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7224 (tp-100) REVERT: I 1018 TYR cc_start: 0.1440 (OUTLIER) cc_final: -0.0538 (t80) REVERT: I 1119 MET cc_start: 0.8386 (tpt) cc_final: 0.7887 (ttt) REVERT: I 1141 LEU cc_start: 0.8043 (mt) cc_final: 0.7795 (mm) REVERT: I 1154 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7825 (t0) REVERT: I 1233 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.8889 (mt) REVERT: I 1331 ARG cc_start: 0.8231 (ttm170) cc_final: 0.7680 (mtt180) REVERT: J 81 ARG cc_start: 0.7802 (ttp-110) cc_final: 0.7460 (tpt-90) REVERT: J 139 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7764 (mp) REVERT: J 183 GLU cc_start: 0.7663 (pt0) cc_final: 0.7420 (pt0) REVERT: J 259 ARG cc_start: 0.7894 (mtp180) cc_final: 0.7625 (mmp-170) REVERT: J 339 ARG cc_start: 0.6420 (OUTLIER) cc_final: 0.6092 (mmt90) REVERT: J 414 GLU cc_start: 0.8391 (tt0) cc_final: 0.7975 (mt-10) REVERT: J 497 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7739 (mm-30) REVERT: J 528 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8574 (p) REVERT: J 712 GLN cc_start: 0.7120 (mp10) cc_final: 0.6802 (mm-40) REVERT: J 751 ASP cc_start: 0.7245 (OUTLIER) cc_final: 0.6923 (m-30) REVERT: J 839 VAL cc_start: 0.8867 (OUTLIER) cc_final: 0.8433 (m) REVERT: J 846 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7978 (pm20) REVERT: J 928 THR cc_start: 0.9118 (t) cc_final: 0.8744 (m) REVERT: J 1025 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6722 (tmm) REVERT: J 1158 GLU cc_start: 0.7285 (tm-30) cc_final: 0.6759 (tm-30) REVERT: J 1284 ARG cc_start: 0.8227 (ttt-90) cc_final: 0.7840 (ttt-90) REVERT: J 1290 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.6128 (ptp90) REVERT: J 1341 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7312 (ttm-80) REVERT: L 369 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8116 (tm-30) REVERT: L 379 MET cc_start: 0.8193 (tpt) cc_final: 0.7780 (tpt) REVERT: L 481 GLU cc_start: 0.8170 (tp30) cc_final: 0.7922 (tp30) REVERT: L 489 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8238 (mtp) REVERT: L 524 GLU cc_start: 0.8895 (pt0) cc_final: 0.8233 (pt0) REVERT: L 567 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.7878 (mtm) REVERT: M 262 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.7675 (pp) REVERT: M 316 MET cc_start: 0.7820 (tpt) cc_final: 0.7334 (pmm) outliers start: 112 outliers final: 63 residues processed: 451 average time/residue: 1.4372 time to fit residues: 765.4957 Evaluate side-chains 446 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 361 time to evaluate : 3.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 423 ASP Chi-restraints excluded: chain I residue 452 ARG Chi-restraints excluded: chain I residue 465 ARG Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 587 LEU Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 611 GLU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 740 GLU Chi-restraints excluded: chain I residue 927 THR Chi-restraints excluded: chain I residue 955 GLN Chi-restraints excluded: chain I residue 1013 GLN Chi-restraints excluded: chain I residue 1018 TYR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1109 ILE Chi-restraints excluded: chain I residue 1154 ASP Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 338 PHE Chi-restraints excluded: chain J residue 339 ARG Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 846 GLU Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 1025 MET Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1095 MET Chi-restraints excluded: chain J residue 1290 ARG Chi-restraints excluded: chain J residue 1341 ARG Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 489 MET Chi-restraints excluded: chain L residue 567 MET Chi-restraints excluded: chain L residue 606 VAL Chi-restraints excluded: chain M residue 262 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 216 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 287 optimal weight: 0.7980 chunk 271 optimal weight: 40.0000 chunk 42 optimal weight: 3.9990 chunk 285 optimal weight: 40.0000 chunk 323 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 256 optimal weight: 0.0980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN I 811 ASN J 777 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.215560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.147013 restraints weight = 32771.866| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.91 r_work: 0.3247 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32003 Z= 0.118 Angle : 0.560 13.471 43552 Z= 0.289 Chirality : 0.041 0.272 5023 Planarity : 0.004 0.068 5416 Dihedral : 13.172 179.880 5257 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.14 % Favored : 94.80 % Rotamer: Outliers : 2.98 % Allowed : 19.13 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.14), residues: 3792 helix: 1.52 (0.14), residues: 1540 sheet: -0.32 (0.25), residues: 415 loop : -1.15 (0.14), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 807 HIS 0.008 0.001 HIS J 777 PHE 0.018 0.001 PHE J1319 TYR 0.027 0.001 TYR L 430 ARG 0.014 0.000 ARG J1369 Details of bonding type rmsd hydrogen bonds : bond 0.03733 ( 1379) hydrogen bonds : angle 4.00940 ( 3865) metal coordination : bond 0.00455 ( 8) metal coordination : angle 3.25609 ( 12) covalent geometry : bond 0.00266 (31995) covalent geometry : angle 0.55741 (43540) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 378 time to evaluate : 3.485 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 233 ASP cc_start: 0.7217 (p0) cc_final: 0.6893 (p0) REVERT: H 75 GLN cc_start: 0.8108 (tm-30) cc_final: 0.7708 (tm-30) REVERT: I 36 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7871 (tm-30) REVERT: I 37 LYS cc_start: 0.8453 (mttm) cc_final: 0.8096 (mttp) REVERT: I 101 ARG cc_start: 0.6667 (ttm110) cc_final: 0.6449 (mtm110) REVERT: I 126 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8496 (mm-30) REVERT: I 151 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8371 (ttm110) REVERT: I 238 GLN cc_start: 0.6712 (OUTLIER) cc_final: 0.6439 (tm-30) REVERT: I 315 MET cc_start: 0.7598 (mmm) cc_final: 0.6365 (ptt) REVERT: I 427 ASP cc_start: 0.7454 (t0) cc_final: 0.7244 (m-30) REVERT: I 465 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.6378 (tmt170) REVERT: I 516 ASP cc_start: 0.8491 (m-30) cc_final: 0.8115 (t70) REVERT: I 820 GLU cc_start: 0.8630 (tp30) cc_final: 0.8333 (tt0) REVERT: I 899 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7519 (mt-10) REVERT: I 943 LYS cc_start: 0.7727 (mptt) cc_final: 0.7493 (mttp) REVERT: I 955 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7343 (tp-100) REVERT: I 958 LYS cc_start: 0.7690 (ttmm) cc_final: 0.7241 (ttpp) REVERT: I 1018 TYR cc_start: 0.1407 (OUTLIER) cc_final: -0.0548 (t80) REVERT: I 1119 MET cc_start: 0.8389 (tpt) cc_final: 0.7897 (ttt) REVERT: I 1154 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7813 (t0) REVERT: I 1233 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.8903 (mt) REVERT: I 1331 ARG cc_start: 0.8240 (ttm170) cc_final: 0.7998 (mtt90) REVERT: J 81 ARG cc_start: 0.7776 (ttp-110) cc_final: 0.7459 (tpt-90) REVERT: J 183 GLU cc_start: 0.7659 (pt0) cc_final: 0.7398 (pt0) REVERT: J 259 ARG cc_start: 0.7902 (mtp180) cc_final: 0.7624 (mmp-170) REVERT: J 414 GLU cc_start: 0.8401 (tt0) cc_final: 0.7966 (mt-10) REVERT: J 497 GLU cc_start: 0.8407 (mt-10) cc_final: 0.7782 (mm-30) REVERT: J 528 THR cc_start: 0.8910 (m) cc_final: 0.8568 (p) REVERT: J 712 GLN cc_start: 0.7120 (mp10) cc_final: 0.6806 (mm-40) REVERT: J 751 ASP cc_start: 0.7163 (OUTLIER) cc_final: 0.6848 (m-30) REVERT: J 839 VAL cc_start: 0.8888 (OUTLIER) cc_final: 0.8454 (m) REVERT: J 928 THR cc_start: 0.9088 (t) cc_final: 0.8736 (m) REVERT: J 1025 MET cc_start: 0.7149 (OUTLIER) cc_final: 0.6735 (tmm) REVERT: J 1158 GLU cc_start: 0.7254 (tm-30) cc_final: 0.6715 (tm-30) REVERT: J 1284 ARG cc_start: 0.8255 (ttt-90) cc_final: 0.7877 (ttt-90) REVERT: J 1290 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.6140 (ptp90) REVERT: K 56 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8057 (mt-10) REVERT: K 61 ASN cc_start: 0.7777 (t0) cc_final: 0.7514 (t0) REVERT: L 369 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8159 (tm-30) REVERT: L 379 MET cc_start: 0.8216 (tpt) cc_final: 0.7948 (mmm) REVERT: L 481 GLU cc_start: 0.8183 (tp30) cc_final: 0.7940 (tp30) REVERT: L 524 GLU cc_start: 0.8901 (pt0) cc_final: 0.8243 (pt0) REVERT: L 567 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8135 (mtt) REVERT: M 262 LEU cc_start: 0.8441 (pt) cc_final: 0.7608 (pp) REVERT: M 316 MET cc_start: 0.7838 (tpt) cc_final: 0.7355 (pmm) outliers start: 96 outliers final: 59 residues processed: 444 average time/residue: 1.4691 time to fit residues: 771.5415 Evaluate side-chains 435 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 363 time to evaluate : 3.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 238 GLN Chi-restraints excluded: chain I residue 365 GLU Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 452 ARG Chi-restraints excluded: chain I residue 465 ARG Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 587 LEU Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 611 GLU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 740 GLU Chi-restraints excluded: chain I residue 811 ASN Chi-restraints excluded: chain I residue 927 THR Chi-restraints excluded: chain I residue 955 GLN Chi-restraints excluded: chain I residue 1005 GLU Chi-restraints excluded: chain I residue 1013 GLN Chi-restraints excluded: chain I residue 1018 TYR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1154 ASP Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 338 PHE Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 1025 MET Chi-restraints excluded: chain J residue 1039 ASP Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1095 MET Chi-restraints excluded: chain J residue 1290 ARG Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 487 MET Chi-restraints excluded: chain L residue 567 MET Chi-restraints excluded: chain L residue 606 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 51 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 314 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 259 optimal weight: 4.9990 chunk 269 optimal weight: 8.9990 chunk 364 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 336 optimal weight: 50.0000 chunk 344 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN I 450 ASN I 808 ASN I 955 GLN ** J 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.210083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.134121 restraints weight = 32141.584| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.76 r_work: 0.3151 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.082 32003 Z= 0.413 Angle : 0.818 20.092 43552 Z= 0.418 Chirality : 0.055 0.342 5023 Planarity : 0.007 0.107 5416 Dihedral : 13.483 179.831 5253 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.04 % Favored : 93.86 % Rotamer: Outliers : 3.75 % Allowed : 18.82 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.13), residues: 3792 helix: 0.85 (0.13), residues: 1555 sheet: -0.59 (0.25), residues: 414 loop : -1.40 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP J 868 HIS 0.011 0.002 HIS J 777 PHE 0.021 0.003 PHE I 514 TYR 0.044 0.003 TYR G 177 ARG 0.015 0.001 ARG J1369 Details of bonding type rmsd hydrogen bonds : bond 0.06470 ( 1379) hydrogen bonds : angle 4.51050 ( 3865) metal coordination : bond 0.01436 ( 8) metal coordination : angle 6.85921 ( 12) covalent geometry : bond 0.01044 (31995) covalent geometry : angle 0.81042 (43540) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 343 time to evaluate : 3.417 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 58 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8531 (mt-10) REVERT: G 181 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7955 (mt-10) REVERT: G 233 ASP cc_start: 0.7364 (p0) cc_final: 0.6992 (p0) REVERT: I 36 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.8018 (tm-30) REVERT: I 99 LYS cc_start: 0.7750 (ttmm) cc_final: 0.7438 (ttmt) REVERT: I 151 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8433 (ttm110) REVERT: I 315 MET cc_start: 0.7580 (mmm) cc_final: 0.6394 (ptt) REVERT: I 427 ASP cc_start: 0.7507 (t0) cc_final: 0.7209 (m-30) REVERT: I 452 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8521 (mtp85) REVERT: I 516 ASP cc_start: 0.8466 (m-30) cc_final: 0.8176 (t0) REVERT: I 539 THR cc_start: 0.8385 (OUTLIER) cc_final: 0.8140 (p) REVERT: I 641 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7365 (mp0) REVERT: I 646 SER cc_start: 0.8662 (t) cc_final: 0.8340 (p) REVERT: I 820 GLU cc_start: 0.8533 (tp30) cc_final: 0.8222 (tt0) REVERT: I 899 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7621 (mt-10) REVERT: I 1018 TYR cc_start: 0.1264 (OUTLIER) cc_final: -0.0796 (t80) REVERT: I 1119 MET cc_start: 0.8466 (tpt) cc_final: 0.7949 (ttt) REVERT: I 1142 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7080 (mtm180) REVERT: I 1154 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7829 (t0) REVERT: I 1331 ARG cc_start: 0.8400 (ttm170) cc_final: 0.7917 (mtt180) REVERT: J 81 ARG cc_start: 0.7922 (ttp-110) cc_final: 0.7632 (tpt90) REVERT: J 183 GLU cc_start: 0.7838 (pt0) cc_final: 0.7622 (pt0) REVERT: J 259 ARG cc_start: 0.8013 (mtp180) cc_final: 0.7662 (mmp-170) REVERT: J 339 ARG cc_start: 0.6290 (OUTLIER) cc_final: 0.6042 (mmt90) REVERT: J 414 GLU cc_start: 0.8515 (tt0) cc_final: 0.8122 (mt-10) REVERT: J 528 THR cc_start: 0.9026 (OUTLIER) cc_final: 0.8664 (p) REVERT: J 839 VAL cc_start: 0.8913 (OUTLIER) cc_final: 0.8460 (m) REVERT: J 1025 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.6809 (tmm) REVERT: J 1158 GLU cc_start: 0.7491 (tm-30) cc_final: 0.6967 (tm-30) REVERT: J 1231 ARG cc_start: 0.8134 (ttp80) cc_final: 0.7701 (ttp-110) REVERT: J 1290 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.6146 (ptp90) REVERT: K 61 ASN cc_start: 0.7831 (t0) cc_final: 0.7593 (t0) REVERT: L 369 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8177 (tm-30) REVERT: L 481 GLU cc_start: 0.8233 (tp30) cc_final: 0.7938 (tp30) REVERT: L 567 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8198 (mtt) REVERT: M 316 MET cc_start: 0.7856 (tpt) cc_final: 0.7368 (pmm) outliers start: 121 outliers final: 71 residues processed: 429 average time/residue: 1.4816 time to fit residues: 745.5735 Evaluate side-chains 424 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 338 time to evaluate : 3.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 365 GLU Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 423 ASP Chi-restraints excluded: chain I residue 452 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 587 LEU Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 740 GLU Chi-restraints excluded: chain I residue 927 THR Chi-restraints excluded: chain I residue 1005 GLU Chi-restraints excluded: chain I residue 1013 GLN Chi-restraints excluded: chain I residue 1018 TYR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1109 ILE Chi-restraints excluded: chain I residue 1142 ARG Chi-restraints excluded: chain I residue 1154 ASP Chi-restraints excluded: chain I residue 1162 SER Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 338 PHE Chi-restraints excluded: chain J residue 339 ARG Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 1025 MET Chi-restraints excluded: chain J residue 1039 ASP Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1095 MET Chi-restraints excluded: chain J residue 1290 ARG Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 567 MET Chi-restraints excluded: chain L residue 606 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 227 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 142 optimal weight: 30.0000 chunk 70 optimal weight: 50.0000 chunk 207 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 256 optimal weight: 0.8980 chunk 279 optimal weight: 20.0000 chunk 171 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 186 ASN H 103 ASN I 811 ASN J 777 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.213304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.142929 restraints weight = 32567.223| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.85 r_work: 0.3226 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 32003 Z= 0.140 Angle : 0.610 13.762 43552 Z= 0.314 Chirality : 0.043 0.375 5023 Planarity : 0.005 0.071 5416 Dihedral : 13.303 179.955 5252 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.09 % Favored : 94.86 % Rotamer: Outliers : 2.42 % Allowed : 20.28 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.05 % 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: -0.20 (0.14), residues: 3792 helix: 1.23 (0.14), residues: 1542 sheet: -0.31 (0.25), residues: 401 loop : -1.30 (0.14), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 807 HIS 0.008 0.001 HIS J 777 PHE 0.015 0.001 PHE J1319 TYR 0.028 0.001 TYR L 430 ARG 0.015 0.000 ARG J1369 Details of bonding type rmsd hydrogen bonds : bond 0.04244 ( 1379) hydrogen bonds : angle 4.20431 ( 3865) metal coordination : bond 0.00605 ( 8) metal coordination : angle 4.90224 ( 12) covalent geometry : bond 0.00325 (31995) covalent geometry : angle 0.60443 (43540) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 344 time to evaluate : 3.761 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 233 ASP cc_start: 0.7252 (p0) cc_final: 0.6912 (p0) REVERT: I 32 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8991 (mp) REVERT: I 101 ARG cc_start: 0.6785 (ttp-170) cc_final: 0.6350 (mtm110) REVERT: I 151 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8404 (ttm110) REVERT: I 315 MET cc_start: 0.7679 (mmm) cc_final: 0.6501 (ptt) REVERT: I 427 ASP cc_start: 0.7420 (t0) cc_final: 0.7161 (m-30) REVERT: I 516 ASP cc_start: 0.8488 (m-30) cc_final: 0.8132 (t70) REVERT: I 646 SER cc_start: 0.8628 (t) cc_final: 0.8306 (p) REVERT: I 820 GLU cc_start: 0.8581 (tp30) cc_final: 0.8275 (tt0) REVERT: I 899 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7481 (mt-10) REVERT: I 943 LYS cc_start: 0.7774 (mptt) cc_final: 0.7459 (mttp) REVERT: I 955 GLN cc_start: 0.7680 (mm-40) cc_final: 0.7233 (tp-100) REVERT: I 1018 TYR cc_start: 0.1218 (OUTLIER) cc_final: -0.0886 (t80) REVERT: I 1119 MET cc_start: 0.8363 (tpt) cc_final: 0.7869 (ttt) REVERT: I 1331 ARG cc_start: 0.8227 (ttm170) cc_final: 0.7736 (mtt180) REVERT: J 81 ARG cc_start: 0.7885 (ttp-110) cc_final: 0.7564 (tpt90) REVERT: J 183 GLU cc_start: 0.7708 (pt0) cc_final: 0.7473 (pt0) REVERT: J 259 ARG cc_start: 0.7870 (mtp180) cc_final: 0.7576 (mmp-170) REVERT: J 414 GLU cc_start: 0.8471 (tt0) cc_final: 0.8063 (mt-10) REVERT: J 528 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8583 (p) REVERT: J 712 GLN cc_start: 0.7393 (mp10) cc_final: 0.6954 (mm-40) REVERT: J 839 VAL cc_start: 0.8883 (OUTLIER) cc_final: 0.8440 (m) REVERT: J 928 THR cc_start: 0.9164 (t) cc_final: 0.8752 (m) REVERT: J 1025 MET cc_start: 0.7282 (OUTLIER) cc_final: 0.6924 (tmm) REVERT: J 1158 GLU cc_start: 0.7318 (tm-30) cc_final: 0.6801 (tm-30) REVERT: J 1247 LYS cc_start: 0.8402 (mtpp) cc_final: 0.7542 (tmtm) REVERT: J 1284 ARG cc_start: 0.8245 (ttt-90) cc_final: 0.7972 (ttt-90) REVERT: J 1290 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.6074 (ptp90) REVERT: K 31 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8713 (tt0) REVERT: L 369 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8141 (tm-30) REVERT: L 481 GLU cc_start: 0.8149 (tp30) cc_final: 0.7932 (tp30) REVERT: L 524 GLU cc_start: 0.8918 (pt0) cc_final: 0.8270 (pt0) REVERT: L 567 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8211 (mtt) REVERT: M 316 MET cc_start: 0.7803 (tpt) cc_final: 0.7340 (pmm) outliers start: 78 outliers final: 58 residues processed: 402 average time/residue: 1.5447 time to fit residues: 728.3347 Evaluate side-chains 401 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 334 time to evaluate : 3.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 365 GLU Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 452 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 587 LEU Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 740 GLU Chi-restraints excluded: chain I residue 927 THR Chi-restraints excluded: chain I residue 1005 GLU Chi-restraints excluded: chain I residue 1013 GLN Chi-restraints excluded: chain I residue 1018 TYR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1162 SER Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 338 PHE Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 1025 MET Chi-restraints excluded: chain J residue 1039 ASP Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1095 MET Chi-restraints excluded: chain J residue 1168 GLU Chi-restraints excluded: chain J residue 1290 ARG Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 567 MET Chi-restraints excluded: chain L residue 606 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 258 optimal weight: 0.1980 chunk 237 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 339 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 301 optimal weight: 4.9990 chunk 329 optimal weight: 5.9990 chunk 280 optimal weight: 10.0000 chunk 335 optimal weight: 50.0000 chunk 98 optimal weight: 2.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 186 ASN H 103 ASN I 811 ASN J 777 HIS K 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.211675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.142191 restraints weight = 32466.620| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.93 r_work: 0.3187 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 32003 Z= 0.208 Angle : 0.653 14.762 43552 Z= 0.337 Chirality : 0.045 0.283 5023 Planarity : 0.005 0.074 5416 Dihedral : 13.333 179.742 5252 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.93 % Favored : 94.01 % Rotamer: Outliers : 2.57 % Allowed : 20.12 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.05 % 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: -0.27 (0.13), residues: 3792 helix: 1.15 (0.14), residues: 1548 sheet: -0.30 (0.25), residues: 402 loop : -1.34 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 807 HIS 0.010 0.001 HIS J 777 PHE 0.015 0.002 PHE J1319 TYR 0.029 0.002 TYR G 177 ARG 0.015 0.001 ARG J1369 Details of bonding type rmsd hydrogen bonds : bond 0.04875 ( 1379) hydrogen bonds : angle 4.25829 ( 3865) metal coordination : bond 0.00845 ( 8) metal coordination : angle 5.12704 ( 12) covalent geometry : bond 0.00513 (31995) covalent geometry : angle 0.64737 (43540) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31691.72 seconds wall clock time: 544 minutes 6.84 seconds (32646.84 seconds total)