Starting phenix.real_space_refine on Thu Oct 29 09:42:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oul_20203/10_2026/6oul_20203_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oul_20203/10_2026/6oul_20203.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6oul_20203/10_2026/6oul_20203_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oul_20203/10_2026/6oul_20203_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6oul_20203/10_2026/6oul_20203.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oul_20203/10_2026/6oul_20203.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 117 5.49 5 Mg 1 5.21 5 S 130 5.16 5 C 19682 2.51 5 N 5632 2.21 5 O 6363 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31927 Number of models: 1 Model: "" Number of chains: 12 Chain: "G" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1785 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 219} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1681 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 10575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10575 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 10386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10386 Classifications: {'peptide': 1337} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 5, 'PTRANS': 55, 'TRANS': 1276} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 75} Chain: "L" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3821 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 455} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "P" Number of atoms: 1253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1253 Classifications: {'DNA': 61} Link IDs: {'rna3p': 60} Chain breaks: 1 Chain: "Q" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1143 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Chain breaks: 1 Chain: "R" 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: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14490 SG CYS J 70 101.624 65.443 73.534 1.00 26.34 S ATOM 14504 SG CYS J 72 99.773 63.370 71.559 1.00 30.73 S ATOM 14612 SG CYS J 85 103.176 63.770 70.385 1.00 24.78 S ATOM 14636 SG CYS J 88 100.008 66.956 70.982 1.00 29.58 S ATOM 20324 SG CYS J 814 132.497 114.536 104.965 1.00 26.70 S ATOM 20889 SG CYS J 888 128.900 114.353 103.856 1.00 24.43 S ATOM 20940 SG CYS J 895 130.617 112.682 107.101 1.00 18.04 S ATOM 20961 SG CYS J 898 130.695 116.116 107.359 1.00 19.69 S Time building chain proxies: 6.41, per 1000 atoms: 0.20 Number of scatterers: 31927 At special positions: 0 Unit cell: (154.7, 189.8, 191.1, 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 130 16.00 P 117 15.00 Mg 1 11.99 O 6363 8.00 N 5632 7.00 C 19682 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: 2.81 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " 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 814 " Number of angles added : 12 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6966 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 51 sheets defined 40.7% alpha, 11.0% beta 53 base pairs and 93 stacking pairs defined. Time for finding SS restraints: 3.63 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.573A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 86 Processing helix chain 'G' and resid 154 through 159 Processing helix chain 'G' and resid 212 through 229 Processing helix chain 'H' and resid 34 through 50 removed outlier: 4.163A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.878A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 212 through 227 removed outlier: 4.264A pdb=" N ARG H 218 " --> pdb=" O GLU H 214 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 39 removed outlier: 3.599A pdb=" N LEU I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.968A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 292 Processing helix chain 'I' and resid 318 through 327 Processing helix chain 'I' and resid 346 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 389 removed outlier: 3.816A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 399 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 481 removed outlier: 3.604A pdb=" N MET I 459 " --> pdb=" O SER I 455 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU I 481 " --> pdb=" O GLU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 Processing helix chain 'I' and resid 519 through 525 removed outlier: 3.628A pdb=" N GLU I 523 " --> pdb=" O ASN I 519 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 686 Processing helix chain 'I' and resid 703 through 711 removed outlier: 4.691A pdb=" N ALA I 707 " --> pdb=" O GLY I 703 " (cutoff:3.500A) Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 861 through 865 removed outlier: 4.279A pdb=" N LYS I 864 " --> pdb=" O ALA I 861 " (cutoff:3.500A) Processing helix chain 'I' and resid 898 through 906 Processing helix chain 'I' and resid 942 through 981 removed outlier: 3.516A pdb=" N GLY I 970 " --> pdb=" O ILE I 966 " (cutoff:3.500A) Processing helix chain 'I' and resid 1010 through 1038 Processing helix chain 'I' and resid 1099 through 1101 No H-bonds generated for 'chain 'I' and resid 1099 through 1101' Processing helix chain 'I' and resid 1102 through 1107 Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.547A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.623A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1165 through 1176 removed outlier: 3.594A pdb=" N MET I1170 " --> pdb=" O ASP I1166 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG I1171 " --> pdb=" O GLU I1167 " (cutoff:3.500A) Processing helix chain 'I' and resid 1185 through 1189 removed outlier: 3.870A pdb=" N GLY I1189 " --> pdb=" O VAL I1186 " (cutoff:3.500A) 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 removed outlier: 3.794A pdb=" N TYR I1281 " --> pdb=" O ALA I1277 " (cutoff:3.500A) Processing helix chain 'I' and resid 1283 through 1292 Processing helix chain 'I' and resid 1299 through 1310 Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.533A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 Processing helix chain 'J' and resid 114 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 removed outlier: 3.811A pdb=" N GLU J 170 " --> pdb=" O LEU J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 192 removed outlier: 3.670A pdb=" N ALA J 184 " --> pdb=" O MET J 180 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 208 Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 233 through 236 removed outlier: 3.620A pdb=" N TRP J 236 " --> pdb=" O LYS J 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 233 through 236' Processing helix chain 'J' and resid 264 through 285 Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 326 through 332 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: 4.138A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 removed outlier: 3.514A pdb=" N GLN J 477 " --> pdb=" O THR J 473 " (cutoff:3.500A) Processing helix chain 'J' and resid 504 through 514 removed outlier: 3.541A pdb=" N LEU J 508 " --> pdb=" O GLN J 504 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 573 through 580 Processing helix chain 'J' and resid 588 through 592 removed outlier: 3.529A pdb=" N ILE J 591 " --> pdb=" O PRO J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 598 through 613 Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.587A 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 Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 741 Processing helix chain 'J' and resid 768 through 802 removed outlier: 3.979A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N THR J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR J 795 " --> pdb=" O ALA J 791 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG J 798 " --> pdb=" O GLY J 794 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 884 through 888 Processing helix chain 'J' and resid 914 through 925 removed outlier: 3.664A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) 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 1138 through 1147 Processing helix chain 'J' and resid 1216 through 1244 removed outlier: 3.571A pdb=" N GLY J1225 " --> pdb=" O LEU J1221 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL J1226 " --> pdb=" O ARG J1222 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N HIS J1227 " --> pdb=" O LEU J1223 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA J1228 " --> pdb=" O ARG J1224 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.323A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1319 through 1324 Processing helix chain 'J' and resid 1327 through 1339 removed outlier: 3.855A pdb=" N VAL J1331 " --> pdb=" O GLU J1327 " (cutoff:3.500A) Processing helix chain 'J' and resid 1347 through 1353 Processing helix chain 'J' and resid 1361 through 1373 removed outlier: 4.389A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 32 Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 77 removed outlier: 3.547A pdb=" N GLN K 75 " --> pdb=" O GLU K 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 108 removed outlier: 3.647A pdb=" N MET L 100 " --> pdb=" O ASP L 96 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU L 104 " --> pdb=" O MET L 100 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL L 108 " --> pdb=" O GLU L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 136 Processing helix chain 'L' and resid 137 through 153 removed outlier: 3.741A pdb=" N ILE L 141 " --> pdb=" O TYR L 137 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU L 144 " --> pdb=" O ALA L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 215 through 234 Processing helix chain 'L' and resid 244 through 258 removed outlier: 3.919A pdb=" N GLN L 258 " --> pdb=" O GLU L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 290 Processing helix chain 'L' and resid 298 through 307 removed outlier: 4.315A pdb=" N LEU L 305 " --> pdb=" O ASN L 301 " (cutoff:3.500A) Processing helix chain 'L' and resid 316 through 321 removed outlier: 3.884A pdb=" N ILE L 320 " --> pdb=" O PHE L 316 " (cutoff:3.500A) Processing helix chain 'L' and resid 330 through 352 removed outlier: 4.051A pdb=" N GLU L 335 " --> pdb=" O HIS L 331 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLU L 336 " --> pdb=" O ASP L 332 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG L 339 " --> pdb=" O GLU L 335 " (cutoff:3.500A) Processing helix chain 'L' and resid 355 through 392 removed outlier: 5.372A pdb=" N ARG L 385 " --> pdb=" O GLU L 381 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU L 386 " --> pdb=" O ALA L 382 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 417 Processing helix chain 'L' and resid 426 through 446 removed outlier: 3.669A pdb=" N TYR L 430 " --> pdb=" O LYS L 426 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N TRP L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TRP L 434 " --> pdb=" O TYR L 430 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 474 Processing helix chain 'L' and resid 481 through 487 removed outlier: 3.522A pdb=" N GLU L 485 " --> pdb=" O GLU L 481 " (cutoff:3.500A) Processing helix chain 'L' and resid 492 through 500 Processing helix chain 'L' and resid 518 through 523 removed outlier: 3.806A pdb=" N ILE L 523 " --> pdb=" O GLY L 520 " (cutoff:3.500A) Processing helix chain 'L' and resid 530 through 549 Processing helix chain 'L' and resid 552 through 563 Processing helix chain 'L' and resid 572 through 581 Processing helix chain 'L' and resid 583 through 600 Processing helix chain 'L' and resid 604 through 610 Processing helix chain 'R' and resid 263 through 274 Processing helix chain 'R' and resid 277 through 282 Processing helix chain 'R' and resid 285 through 291 removed outlier: 3.845A pdb=" N LEU R 289 " --> pdb=" O THR R 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 296 through 310 removed outlier: 3.834A pdb=" N LEU R 300 " --> pdb=" O GLY R 296 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 13 through 17 removed outlier: 6.422A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLU G 204 " --> pdb=" O ILE G 183 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE G 183 " --> pdb=" O GLU G 204 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLU G 206 " --> pdb=" O GLU G 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 13 through 17 removed outlier: 6.422A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU G 198 " --> pdb=" O ALA G 190 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 98 through 105 removed outlier: 3.738A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AA5, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.694A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 52 through 61 removed outlier: 3.824A pdb=" N ALA H 55 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL H 98 " --> pdb=" O VAL H 146 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AA8, first strand: chain 'H' and resid 109 through 111 removed outlier: 6.743A pdb=" N VAL H 110 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 152 through 153 removed outlier: 3.680A pdb=" N VAL H 153 " --> pdb=" O ALA H 175 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA H 175 " --> pdb=" O VAL H 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'H' and resid 180 through 183 removed outlier: 6.127A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.753A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'I' and resid 59 through 60 removed outlier: 6.481A pdb=" N LEU I 102 " --> pdb=" O ILE I 117 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE I 117 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE I 104 " --> pdb=" O LYS I 115 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 73 through 75 removed outlier: 6.292A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB6, first strand: chain 'I' and resid 147 through 148 removed outlier: 6.299A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.561A pdb=" N ALA I 174 " --> pdb=" O PHE I 186 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 227 through 228 Processing sheet with id=AB9, first strand: chain 'I' and resid 230 through 231 Processing sheet with id=AC1, first strand: chain 'I' and resid 250 through 251 removed outlier: 3.526A pdb=" N ARG I 267 " --> pdb=" O ALA I 251 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 256 through 257 Processing sheet with id=AC3, first strand: chain 'I' and resid 301 through 302 Processing sheet with id=AC4, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC5, first strand: chain 'I' and resid 599 through 603 removed outlier: 4.970A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 633 through 637 Processing sheet with id=AC7, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.429A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 748 through 751 removed outlier: 6.685A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AD1, first strand: chain 'I' and resid 798 through 803 removed outlier: 3.776A pdb=" N MET I1230 " --> pdb=" O MET I 800 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA I1067 " --> pdb=" O LEU I1233 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 798 through 803 removed outlier: 3.776A pdb=" N MET I1230 " --> pdb=" O MET I 800 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 832 through 835 Processing sheet with id=AD4, first strand: chain 'I' and resid 846 through 847 removed outlier: 6.937A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 876 through 877 Processing sheet with id=AD6, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.617A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 887 through 889 Processing sheet with id=AD8, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 3.676A pdb=" N GLN J 435 " --> pdb=" O LEU J 423 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS J 366 " --> pdb=" O GLU J 438 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 1268 through 1270 removed outlier: 3.500A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS J 345 " --> pdb=" O PHE I1270 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 1335 through 1340 removed outlier: 3.818A pdb=" N ALA J 19 " --> pdb=" O GLU I1340 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.470A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 10.175A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 9.939A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 144 through 145 Processing sheet with id=AE4, first strand: chain 'J' and resid 548 through 549 Processing sheet with id=AE5, first strand: chain 'J' and resid 555 through 556 Processing sheet with id=AE6, first strand: chain 'J' and resid 706 through 707 Processing sheet with id=AE7, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE8, first strand: chain 'J' and resid 825 through 826 removed outlier: 6.526A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 991 through 997 removed outlier: 4.017A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 965 through 966 Processing sheet with id=AF2, first strand: chain 'J' and resid 1002 through 1003 Processing sheet with id=AF3, first strand: chain 'J' and resid 1037 through 1038 Processing sheet with id=AF4, first strand: chain 'J' and resid 1106 through 1107 Processing sheet with id=AF5, first strand: chain 'J' and resid 1188 through 1190 Processing sheet with id=AF6, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.862A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1215 hydrogen bonds defined for protein. 3447 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 125 hydrogen bonds 250 hydrogen bond angles 0 basepair planarities 53 basepair parallelities 93 stacking parallelities Total time for adding SS restraints: 7.96 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8386 1.33 - 1.46: 8154 1.46 - 1.58: 15628 1.58 - 1.71: 245 1.71 - 1.84: 234 Bond restraints: 32647 Sorted by residual: bond pdb=" C19 1N7 J1504 " pdb=" C3 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.841 -0.309 2.00e-02 2.50e+03 2.38e+02 bond pdb=" C19 1N7 L 701 " pdb=" C3 1N7 L 701 " ideal model delta sigma weight residual 1.532 1.840 -0.308 2.00e-02 2.50e+03 2.38e+02 bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.832 -0.300 2.00e-02 2.50e+03 2.25e+02 bond pdb=" C3 1N7 I1401 " pdb=" C4 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.735 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C3 1N7 L 701 " pdb=" C4 1N7 L 701 " ideal model delta sigma weight residual 1.532 1.725 -0.193 2.00e-02 2.50e+03 9.32e+01 ... (remaining 32642 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 43495 3.27 - 6.53: 990 6.53 - 9.80: 98 9.80 - 13.06: 14 13.06 - 16.33: 4 Bond angle restraints: 44601 Sorted by residual: angle pdb=" N GLN I 517 " pdb=" CA GLN I 517 " pdb=" C GLN I 517 " ideal model delta sigma weight residual 109.62 119.91 -10.29 1.50e+00 4.44e-01 4.71e+01 angle pdb=" C GLU J 765 " pdb=" N GLY J 766 " pdb=" CA GLY J 766 " ideal model delta sigma weight residual 122.73 116.71 6.02 9.30e-01 1.16e+00 4.20e+01 angle pdb=" C GLY L 512 " pdb=" N ASP L 513 " pdb=" CA ASP L 513 " ideal model delta sigma weight residual 121.70 132.02 -10.32 1.80e+00 3.09e-01 3.29e+01 angle pdb=" O4' DC P 74 " pdb=" C4' DC P 74 " pdb=" C3' DC P 74 " ideal model delta sigma weight residual 106.00 102.65 3.35 6.00e-01 2.78e+00 3.12e+01 angle pdb=" C GLY J1171 " pdb=" N LYS J1172 " pdb=" CA LYS J1172 " ideal model delta sigma weight residual 121.70 131.74 -10.04 1.80e+00 3.09e-01 3.11e+01 ... (remaining 44596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.19: 19088 30.19 - 60.38: 871 60.38 - 90.57: 33 90.57 - 120.77: 2 120.77 - 150.96: 1 Dihedral angle restraints: 19995 sinusoidal: 9193 harmonic: 10802 Sorted by residual: dihedral pdb=" CA GLU J1168 " pdb=" C GLU J1168 " pdb=" N THR J1169 " pdb=" CA THR J1169 " ideal model delta harmonic sigma weight residual 180.00 120.77 59.23 0 5.00e+00 4.00e-02 1.40e+02 dihedral pdb=" CA THR J 853 " pdb=" C THR J 853 " pdb=" N ALA J 854 " pdb=" CA ALA J 854 " ideal model delta harmonic sigma weight residual 180.00 130.72 49.28 0 5.00e+00 4.00e-02 9.71e+01 dihedral pdb=" CA GLN J1326 " pdb=" C GLN J1326 " pdb=" N GLU J1327 " pdb=" CA GLU J1327 " ideal model delta harmonic sigma weight residual -180.00 -137.51 -42.49 0 5.00e+00 4.00e-02 7.22e+01 ... (remaining 19992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 4154 0.077 - 0.155: 868 0.155 - 0.232: 78 0.232 - 0.309: 11 0.309 - 0.387: 1 Chirality restraints: 5112 Sorted by residual: chirality pdb=" CA GLN I 517 " pdb=" N GLN I 517 " pdb=" C GLN I 517 " pdb=" CB GLN I 517 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" CB ILE J 442 " pdb=" CA ILE J 442 " pdb=" CG1 ILE J 442 " pdb=" CG2 ILE J 442 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CB ILE L 511 " pdb=" CA ILE L 511 " pdb=" CG1 ILE L 511 " pdb=" CG2 ILE L 511 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 5109 not shown) Planarity restraints: 5398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU J1138 " 0.025 2.00e-02 2.50e+03 4.87e-02 2.37e+01 pdb=" C LEU J1138 " -0.084 2.00e-02 2.50e+03 pdb=" O LEU J1138 " 0.031 2.00e-02 2.50e+03 pdb=" N PRO J1139 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU J1138 " -0.075 5.00e-02 4.00e+02 1.13e-01 2.05e+01 pdb=" N PRO J1139 " 0.196 5.00e-02 4.00e+02 pdb=" CA PRO J1139 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO J1139 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO J 246 " -0.064 5.00e-02 4.00e+02 9.65e-02 1.49e+01 pdb=" N PRO J 247 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO J 247 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO J 247 " -0.052 5.00e-02 4.00e+02 ... (remaining 5395 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 404 2.59 - 3.17: 29573 3.17 - 3.74: 48069 3.74 - 4.32: 69322 4.32 - 4.90: 112267 Nonbonded interactions: 259635 Sorted by model distance: nonbonded pdb=" OD1 ASN J1268 " pdb=" OG1 THR J1301 " model vdw 2.011 3.040 nonbonded pdb=" OG1 THR I 6 " pdb=" OD1 ASP I 781 " model vdw 2.020 3.040 nonbonded pdb=" O LEU L 598 " pdb=" OG SER L 604 " model vdw 2.047 3.040 nonbonded pdb=" OD2 ASP J 464 " pdb="MG MG J1501 " model vdw 2.054 2.170 nonbonded pdb=" O ILE I 11 " pdb=" OH TYR I1149 " model vdw 2.058 3.040 ... (remaining 259630 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 158 or resid 171 through 233 or (resid 234 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain 'H' and ((resid 5 through 7 and (name N or name CA or name C or name O or \ name CB )) or resid 8 through 234)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 36.630 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 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 : 0.015 0.309 32655 Z= 0.690 Angle : 1.247 35.606 44613 Z= 0.707 Chirality : 0.062 0.387 5112 Planarity : 0.007 0.113 5398 Dihedral : 15.135 150.957 13029 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 34.22 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.15 % Favored : 87.58 % Rotamer: Outliers : 0.31 % Allowed : 3.50 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.22 % Twisted Proline : 0.68 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.17 (0.11), residues: 3727 helix: -2.10 (0.11), residues: 1430 sheet: -3.45 (0.23), residues: 366 loop : -3.21 (0.12), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG I 143 TYR 0.050 0.005 TYR J 144 PHE 0.051 0.005 PHE I1187 TRP 0.039 0.005 TRP J 33 HIS 0.015 0.003 HIS I 832 Details of bonding type rmsd/Z covalent geometry : bond 0.01519 / 0.69 (32647) covalent geometry : angle 1.21257 / 0.71 (44601) hydrogen bonds : bond 0.16481 / 10.79 ( 1332) hydrogen bonds : angle 7.83552 / 5.39 ( 3697) metal coordination : bond 0.04497 / 2.78 ( 8) metal coordination : angle 17.76550 / 10.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 645 time to evaluate : 1.173 Fit side-chains revert: symmetry clash REVERT: G 130 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8663 (mt) REVERT: G 157 THR cc_start: 0.8584 (m) cc_final: 0.8175 (p) REVERT: I 158 ASP cc_start: 0.7803 (t70) cc_final: 0.7581 (t0) REVERT: I 337 PHE cc_start: 0.7891 (t80) cc_final: 0.7678 (t80) REVERT: I 369 MET cc_start: 0.8395 (tmm) cc_final: 0.8182 (ttp) REVERT: I 516 ASP cc_start: 0.8368 (t0) cc_final: 0.8098 (t70) REVERT: I 582 ASN cc_start: 0.8340 (t0) cc_final: 0.8115 (t0) REVERT: I 684 ASN cc_start: 0.9014 (OUTLIER) cc_final: 0.8696 (m-40) REVERT: I 1232 MET cc_start: 0.8452 (mtp) cc_final: 0.8186 (mtp) REVERT: J 129 ASP cc_start: 0.7748 (t70) cc_final: 0.7500 (t0) REVERT: J 137 ARG cc_start: 0.8161 (mtp180) cc_final: 0.7861 (mtm-85) REVERT: J 821 MET cc_start: 0.7322 (mmm) cc_final: 0.7077 (mmm) REVERT: L 430 TYR cc_start: 0.8730 (t80) cc_final: 0.8473 (t80) REVERT: L 507 MET cc_start: 0.8487 (ttp) cc_final: 0.8149 (ttm) outliers start: 10 outliers final: 4 residues processed: 654 average time/residue: 0.2323 time to fit residues: 232.1571 Evaluate side-chains 395 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 389 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 684 ASN Chi-restraints excluded: chain I residue 802 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 23 HIS G 132 HIS H 84 ASN H 103 ASN H 127 GLN H 208 ASN I 69 GLN I 165 HIS ** I 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 214 ASN I 273 HIS I 330 HIS ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 580 GLN I 760 ASN I 808 ASN I 856 ASN I1116 HIS ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1237 HIS I1268 GLN ** I1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 ASN J 80 HIS ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 488 ASN J 720 ASN J 817 HIS J1010 GLN J1197 ASN ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1326 GLN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 518 HIS L 600 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.177744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.139732 restraints weight = 37761.965| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.54 r_work: 0.3102 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 32655 Z= 0.205 Angle : 0.832 14.940 44613 Z= 0.424 Chirality : 0.049 0.340 5112 Planarity : 0.006 0.100 5398 Dihedral : 18.314 150.694 5638 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.54 % Favored : 92.33 % Rotamer: Outliers : 2.62 % Allowed : 9.24 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.13), residues: 3727 helix: -0.79 (0.13), residues: 1453 sheet: -3.11 (0.23), residues: 380 loop : -2.67 (0.13), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J1036 TYR 0.025 0.002 TYR L 137 PHE 0.017 0.002 PHE I 405 TRP 0.017 0.002 TRP I 807 HIS 0.007 0.001 HIS G 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 (32647) covalent geometry : angle 0.82562 / 0.42 (44601) hydrogen bonds : bond 0.05524 / 3.68 ( 1332) hydrogen bonds : angle 5.64868 / 3.86 ( 3697) metal coordination : bond 0.01551 / 0.84 ( 8) metal coordination : angle 6.49911 / 3.81 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 470 time to evaluate : 1.120 Fit side-chains revert: symmetry clash REVERT: G 181 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7816 (mp0) REVERT: H 15 ASP cc_start: 0.6697 (m-30) cc_final: 0.6379 (m-30) REVERT: I 158 ASP cc_start: 0.8360 (t70) cc_final: 0.8109 (t0) REVERT: I 169 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8047 (tttt) REVERT: I 315 MET cc_start: 0.7601 (ttm) cc_final: 0.7371 (ttp) REVERT: I 337 PHE cc_start: 0.8201 (t80) cc_final: 0.7869 (t80) REVERT: I 371 ARG cc_start: 0.7324 (mtt-85) cc_final: 0.7046 (mtt180) REVERT: I 508 SER cc_start: 0.8937 (t) cc_final: 0.8667 (p) REVERT: I 516 ASP cc_start: 0.8274 (t0) cc_final: 0.7776 (t70) REVERT: I 545 PHE cc_start: 0.7473 (t80) cc_final: 0.7127 (t80) REVERT: I 572 ILE cc_start: 0.9299 (mm) cc_final: 0.9068 (mt) REVERT: I 779 ARG cc_start: 0.8180 (ttm-80) cc_final: 0.7913 (ttp-110) REVERT: I 1041 ASP cc_start: 0.8148 (t0) cc_final: 0.7886 (m-30) REVERT: I 1171 ARG cc_start: 0.8407 (ttp80) cc_final: 0.8099 (ttm-80) REVERT: I 1304 MET cc_start: 0.8879 (tpt) cc_final: 0.8459 (tpp) REVERT: I 1338 GLU cc_start: 0.8119 (pm20) cc_final: 0.7917 (pt0) REVERT: J 77 ARG cc_start: 0.7993 (mmm-85) cc_final: 0.7762 (ttp-110) REVERT: J 96 LYS cc_start: 0.9141 (ptpt) cc_final: 0.8758 (pttp) REVERT: J 102 MET cc_start: 0.9150 (ttm) cc_final: 0.8749 (ttm) REVERT: J 129 ASP cc_start: 0.8149 (t70) cc_final: 0.7715 (t0) REVERT: J 162 GLU cc_start: 0.8180 (tp30) cc_final: 0.7975 (tp30) REVERT: J 214 ARG cc_start: 0.5204 (ttp-110) cc_final: 0.4851 (ttm110) REVERT: J 368 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8571 (tt) REVERT: J 460 ASP cc_start: 0.8460 (m-30) cc_final: 0.8145 (m-30) REVERT: J 663 GLU cc_start: 0.7252 (tm-30) cc_final: 0.6987 (mm-30) REVERT: J 788 LEU cc_start: 0.8129 (tt) cc_final: 0.7790 (tt) REVERT: J 1146 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8286 (mm-30) REVERT: J 1284 ARG cc_start: 0.7962 (mtm-85) cc_final: 0.7313 (mtp85) REVERT: L 102 MET cc_start: 0.8116 (mmm) cc_final: 0.7912 (mmm) REVERT: L 221 PHE cc_start: 0.4155 (m-80) cc_final: 0.3107 (m-80) REVERT: L 268 TYR cc_start: 0.5254 (t80) cc_final: 0.4995 (t80) REVERT: L 529 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8109 (tt0) outliers start: 84 outliers final: 47 residues processed: 528 average time/residue: 0.2011 time to fit residues: 170.5238 Evaluate side-chains 429 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 378 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 169 LYS Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 576 SER Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 730 SER Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 853 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 228 VAL Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 532 GLU Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 682 VAL Chi-restraints excluded: chain J residue 684 ASP Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 753 SER Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 1173 ARG Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain L residue 270 VAL Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 517 SER Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 529 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: [344, 268, 343, 312, 109, 146, 74, 202, 187, 96, 94] chunk 344 optimal weight: 3.9990 chunk 268 optimal weight: 0.9980 chunk 343 optimal weight: 0.5980 chunk 312 optimal weight: 0.3980 chunk 109 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 74 optimal weight: 0.4980 chunk 202 optimal weight: 5.9990 chunk 187 optimal weight: 0.2980 chunk 96 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 66 HIS H 103 ASN I 193 ASN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 383 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.190749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.151671 restraints weight = 37416.052| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 3.17 r_work: 0.3050 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 32655 Z= 0.143 Angle : 0.700 14.435 44613 Z= 0.362 Chirality : 0.045 0.245 5112 Planarity : 0.005 0.125 5398 Dihedral : 17.872 149.680 5633 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.98 % Favored : 92.92 % Rotamer: Outliers : 3.19 % Allowed : 11.15 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.13), residues: 3727 helix: -0.07 (0.13), residues: 1480 sheet: -2.84 (0.23), residues: 398 loop : -2.30 (0.13), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J1036 TYR 0.026 0.002 TYR L 430 PHE 0.018 0.002 PHE I 405 TRP 0.013 0.001 TRP I 997 HIS 0.007 0.001 HIS G 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (32647) covalent geometry : angle 0.69715 / 0.36 (44601) hydrogen bonds : bond 0.04561 / 3.08 ( 1332) hydrogen bonds : angle 5.01732 / 3.42 ( 3697) metal coordination : bond 0.00692 / 0.38 ( 8) metal coordination : angle 3.75793 / 2.17 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 406 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 50 SER cc_start: 0.9057 (OUTLIER) cc_final: 0.8496 (p) REVERT: G 123 ILE cc_start: 0.8918 (mm) cc_final: 0.8666 (mm) REVERT: G 156 SER cc_start: 0.8479 (m) cc_final: 0.8219 (t) REVERT: G 181 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7476 (mp0) REVERT: H 145 LYS cc_start: 0.7251 (tttm) cc_final: 0.6922 (tttp) REVERT: H 183 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8636 (tp) REVERT: I 81 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7469 (p0) REVERT: I 130 MET cc_start: 0.9035 (ttm) cc_final: 0.8764 (ttm) REVERT: I 299 LYS cc_start: 0.6961 (mtmt) cc_final: 0.6609 (pttt) REVERT: I 334 GLU cc_start: 0.7339 (pp20) cc_final: 0.6903 (pp20) REVERT: I 337 PHE cc_start: 0.8263 (t80) cc_final: 0.7948 (t80) REVERT: I 371 ARG cc_start: 0.7283 (mtt-85) cc_final: 0.7056 (mtt180) REVERT: I 508 SER cc_start: 0.8792 (t) cc_final: 0.8563 (p) REVERT: I 516 ASP cc_start: 0.8176 (t0) cc_final: 0.7589 (t70) REVERT: I 572 ILE cc_start: 0.9235 (mm) cc_final: 0.8981 (mt) REVERT: I 601 ASP cc_start: 0.7645 (p0) cc_final: 0.6688 (t0) REVERT: I 765 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8758 (pt) REVERT: I 1082 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8163 (mp) REVERT: I 1114 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7897 (tt0) REVERT: I 1171 ARG cc_start: 0.8371 (ttp80) cc_final: 0.7968 (ttm-80) REVERT: J 96 LYS cc_start: 0.9039 (ptpt) cc_final: 0.8641 (pttp) REVERT: J 102 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8764 (ttm) REVERT: J 129 ASP cc_start: 0.8034 (t70) cc_final: 0.7570 (t0) REVERT: J 132 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7858 (tp) REVERT: J 214 ARG cc_start: 0.5297 (ttp-110) cc_final: 0.4946 (ttm110) REVERT: J 698 MET cc_start: 0.8839 (tpt) cc_final: 0.8446 (tpt) REVERT: J 738 ARG cc_start: 0.7429 (ttm170) cc_final: 0.6854 (mtm110) REVERT: J 753 SER cc_start: 0.9108 (OUTLIER) cc_final: 0.8458 (p) REVERT: J 1095 MET cc_start: 0.2860 (ttp) cc_final: 0.2603 (ppp) REVERT: J 1115 ILE cc_start: 0.4159 (OUTLIER) cc_final: 0.3815 (pt) REVERT: J 1173 ARG cc_start: 0.6465 (OUTLIER) cc_final: 0.5819 (mtp85) REVERT: J 1284 ARG cc_start: 0.7829 (mtm-85) cc_final: 0.7603 (mpt180) REVERT: K 74 GLU cc_start: 0.5877 (mt-10) cc_final: 0.5507 (tt0) REVERT: L 221 PHE cc_start: 0.4039 (m-80) cc_final: 0.3102 (m-80) REVERT: L 268 TYR cc_start: 0.5664 (t80) cc_final: 0.5433 (t80) outliers start: 102 outliers final: 46 residues processed: 480 average time/residue: 0.1945 time to fit residues: 150.8632 Evaluate side-chains 406 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 348 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 476 LYS Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 730 SER Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1114 GLU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 228 VAL Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 684 ASP Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 753 SER Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1115 ILE Chi-restraints excluded: chain J residue 1173 ARG Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain L residue 347 ILE Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 529 GLU Chi-restraints excluded: chain L residue 609 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: [189, 43, 244, 290, 341, 373, 132, 233, 229, 195, 313] chunk 189 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 244 optimal weight: 8.9990 chunk 290 optimal weight: 9.9990 chunk 341 optimal weight: 7.9990 chunk 373 optimal weight: 40.0000 chunk 132 optimal weight: 0.9990 chunk 233 optimal weight: 4.9990 chunk 229 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 313 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 103 ASN I 193 ASN I 214 ASN I 219 GLN I1244 HIS ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.175769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.137549 restraints weight = 37729.396| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.57 r_work: 0.3069 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 32655 Z= 0.262 Angle : 0.754 15.919 44613 Z= 0.387 Chirality : 0.047 0.309 5112 Planarity : 0.005 0.088 5398 Dihedral : 17.853 149.200 5632 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.57 % Favored : 92.33 % Rotamer: Outliers : 4.06 % Allowed : 11.87 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.13), residues: 3727 helix: 0.05 (0.13), residues: 1489 sheet: -2.57 (0.24), residues: 384 loop : -2.23 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 352 TYR 0.021 0.002 TYR J 631 PHE 0.020 0.002 PHE I1025 TRP 0.010 0.002 TRP I 997 HIS 0.007 0.002 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00636 / 0.26 (32647) covalent geometry : angle 0.75116 / 0.39 (44601) hydrogen bonds : bond 0.04760 / 3.17 ( 1332) hydrogen bonds : angle 4.95069 / 3.38 ( 3697) metal coordination : bond 0.01398 / 0.85 ( 8) metal coordination : angle 3.70802 / 2.20 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 358 time to evaluate : 1.191 Fit side-chains REVERT: G 50 SER cc_start: 0.9310 (OUTLIER) cc_final: 0.8820 (p) REVERT: G 130 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8953 (mt) REVERT: G 156 SER cc_start: 0.8507 (m) cc_final: 0.8234 (t) REVERT: G 181 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: H 145 LYS cc_start: 0.7218 (tttm) cc_final: 0.6902 (tttt) REVERT: I 81 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7596 (p0) REVERT: I 299 LYS cc_start: 0.7137 (mtmt) cc_final: 0.6683 (pttt) REVERT: I 334 GLU cc_start: 0.7547 (pp20) cc_final: 0.7251 (pp20) REVERT: I 337 PHE cc_start: 0.8280 (t80) cc_final: 0.8050 (t80) REVERT: I 354 ASP cc_start: 0.7398 (t0) cc_final: 0.7195 (t0) REVERT: I 367 TYR cc_start: 0.8766 (t80) cc_final: 0.8519 (t80) REVERT: I 445 ILE cc_start: 0.7652 (OUTLIER) cc_final: 0.7441 (mm) REVERT: I 516 ASP cc_start: 0.8388 (t0) cc_final: 0.7890 (t70) REVERT: I 572 ILE cc_start: 0.9380 (mm) cc_final: 0.9093 (mt) REVERT: I 601 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.6752 (t0) REVERT: I 728 ASP cc_start: 0.8406 (t0) cc_final: 0.8206 (t0) REVERT: I 731 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8501 (ptp90) REVERT: I 765 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8782 (pt) REVERT: I 779 ARG cc_start: 0.8279 (ttm-80) cc_final: 0.7972 (ttp-110) REVERT: I 1126 ASP cc_start: 0.7746 (m-30) cc_final: 0.7533 (m-30) REVERT: I 1171 ARG cc_start: 0.8561 (ttp80) cc_final: 0.8176 (ttm-80) REVERT: I 1172 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8741 (tp) REVERT: J 96 LYS cc_start: 0.9192 (ptpt) cc_final: 0.8827 (pttp) REVERT: J 129 ASP cc_start: 0.8120 (t70) cc_final: 0.7645 (t0) REVERT: J 132 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8095 (tp) REVERT: J 163 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7396 (pt0) REVERT: J 214 ARG cc_start: 0.5418 (ttp-110) cc_final: 0.5200 (ttm110) REVERT: J 227 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.7920 (t80) REVERT: J 368 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8692 (tt) REVERT: J 460 ASP cc_start: 0.8478 (m-30) cc_final: 0.8199 (m-30) REVERT: J 663 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7111 (mm-30) REVERT: J 698 MET cc_start: 0.8957 (tpt) cc_final: 0.8646 (tpt) REVERT: J 701 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8648 (tp) REVERT: J 738 ARG cc_start: 0.7776 (ttm170) cc_final: 0.7373 (mtm110) REVERT: J 753 SER cc_start: 0.9090 (OUTLIER) cc_final: 0.8513 (p) REVERT: J 1079 LYS cc_start: 0.6560 (OUTLIER) cc_final: 0.5465 (tptt) REVERT: J 1095 MET cc_start: 0.2672 (OUTLIER) cc_final: 0.2428 (ppp) REVERT: J 1115 ILE cc_start: 0.4295 (OUTLIER) cc_final: 0.3794 (pt) REVERT: J 1284 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7657 (mpt180) REVERT: L 221 PHE cc_start: 0.3927 (m-80) cc_final: 0.3090 (m-80) REVERT: L 268 TYR cc_start: 0.5398 (t80) cc_final: 0.5154 (t80) REVERT: L 356 GLU cc_start: 0.6843 (tp30) cc_final: 0.6471 (mt-10) REVERT: L 585 GLU cc_start: 0.7644 (tp30) cc_final: 0.7347 (tp30) REVERT: L 587 ILE cc_start: 0.7443 (tt) cc_final: 0.7237 (mt) outliers start: 130 outliers final: 84 residues processed: 460 average time/residue: 0.2058 time to fit residues: 152.4466 Evaluate side-chains 445 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 343 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 152 SER Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 169 LYS Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 397 LEU Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 576 SER Chi-restraints excluded: chain I residue 601 ASP Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 730 SER Chi-restraints excluded: chain I residue 731 ARG Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 853 ASP Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1098 LEU Chi-restraints excluded: chain I residue 1172 LEU 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 I residue 1254 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 228 VAL Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 682 VAL Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 753 SER Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 901 ARG Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 1079 LYS Chi-restraints excluded: chain J residue 1095 MET Chi-restraints excluded: chain J residue 1115 ILE Chi-restraints excluded: chain J residue 1173 ARG Chi-restraints excluded: chain J residue 1221 LEU Chi-restraints excluded: chain J residue 1284 ARG Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain L residue 270 VAL Chi-restraints excluded: chain L residue 379 MET Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 529 GLU Chi-restraints excluded: chain L residue 609 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: [75, 90, 115, 149, 127, 300, 3, 204, 362, 78, 0] chunk 75 optimal weight: 20.0000 chunk 90 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 300 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 362 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 147 GLN I 193 ASN I 214 ASN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.177699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.141040 restraints weight = 37625.447| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.44 r_work: 0.2980 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 32655 Z= 0.161 Angle : 0.667 15.305 44613 Z= 0.345 Chirality : 0.044 0.332 5112 Planarity : 0.005 0.083 5398 Dihedral : 17.677 148.038 5632 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.41 % Favored : 93.48 % Rotamer: Outliers : 3.47 % Allowed : 13.71 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.13), residues: 3727 helix: 0.36 (0.13), residues: 1495 sheet: -2.24 (0.25), residues: 400 loop : -2.04 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 33 TYR 0.019 0.001 TYR G 177 PHE 0.020 0.002 PHE I1025 TRP 0.010 0.001 TRP I 807 HIS 0.007 0.001 HIS G 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (32647) covalent geometry : angle 0.66462 / 0.34 (44601) hydrogen bonds : bond 0.04277 / 2.88 ( 1332) hydrogen bonds : angle 4.75193 / 3.24 ( 3697) metal coordination : bond 0.00866 / 0.51 ( 8) metal coordination : angle 3.12078 / 1.83 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 366 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 156 SER cc_start: 0.8480 (m) cc_final: 0.8214 (t) REVERT: G 181 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7660 (mp0) REVERT: I 59 ILE cc_start: 0.8338 (tp) cc_final: 0.8047 (mt) REVERT: I 81 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7632 (p0) REVERT: I 367 TYR cc_start: 0.8763 (t80) cc_final: 0.8403 (t80) REVERT: I 371 ARG cc_start: 0.7639 (mtt-85) cc_final: 0.7406 (mtt180) REVERT: I 516 ASP cc_start: 0.8224 (t0) cc_final: 0.7671 (t70) REVERT: I 572 ILE cc_start: 0.9334 (mm) cc_final: 0.9067 (mt) REVERT: I 601 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.6937 (t0) REVERT: I 728 ASP cc_start: 0.8313 (t0) cc_final: 0.8060 (t0) REVERT: I 765 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8727 (pt) REVERT: I 779 ARG cc_start: 0.8218 (ttm-80) cc_final: 0.7865 (ttp-110) REVERT: I 788 SER cc_start: 0.9209 (m) cc_final: 0.8973 (m) REVERT: I 1171 ARG cc_start: 0.8516 (ttp80) cc_final: 0.8113 (ttm-80) REVERT: I 1172 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8685 (tp) REVERT: J 96 LYS cc_start: 0.9134 (ptpt) cc_final: 0.8754 (pttp) REVERT: J 102 MET cc_start: 0.9231 (ttm) cc_final: 0.8885 (ttm) REVERT: J 129 ASP cc_start: 0.8056 (t70) cc_final: 0.7543 (t0) REVERT: J 132 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7883 (tp) REVERT: J 163 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7365 (pt0) REVERT: J 214 ARG cc_start: 0.5479 (ttp-110) cc_final: 0.5247 (ttm110) REVERT: J 227 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.7814 (t80) REVERT: J 486 SER cc_start: 0.8722 (t) cc_final: 0.8503 (p) REVERT: J 513 MET cc_start: 0.8960 (ttp) cc_final: 0.8552 (ttp) REVERT: J 525 MET cc_start: 0.8336 (ptp) cc_final: 0.8045 (ptm) REVERT: J 698 MET cc_start: 0.8894 (tpt) cc_final: 0.8660 (tpt) REVERT: J 701 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8550 (tp) REVERT: J 738 ARG cc_start: 0.7565 (ttm170) cc_final: 0.6995 (mtm110) REVERT: J 753 SER cc_start: 0.9071 (OUTLIER) cc_final: 0.8494 (p) REVERT: J 1079 LYS cc_start: 0.6772 (OUTLIER) cc_final: 0.5759 (tptt) REVERT: J 1095 MET cc_start: 0.2643 (ttp) cc_final: 0.2378 (ppp) REVERT: J 1115 ILE cc_start: 0.4130 (OUTLIER) cc_final: 0.3720 (pt) REVERT: J 1284 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7525 (mpt180) REVERT: L 221 PHE cc_start: 0.4132 (m-80) cc_final: 0.3449 (m-80) REVERT: L 268 TYR cc_start: 0.5611 (t80) cc_final: 0.5224 (t80) REVERT: L 356 GLU cc_start: 0.6622 (tp30) cc_final: 0.6200 (mt-10) outliers start: 111 outliers final: 73 residues processed: 453 average time/residue: 0.1994 time to fit residues: 145.2369 Evaluate side-chains 419 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 334 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 214 ASN Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 397 LEU Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 504 GLU Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 576 SER Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 601 ASP Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 730 SER Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 853 ASP Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 1010 GLN Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 228 VAL Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 753 SER Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 1079 LYS Chi-restraints excluded: chain J residue 1115 ILE Chi-restraints excluded: chain J residue 1221 LEU Chi-restraints excluded: chain J residue 1284 ARG Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 529 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: [132, 56, 67, 164, 363, 13, 19, 27, 205, 213, 78] chunk 132 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 67 optimal weight: 20.0000 chunk 164 optimal weight: 3.9990 chunk 363 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 205 optimal weight: 3.9990 chunk 213 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 193 ASN I 214 ASN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 799 ASN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 331 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.177491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.138998 restraints weight = 37407.226| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.61 r_work: 0.3130 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 32655 Z= 0.166 Angle : 0.660 15.293 44613 Z= 0.341 Chirality : 0.044 0.324 5112 Planarity : 0.005 0.082 5398 Dihedral : 17.609 147.484 5632 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.63 % Favored : 93.27 % Rotamer: Outliers : 3.44 % Allowed : 14.43 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.13), residues: 3727 helix: 0.52 (0.13), residues: 1496 sheet: -2.18 (0.25), residues: 402 loop : -1.96 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 33 TYR 0.019 0.001 TYR G 177 PHE 0.019 0.002 PHE I1025 TRP 0.008 0.001 TRP I 997 HIS 0.007 0.001 HIS G 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (32647) covalent geometry : angle 0.65806 / 0.34 (44601) hydrogen bonds : bond 0.04160 / 2.80 ( 1332) hydrogen bonds : angle 4.65936 / 3.17 ( 3697) metal coordination : bond 0.00865 / 0.52 ( 8) metal coordination : angle 2.91276 / 1.71 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 351 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 156 SER cc_start: 0.8466 (m) cc_final: 0.8210 (t) REVERT: G 181 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7727 (mp0) REVERT: H 143 ARG cc_start: 0.6322 (mtm110) cc_final: 0.6000 (mtm110) REVERT: I 59 ILE cc_start: 0.8322 (tp) cc_final: 0.8036 (mt) REVERT: I 81 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7722 (p0) REVERT: I 360 LEU cc_start: 0.7444 (tt) cc_final: 0.6755 (mp) REVERT: I 367 TYR cc_start: 0.8775 (t80) cc_final: 0.8458 (t80) REVERT: I 516 ASP cc_start: 0.8225 (t0) cc_final: 0.7645 (t70) REVERT: I 572 ILE cc_start: 0.9350 (mm) cc_final: 0.9092 (mt) REVERT: I 601 ASP cc_start: 0.7746 (OUTLIER) cc_final: 0.7093 (t0) REVERT: I 728 ASP cc_start: 0.8273 (t0) cc_final: 0.8040 (t0) REVERT: I 779 ARG cc_start: 0.8283 (ttm-80) cc_final: 0.8005 (ttp-110) REVERT: I 788 SER cc_start: 0.8908 (m) cc_final: 0.8651 (m) REVERT: I 800 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8203 (ptp) REVERT: I 1171 ARG cc_start: 0.8577 (ttp80) cc_final: 0.8205 (ttm-80) REVERT: I 1172 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8750 (tp) REVERT: J 96 LYS cc_start: 0.9151 (ptpt) cc_final: 0.8794 (pttp) REVERT: J 102 MET cc_start: 0.9181 (ttm) cc_final: 0.8888 (ttm) REVERT: J 129 ASP cc_start: 0.8100 (t70) cc_final: 0.7593 (t0) REVERT: J 132 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.7975 (tp) REVERT: J 214 ARG cc_start: 0.5543 (ttp-110) cc_final: 0.5300 (ttm110) REVERT: J 227 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.7852 (t80) REVERT: J 513 MET cc_start: 0.8829 (ttp) cc_final: 0.8305 (ttp) REVERT: J 525 MET cc_start: 0.8468 (ptp) cc_final: 0.8207 (ptm) REVERT: J 698 MET cc_start: 0.8938 (tpt) cc_final: 0.8681 (tpt) REVERT: J 701 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8658 (tp) REVERT: J 738 ARG cc_start: 0.7720 (ttm170) cc_final: 0.7176 (mtm110) REVERT: J 753 SER cc_start: 0.8989 (OUTLIER) cc_final: 0.8552 (p) REVERT: J 1079 LYS cc_start: 0.6810 (OUTLIER) cc_final: 0.5777 (tptt) REVERT: J 1095 MET cc_start: 0.2942 (ttp) cc_final: 0.2688 (ppp) REVERT: J 1115 ILE cc_start: 0.4416 (OUTLIER) cc_final: 0.3878 (pt) REVERT: J 1194 ARG cc_start: 0.7699 (mtm110) cc_final: 0.7179 (mtm110) REVERT: J 1231 ARG cc_start: 0.8295 (ttm110) cc_final: 0.8076 (ttp-110) REVERT: J 1284 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7607 (mpt180) REVERT: L 102 MET cc_start: 0.8267 (mmm) cc_final: 0.7826 (mmm) REVERT: L 221 PHE cc_start: 0.3998 (m-80) cc_final: 0.3451 (m-80) REVERT: L 268 TYR cc_start: 0.5286 (t80) cc_final: 0.5079 (t80) REVERT: L 356 GLU cc_start: 0.6674 (tp30) cc_final: 0.6261 (mt-10) REVERT: L 566 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7652 (t0) REVERT: L 585 GLU cc_start: 0.7600 (tp30) cc_final: 0.7285 (tp30) outliers start: 110 outliers final: 81 residues processed: 436 average time/residue: 0.2022 time to fit residues: 140.7146 Evaluate side-chains 436 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 342 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 14 ASP Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 152 SER Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 214 ASN Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 397 LEU Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 504 GLU Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 576 SER Chi-restraints excluded: chain I residue 601 ASP Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 730 SER Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 853 ASP Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 1010 GLN Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 753 SER Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 958 ILE Chi-restraints excluded: chain J residue 1079 LYS Chi-restraints excluded: chain J residue 1115 ILE Chi-restraints excluded: chain J residue 1221 LEU Chi-restraints excluded: chain J residue 1284 ARG Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 529 GLU Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 558 VAL Chi-restraints excluded: chain L residue 566 ASP Chi-restraints excluded: chain L residue 587 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: [246, 291, 223, 105, 309, 18, 175, 239, 95, 51, 244] chunk 246 optimal weight: 7.9990 chunk 291 optimal weight: 4.9990 chunk 223 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 309 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 175 optimal weight: 1.9990 chunk 239 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 244 optimal weight: 8.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 193 ASN I 214 ASN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 568 ASN I 799 ASN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.177151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.139668 restraints weight = 37688.765| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.54 r_work: 0.3107 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 32655 Z= 0.176 Angle : 0.659 15.099 44613 Z= 0.340 Chirality : 0.044 0.312 5112 Planarity : 0.005 0.082 5398 Dihedral : 17.554 146.604 5632 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.73 % Favored : 93.16 % Rotamer: Outliers : 3.97 % Allowed : 14.46 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.13), residues: 3727 helix: 0.61 (0.13), residues: 1494 sheet: -2.14 (0.25), residues: 405 loop : -1.90 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J1173 TYR 0.018 0.001 TYR G 177 PHE 0.020 0.002 PHE J1037 TRP 0.008 0.001 TRP I 997 HIS 0.007 0.001 HIS G 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (32647) covalent geometry : angle 0.65728 / 0.34 (44601) hydrogen bonds : bond 0.04127 / 2.78 ( 1332) hydrogen bonds : angle 4.61851 / 3.14 ( 3697) metal coordination : bond 0.00906 / 0.55 ( 8) metal coordination : angle 2.84700 / 1.68 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 350 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 156 SER cc_start: 0.8462 (m) cc_final: 0.8209 (t) REVERT: G 181 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7796 (mp0) REVERT: H 143 ARG cc_start: 0.6433 (mtm110) cc_final: 0.6001 (mtm110) REVERT: I 59 ILE cc_start: 0.8333 (tp) cc_final: 0.8013 (mt) REVERT: I 81 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7803 (p0) REVERT: I 130 MET cc_start: 0.9204 (ttm) cc_final: 0.8968 (ttm) REVERT: I 319 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7354 (mt) REVERT: I 346 TYR cc_start: 0.7260 (m-80) cc_final: 0.6917 (m-80) REVERT: I 360 LEU cc_start: 0.7414 (tt) cc_final: 0.6724 (mp) REVERT: I 367 TYR cc_start: 0.8752 (t80) cc_final: 0.8455 (t80) REVERT: I 516 ASP cc_start: 0.8227 (t0) cc_final: 0.7638 (t70) REVERT: I 572 ILE cc_start: 0.9358 (mm) cc_final: 0.9110 (mt) REVERT: I 601 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.7050 (t0) REVERT: I 728 ASP cc_start: 0.8333 (t0) cc_final: 0.8073 (t0) REVERT: I 779 ARG cc_start: 0.8302 (ttm-80) cc_final: 0.8016 (ttp-110) REVERT: I 788 SER cc_start: 0.8945 (m) cc_final: 0.8690 (m) REVERT: I 800 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8271 (ptp) REVERT: I 1171 ARG cc_start: 0.8618 (ttp80) cc_final: 0.8254 (ttm-80) REVERT: I 1172 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8767 (tp) REVERT: J 26 SER cc_start: 0.8831 (OUTLIER) cc_final: 0.8617 (p) REVERT: J 96 LYS cc_start: 0.9168 (ptpt) cc_final: 0.8802 (pttp) REVERT: J 129 ASP cc_start: 0.8112 (t70) cc_final: 0.7607 (t0) REVERT: J 132 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7966 (tp) REVERT: J 180 MET cc_start: 0.8278 (ttm) cc_final: 0.7975 (ttm) REVERT: J 227 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.7790 (t80) REVERT: J 513 MET cc_start: 0.8847 (ttp) cc_final: 0.8330 (ttp) REVERT: J 525 MET cc_start: 0.8423 (ptp) cc_final: 0.8155 (ptm) REVERT: J 698 MET cc_start: 0.8939 (tpt) cc_final: 0.8647 (tpt) REVERT: J 738 ARG cc_start: 0.7832 (ttm170) cc_final: 0.7204 (mtm110) REVERT: J 753 SER cc_start: 0.8932 (OUTLIER) cc_final: 0.8495 (p) REVERT: J 1079 LYS cc_start: 0.6815 (OUTLIER) cc_final: 0.5736 (tptt) REVERT: J 1095 MET cc_start: 0.2712 (OUTLIER) cc_final: 0.2451 (ppp) REVERT: J 1115 ILE cc_start: 0.4273 (OUTLIER) cc_final: 0.3794 (pt) REVERT: J 1194 ARG cc_start: 0.7637 (mtm110) cc_final: 0.7228 (mtm110) REVERT: J 1284 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7484 (mpt180) REVERT: L 102 MET cc_start: 0.8242 (mmm) cc_final: 0.7675 (mmm) REVERT: L 221 PHE cc_start: 0.4043 (m-80) cc_final: 0.3528 (m-80) REVERT: L 268 TYR cc_start: 0.5428 (t80) cc_final: 0.5180 (t80) REVERT: L 356 GLU cc_start: 0.6637 (tp30) cc_final: 0.6152 (mt-10) REVERT: L 585 GLU cc_start: 0.7535 (tp30) cc_final: 0.7268 (tp30) outliers start: 127 outliers final: 94 residues processed: 448 average time/residue: 0.1944 time to fit residues: 141.1084 Evaluate side-chains 446 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 338 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 14 ASP Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 152 SER Chi-restraints excluded: chain I residue 214 ASN Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 397 LEU Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 476 LYS Chi-restraints excluded: chain I residue 504 GLU Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 576 SER Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 601 ASP Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 730 SER Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 1010 GLN Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1098 LEU Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 228 VAL Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 618 VAL Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 753 SER Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 958 ILE Chi-restraints excluded: chain J residue 1079 LYS Chi-restraints excluded: chain J residue 1095 MET Chi-restraints excluded: chain J residue 1115 ILE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1221 LEU Chi-restraints excluded: chain J residue 1284 ARG Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 529 GLU Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 558 VAL Chi-restraints excluded: chain L residue 566 ASP Chi-restraints excluded: chain L residue 587 ILE Chi-restraints excluded: chain L residue 606 VAL Chi-restraints excluded: chain L residue 609 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: [27, 201, 289, 97, 10, 111, 24, 328, 123, 303, 71] chunk 27 optimal weight: 0.9990 chunk 201 optimal weight: 2.9990 chunk 289 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 24 optimal weight: 0.0870 chunk 328 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 303 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 193 ASN I 214 ASN ** I 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 568 ASN I 799 ASN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 504 GLN ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN L 309 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.181678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.142220 restraints weight = 37606.403| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.66 r_work: 0.3120 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32655 Z= 0.128 Angle : 0.627 14.737 44613 Z= 0.325 Chirality : 0.043 0.308 5112 Planarity : 0.004 0.080 5398 Dihedral : 17.437 145.426 5632 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.25 % Favored : 93.67 % Rotamer: Outliers : 3.78 % Allowed : 14.74 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.14), residues: 3727 helix: 0.76 (0.13), residues: 1497 sheet: -2.00 (0.25), residues: 400 loop : -1.77 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 33 TYR 0.018 0.001 TYR G 177 PHE 0.022 0.001 PHE J1037 TRP 0.011 0.001 TRP I 807 HIS 0.007 0.001 HIS G 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (32647) covalent geometry : angle 0.62542 / 0.32 (44601) hydrogen bonds : bond 0.03899 / 2.63 ( 1332) hydrogen bonds : angle 4.51109 / 3.06 ( 3697) metal coordination : bond 0.00614 / 0.37 ( 8) metal coordination : angle 2.50885 / 1.47 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 366 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 156 SER cc_start: 0.8457 (m) cc_final: 0.8206 (t) REVERT: G 181 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7677 (mp0) REVERT: H 143 ARG cc_start: 0.6398 (mtm110) cc_final: 0.6061 (mtm110) REVERT: I 59 ILE cc_start: 0.8308 (tp) cc_final: 0.8007 (mt) REVERT: I 81 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7796 (p0) REVERT: I 130 MET cc_start: 0.9181 (ttm) cc_final: 0.8959 (ttm) REVERT: I 346 TYR cc_start: 0.7248 (m-80) cc_final: 0.6929 (m-80) REVERT: I 360 LEU cc_start: 0.7412 (tt) cc_final: 0.6727 (mp) REVERT: I 516 ASP cc_start: 0.8210 (t0) cc_final: 0.7617 (t70) REVERT: I 572 ILE cc_start: 0.9359 (mm) cc_final: 0.9105 (mt) REVERT: I 601 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7110 (t0) REVERT: I 728 ASP cc_start: 0.8281 (t0) cc_final: 0.8020 (t0) REVERT: I 800 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8233 (ptp) REVERT: I 1033 ARG cc_start: 0.7307 (ttm110) cc_final: 0.7039 (ttm170) REVERT: I 1171 ARG cc_start: 0.8560 (ttp80) cc_final: 0.8203 (ttm-80) REVERT: I 1172 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8756 (tp) REVERT: J 26 SER cc_start: 0.8774 (OUTLIER) cc_final: 0.8536 (p) REVERT: J 58 CYS cc_start: 0.8362 (t) cc_final: 0.8100 (t) REVERT: J 96 LYS cc_start: 0.9140 (ptpt) cc_final: 0.8770 (pttp) REVERT: J 129 ASP cc_start: 0.8082 (t70) cc_final: 0.7547 (t0) REVERT: J 132 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7956 (tp) REVERT: J 180 MET cc_start: 0.8269 (ttm) cc_final: 0.7981 (ttm) REVERT: J 242 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8669 (tp) REVERT: J 513 MET cc_start: 0.8827 (ttp) cc_final: 0.8327 (ttp) REVERT: J 525 MET cc_start: 0.8437 (ptp) cc_final: 0.8167 (ptm) REVERT: J 669 GLN cc_start: 0.7810 (mt0) cc_final: 0.7521 (mm110) REVERT: J 698 MET cc_start: 0.8910 (tpt) cc_final: 0.8655 (tpt) REVERT: J 701 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8666 (tp) REVERT: J 738 ARG cc_start: 0.7708 (ttm170) cc_final: 0.7095 (mtm110) REVERT: J 753 SER cc_start: 0.8845 (OUTLIER) cc_final: 0.8484 (p) REVERT: J 1079 LYS cc_start: 0.6836 (OUTLIER) cc_final: 0.5856 (tptt) REVERT: J 1115 ILE cc_start: 0.4223 (OUTLIER) cc_final: 0.3737 (pt) REVERT: J 1194 ARG cc_start: 0.7657 (mtm110) cc_final: 0.7334 (mtm110) REVERT: J 1231 ARG cc_start: 0.8248 (ttm110) cc_final: 0.8034 (ttp-110) REVERT: J 1284 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7497 (mpt180) REVERT: L 102 MET cc_start: 0.8281 (mmm) cc_final: 0.7763 (mmm) REVERT: L 221 PHE cc_start: 0.4025 (m-80) cc_final: 0.3512 (m-80) REVERT: L 268 TYR cc_start: 0.5541 (t80) cc_final: 0.5257 (t80) REVERT: L 356 GLU cc_start: 0.6642 (tp30) cc_final: 0.6188 (mt-10) REVERT: L 584 ARG cc_start: 0.7265 (mtt180) cc_final: 0.7007 (mtt-85) REVERT: L 585 GLU cc_start: 0.7594 (tp30) cc_final: 0.7314 (tp30) outliers start: 121 outliers final: 83 residues processed: 458 average time/residue: 0.2015 time to fit residues: 148.8352 Evaluate side-chains 438 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 342 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 14 ASP Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 152 SER Chi-restraints excluded: chain I residue 214 ASN Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 397 LEU Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 504 GLU Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 568 ASN Chi-restraints excluded: chain I residue 576 SER Chi-restraints excluded: chain I residue 601 ASP Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 730 SER Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 1010 GLN Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 228 VAL Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 618 VAL Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 753 SER Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 1079 LYS Chi-restraints excluded: chain J residue 1115 ILE Chi-restraints excluded: chain J residue 1221 LEU Chi-restraints excluded: chain J residue 1284 ARG Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 225 ARG Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 529 GLU Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 558 VAL Chi-restraints excluded: chain L residue 587 ILE Chi-restraints excluded: chain L residue 606 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: [195, 231, 7, 49, 43, 183, 323, 30, 47, 341, 131] chunk 195 optimal weight: 1.9990 chunk 231 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 323 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 341 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 193 ASN I 214 ASN ** I 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 568 ASN I 799 ASN ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 504 GLN ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1350 ASN K 43 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.177742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.140934 restraints weight = 37379.689| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.45 r_work: 0.3121 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 32655 Z= 0.202 Angle : 0.670 14.976 44613 Z= 0.344 Chirality : 0.044 0.242 5112 Planarity : 0.005 0.081 5398 Dihedral : 17.429 144.257 5632 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.73 % Favored : 93.18 % Rotamer: Outliers : 3.78 % Allowed : 15.12 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.14), residues: 3727 helix: 0.74 (0.13), residues: 1499 sheet: -2.02 (0.25), residues: 414 loop : -1.79 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 33 TYR 0.018 0.002 TYR G 177 PHE 0.025 0.002 PHE I 405 TRP 0.008 0.001 TRP I 997 HIS 0.007 0.001 HIS G 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.20 (32647) covalent geometry : angle 0.66891 / 0.34 (44601) hydrogen bonds : bond 0.04083 / 2.74 ( 1332) hydrogen bonds : angle 4.53128 / 3.07 ( 3697) metal coordination : bond 0.00986 / 0.61 ( 8) metal coordination : angle 2.62799 / 1.56 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 351 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 156 SER cc_start: 0.8458 (m) cc_final: 0.8185 (t) REVERT: G 181 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7771 (mp0) REVERT: H 143 ARG cc_start: 0.6419 (mtm110) cc_final: 0.6150 (mtm110) REVERT: I 59 ILE cc_start: 0.8330 (tp) cc_final: 0.7987 (mt) REVERT: I 81 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7877 (p0) REVERT: I 130 MET cc_start: 0.9230 (ttm) cc_final: 0.8994 (ttt) REVERT: I 346 TYR cc_start: 0.7321 (m-80) cc_final: 0.6973 (m-80) REVERT: I 360 LEU cc_start: 0.7440 (tt) cc_final: 0.6753 (mp) REVERT: I 367 TYR cc_start: 0.8759 (t80) cc_final: 0.8484 (t80) REVERT: I 516 ASP cc_start: 0.8224 (t0) cc_final: 0.7618 (t70) REVERT: I 572 ILE cc_start: 0.9313 (mm) cc_final: 0.9057 (mt) REVERT: I 601 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7102 (t0) REVERT: I 728 ASP cc_start: 0.8331 (t0) cc_final: 0.8049 (t0) REVERT: I 800 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8210 (ptp) REVERT: I 1033 ARG cc_start: 0.7311 (ttm110) cc_final: 0.7053 (ttm170) REVERT: I 1171 ARG cc_start: 0.8607 (ttp80) cc_final: 0.8239 (ttm-80) REVERT: I 1172 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8764 (tp) REVERT: J 26 SER cc_start: 0.8796 (OUTLIER) cc_final: 0.8595 (p) REVERT: J 58 CYS cc_start: 0.8411 (t) cc_final: 0.8182 (t) REVERT: J 96 LYS cc_start: 0.9181 (ptpt) cc_final: 0.8812 (pttp) REVERT: J 129 ASP cc_start: 0.8088 (t70) cc_final: 0.7554 (t0) REVERT: J 132 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8015 (tp) REVERT: J 180 MET cc_start: 0.8298 (ttm) cc_final: 0.8014 (ttm) REVERT: J 242 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8643 (tp) REVERT: J 478 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8480 (mm) REVERT: J 513 MET cc_start: 0.8845 (ttp) cc_final: 0.8323 (ttp) REVERT: J 525 MET cc_start: 0.8545 (ptp) cc_final: 0.8277 (ptm) REVERT: J 669 GLN cc_start: 0.7901 (mt0) cc_final: 0.7654 (mm110) REVERT: J 698 MET cc_start: 0.8945 (tpt) cc_final: 0.8657 (tpt) REVERT: J 701 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8688 (tp) REVERT: J 738 ARG cc_start: 0.7835 (ttm170) cc_final: 0.7209 (mtm110) REVERT: J 753 SER cc_start: 0.8829 (OUTLIER) cc_final: 0.8450 (p) REVERT: J 1079 LYS cc_start: 0.6742 (OUTLIER) cc_final: 0.5789 (tptt) REVERT: J 1115 ILE cc_start: 0.4280 (OUTLIER) cc_final: 0.3773 (pt) REVERT: J 1194 ARG cc_start: 0.7699 (mtm110) cc_final: 0.7384 (mtm110) REVERT: J 1284 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7503 (mpt180) REVERT: L 102 MET cc_start: 0.8246 (mmm) cc_final: 0.7699 (mmm) REVERT: L 221 PHE cc_start: 0.3944 (m-80) cc_final: 0.3452 (m-80) REVERT: L 268 TYR cc_start: 0.5438 (t80) cc_final: 0.5208 (t80) REVERT: L 356 GLU cc_start: 0.6648 (tp30) cc_final: 0.6180 (mt-10) REVERT: L 584 ARG cc_start: 0.7280 (mtt180) cc_final: 0.7032 (mtt-85) REVERT: L 585 GLU cc_start: 0.7612 (tp30) cc_final: 0.7363 (tp30) outliers start: 121 outliers final: 91 residues processed: 445 average time/residue: 0.2080 time to fit residues: 148.2056 Evaluate side-chains 438 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 333 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 14 ASP Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 152 SER Chi-restraints excluded: chain I residue 214 ASN Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 397 LEU Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 504 GLU Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 576 SER Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 601 ASP Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 730 SER Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 1010 GLN Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1098 LEU Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 228 VAL Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 618 VAL Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 753 SER Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 1079 LYS Chi-restraints excluded: chain J residue 1115 ILE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1221 LEU Chi-restraints excluded: chain J residue 1284 ARG Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 529 GLU Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 558 VAL Chi-restraints excluded: chain L residue 587 ILE Chi-restraints excluded: chain L residue 606 VAL Chi-restraints excluded: chain L residue 609 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: [253, 290, 352, 118, 97, 46, 180, 218, 127, 191, 202] chunk 253 optimal weight: 2.9990 chunk 290 optimal weight: 9.9990 chunk 352 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 97 optimal weight: 0.0570 chunk 46 optimal weight: 0.7980 chunk 180 optimal weight: 1.9990 chunk 218 optimal weight: 0.9990 chunk 127 optimal weight: 0.0980 chunk 191 optimal weight: 0.6980 chunk 202 optimal weight: 4.9990 overall best weight: 0.5300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 193 ASN I 214 ASN ** I 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 568 ASN I 799 ASN ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 504 GLN J1235 ASN ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.180816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.142935 restraints weight = 37605.320| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.70 r_work: 0.3158 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 32655 Z= 0.120 Angle : 0.627 16.823 44613 Z= 0.324 Chirality : 0.042 0.242 5112 Planarity : 0.004 0.079 5398 Dihedral : 17.302 142.598 5632 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.98 % Favored : 93.94 % Rotamer: Outliers : 3.19 % Allowed : 15.90 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.14), residues: 3727 helix: 0.94 (0.13), residues: 1488 sheet: -1.98 (0.25), residues: 422 loop : -1.61 (0.14), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 33 TYR 0.019 0.001 TYR G 177 PHE 0.023 0.001 PHE I 405 TRP 0.026 0.001 TRP L 315 HIS 0.006 0.001 HIS G 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (32647) covalent geometry : angle 0.62601 / 0.32 (44601) hydrogen bonds : bond 0.03803 / 2.57 ( 1332) hydrogen bonds : angle 4.43089 / 3.00 ( 3697) metal coordination : bond 0.00482 / 0.29 ( 8) metal coordination : angle 2.29683 / 1.34 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 356 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 156 SER cc_start: 0.8434 (m) cc_final: 0.8212 (t) REVERT: G 181 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7683 (mp0) REVERT: H 15 ASP cc_start: 0.6595 (m-30) cc_final: 0.6392 (m-30) REVERT: H 143 ARG cc_start: 0.6378 (mtm110) cc_final: 0.6017 (mtm110) REVERT: I 59 ILE cc_start: 0.8280 (tp) cc_final: 0.7952 (mt) REVERT: I 81 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7843 (p0) REVERT: I 130 MET cc_start: 0.9220 (ttm) cc_final: 0.8998 (ttt) REVERT: I 346 TYR cc_start: 0.7273 (m-80) cc_final: 0.6968 (m-80) REVERT: I 360 LEU cc_start: 0.7490 (tt) cc_final: 0.6837 (mp) REVERT: I 459 MET cc_start: 0.8844 (mtp) cc_final: 0.8397 (mtp) REVERT: I 516 ASP cc_start: 0.8200 (t0) cc_final: 0.7574 (t70) REVERT: I 572 ILE cc_start: 0.9316 (mm) cc_final: 0.9051 (mt) REVERT: I 601 ASP cc_start: 0.7747 (OUTLIER) cc_final: 0.7110 (t0) REVERT: I 728 ASP cc_start: 0.8326 (t0) cc_final: 0.8018 (t0) REVERT: I 800 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8232 (ptp) REVERT: I 1033 ARG cc_start: 0.7279 (ttm110) cc_final: 0.7020 (ttm170) REVERT: I 1082 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8231 (mp) REVERT: I 1171 ARG cc_start: 0.8585 (ttp80) cc_final: 0.8229 (ttm-80) REVERT: I 1172 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8784 (tp) REVERT: J 26 SER cc_start: 0.8838 (OUTLIER) cc_final: 0.8624 (p) REVERT: J 58 CYS cc_start: 0.8409 (t) cc_final: 0.8185 (t) REVERT: J 96 LYS cc_start: 0.9147 (ptpt) cc_final: 0.8779 (pttp) REVERT: J 129 ASP cc_start: 0.8083 (t70) cc_final: 0.7529 (t0) REVERT: J 132 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7968 (tp) REVERT: J 180 MET cc_start: 0.8225 (ttm) cc_final: 0.7975 (ttm) REVERT: J 242 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8627 (tp) REVERT: J 478 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8311 (mm) REVERT: J 513 MET cc_start: 0.8782 (ttp) cc_final: 0.8282 (ttp) REVERT: J 698 MET cc_start: 0.8853 (tpt) cc_final: 0.8609 (tpt) REVERT: J 701 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8636 (tp) REVERT: J 738 ARG cc_start: 0.7748 (ttm170) cc_final: 0.7201 (mtm110) REVERT: J 753 SER cc_start: 0.8792 (OUTLIER) cc_final: 0.8475 (p) REVERT: J 788 LEU cc_start: 0.8163 (tt) cc_final: 0.7714 (tt) REVERT: J 1079 LYS cc_start: 0.6711 (OUTLIER) cc_final: 0.5783 (tptt) REVERT: J 1115 ILE cc_start: 0.3954 (OUTLIER) cc_final: 0.3493 (pt) REVERT: J 1173 ARG cc_start: 0.6856 (tpp80) cc_final: 0.6420 (mtp85) REVERT: J 1194 ARG cc_start: 0.7671 (mtm110) cc_final: 0.7433 (mtm110) REVERT: J 1284 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7473 (mpt180) REVERT: L 102 MET cc_start: 0.8185 (mmm) cc_final: 0.7756 (mmm) REVERT: L 221 PHE cc_start: 0.3830 (m-80) cc_final: 0.3323 (m-80) REVERT: L 268 TYR cc_start: 0.5366 (t80) cc_final: 0.5132 (t80) REVERT: L 356 GLU cc_start: 0.6658 (tp30) cc_final: 0.6210 (mt-10) REVERT: L 529 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8105 (tt0) REVERT: L 584 ARG cc_start: 0.7165 (mtt180) cc_final: 0.6925 (mtt-85) REVERT: L 585 GLU cc_start: 0.7591 (tp30) cc_final: 0.7334 (tp30) outliers start: 102 outliers final: 75 residues processed: 434 average time/residue: 0.1957 time to fit residues: 137.4910 Evaluate side-chains 431 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 340 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 14 ASP Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 152 SER Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 397 LEU Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 504 GLU Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 568 ASN Chi-restraints excluded: chain I residue 576 SER Chi-restraints excluded: chain I residue 601 ASP Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 730 SER Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 1010 GLN Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 618 VAL Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 753 SER Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 1079 LYS Chi-restraints excluded: chain J residue 1115 ILE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1221 LEU Chi-restraints excluded: chain J residue 1284 ARG Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 225 ARG Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 529 GLU Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 558 VAL Chi-restraints excluded: chain L residue 587 ILE Chi-restraints excluded: chain L residue 606 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: [38, 291, 25, 93, 215, 5, 190, 69, 312, 370, 164] chunk 38 optimal weight: 0.9980 chunk 291 optimal weight: 0.0870 chunk 25 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 190 optimal weight: 3.9990 chunk 69 optimal weight: 20.0000 chunk 312 optimal weight: 0.0570 chunk 370 optimal weight: 40.0000 chunk 164 optimal weight: 0.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 193 ASN I 214 ASN ** I 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 517 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 568 ASN I 799 ASN ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.182903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.137288 restraints weight = 37857.081| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 3.27 r_work: 0.2990 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32655 Z= 0.120 Angle : 0.624 17.030 44613 Z= 0.321 Chirality : 0.042 0.243 5112 Planarity : 0.004 0.078 5398 Dihedral : 17.238 141.195 5632 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.01 % Favored : 93.91 % Rotamer: Outliers : 2.97 % Allowed : 16.21 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.14), residues: 3727 helix: 1.03 (0.13), residues: 1494 sheet: -1.93 (0.25), residues: 422 loop : -1.55 (0.14), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J1231 TYR 0.017 0.001 TYR G 177 PHE 0.022 0.001 PHE I 405 TRP 0.016 0.001 TRP L 315 HIS 0.006 0.001 HIS G 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (32647) covalent geometry : angle 0.62319 / 0.32 (44601) hydrogen bonds : bond 0.03740 / 2.52 ( 1332) hydrogen bonds : angle 4.38004 / 2.96 ( 3697) metal coordination : bond 0.00478 / 0.29 ( 8) metal coordination : angle 2.14894 / 1.26 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7874.26 seconds wall clock time: 135 minutes 13.31 seconds (8113.31 seconds total)