Starting phenix.real_space_refine on Tue Aug 26 03:08:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6psw_20466/08_2025/6psw_20466_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6psw_20466/08_2025/6psw_20466.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6psw_20466/08_2025/6psw_20466_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6psw_20466/08_2025/6psw_20466_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6psw_20466/08_2025/6psw_20466.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6psw_20466/08_2025/6psw_20466.map" } resolution = 3.7 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= 0.006 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 3 6.06 5 P 124 5.49 5 Mg 1 5.21 5 S 136 5.16 5 C 20127 2.51 5 N 5780 2.21 5 O 6524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 137 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32695 Number of models: 1 Model: "" Number of chains: 13 Chain: "G" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1762 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 219} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1678 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 10571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10571 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 56, 'TRANS': 1284} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 10460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1345, 10460 Classifications: {'peptide': 1345} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 54, 'TRANS': 1288} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "L" Number of atoms: 3854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3854 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 14, 'TRANS': 458} Chain breaks: 2 Chain: "M" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 572 Classifications: {'peptide': 73} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 68} Chain: "N" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 571 Classifications: {'peptide': 72} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 66} Chain: "O" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1270 Classifications: {'DNA': 62} Link IDs: {'rna3p': 61} Chain: "P" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1272 Classifications: {'DNA': 62} Link IDs: {'rna3p': 61} 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: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14460 SG CYS J 70 76.872 99.753 110.158 1.00 33.15 S ATOM 14474 SG CYS J 72 77.146 102.675 111.995 1.00 38.61 S ATOM 14582 SG CYS J 85 74.415 101.147 113.335 1.00 42.93 S ATOM 14606 SG CYS J 88 73.523 100.283 110.077 1.00 47.24 S ATOM 20288 SG CYS J 814 73.930 38.981 83.279 1.00 26.40 S ATOM 20853 SG CYS J 888 73.547 42.857 82.747 1.00 23.18 S ATOM 20925 SG CYS J 898 75.066 40.229 80.222 1.00 16.65 S ATOM 29825 SG CYS N 40 53.649 54.250 22.072 1.00 73.58 S ATOM 29984 SG CYS N 61 56.367 55.850 24.356 1.00 81.89 S Time building chain proxies: 7.77, per 1000 atoms: 0.24 Number of scatterers: 32695 At special positions: 0 Unit cell: (163.8, 156, 166.4, 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 3 29.99 S 136 16.00 P 124 15.00 Mg 1 11.99 O 6524 8.00 N 5780 7.00 C 20127 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: 3.00 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 238.4 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 40 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 61 " Number of angles added : 6 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7118 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 54 sheets defined 42.9% alpha, 12.6% beta 48 base pairs and 91 stacking pairs defined. Time for finding SS restraints: 4.48 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.736A pdb=" N SER G 49 " --> pdb=" O ARG G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 86 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 155 through 160 Processing helix chain 'G' and resid 161 through 165 removed outlier: 4.511A pdb=" N ASP G 164 " --> pdb=" O SER G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 234 removed outlier: 4.126A pdb=" N LEU G 234 " --> pdb=" O ALA G 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 49 removed outlier: 3.813A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU H 39 " --> pdb=" O PHE H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 88 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 Processing helix chain 'I' and resid 4 through 9 Processing helix chain 'I' and resid 28 through 40 removed outlier: 4.112A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 57 removed outlier: 3.655A pdb=" N ALA I 52 " --> pdb=" O GLY I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 165 through 169 removed outlier: 4.244A pdb=" N GLY I 168 " --> pdb=" O HIS I 165 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.880A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 removed outlier: 3.553A pdb=" N ILE I 220 " --> pdb=" O THR I 216 " (cutoff:3.500A) Processing helix chain 'I' and resid 242 through 247 Processing helix chain 'I' and resid 270 through 280 Processing helix chain 'I' and resid 318 through 329 removed outlier: 3.626A pdb=" N SER I 328 " --> pdb=" O LYS I 324 " (cutoff:3.500A) 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: 4.033A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 437 Processing helix chain 'I' and resid 455 through 479 removed outlier: 4.314A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 494 through 508 removed outlier: 4.455A pdb=" N ILE I 498 " --> pdb=" O ASN I 494 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 removed outlier: 3.506A pdb=" N ARG I 528 " --> pdb=" O ILE I 524 " (cutoff:3.500A) Processing helix chain 'I' and resid 540 through 544 removed outlier: 3.882A pdb=" N GLY I 544 " --> pdb=" O GLU I 541 " (cutoff:3.500A) Processing helix chain 'I' and resid 648 through 650 No H-bonds generated for 'chain 'I' and resid 648 through 650' Processing helix chain 'I' and resid 664 through 668 removed outlier: 3.840A pdb=" N LEU I 667 " --> pdb=" O GLY I 664 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 688 removed outlier: 3.639A pdb=" N GLN I 688 " --> pdb=" O ASN I 684 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 898 through 907 Processing helix chain 'I' and resid 942 through 979 removed outlier: 3.519A pdb=" N LEU I 946 " --> pdb=" O ASP I 942 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA I 977 " --> pdb=" O SER I 973 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 3.881A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.650A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1149 removed outlier: 3.813A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1176 removed outlier: 3.627A pdb=" N ARG I1171 " --> pdb=" O GLU I1167 " (cutoff:3.500A) Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.591A pdb=" N GLY I1202 " --> pdb=" O LEU I1198 " (cutoff:3.500A) Processing helix chain 'I' and resid 1238 through 1243 removed outlier: 3.528A pdb=" N LYS I1242 " --> pdb=" O LEU I1238 " (cutoff:3.500A) Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1284 through 1292 Processing helix chain 'I' and resid 1299 through 1310 removed outlier: 3.955A pdb=" N TYR I1305 " --> pdb=" O ARG I1301 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE I1308 " --> pdb=" O MET I1304 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1331 removed outlier: 3.512A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 34 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.585A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 Processing helix chain 'J' and resid 122 through 128 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 removed outlier: 3.884A pdb=" N GLU J 170 " --> pdb=" O LEU J 166 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU J 171 " --> pdb=" O ASP J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 192 removed outlier: 3.533A pdb=" N ALA J 184 " --> pdb=" O MET J 180 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 208 removed outlier: 4.061A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 removed outlier: 3.657A pdb=" N LEU J 249 " --> pdb=" O PRO J 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 256 through 258 No H-bonds generated for 'chain 'J' and resid 256 through 258' Processing helix chain 'J' and resid 263 through 286 removed outlier: 3.872A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU J 285 " --> pdb=" O ARG J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 336 through 341 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 407 through 416 Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 removed outlier: 3.644A pdb=" N ASN J 489 " --> pdb=" O SER J 486 " (cutoff:3.500A) Processing helix chain 'J' and resid 504 through 515 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 593 Processing helix chain 'J' and resid 598 through 613 Processing helix chain 'J' and resid 614 through 636 removed outlier: 4.028A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 644 removed outlier: 3.535A pdb=" N ASP J 643 " --> pdb=" O GLY J 640 " (cutoff:3.500A) Processing helix chain 'J' and resid 648 through 670 removed outlier: 4.679A pdb=" N GLU J 652 " --> pdb=" O GLU J 648 " (cutoff:3.500A) Processing helix chain 'J' and resid 674 through 703 removed outlier: 3.798A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 741 removed outlier: 3.571A pdb=" N ILE J 737 " --> pdb=" O SER J 733 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 790 removed outlier: 4.016A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS J 781 " --> pdb=" O HIS J 777 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU J 788 " --> pdb=" O ALA J 784 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) Processing helix chain 'J' and resid 790 through 804 removed outlier: 3.561A pdb=" N GLY J 794 " --> pdb=" O THR J 790 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU J 796 " --> pdb=" O ASN J 792 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 839 Processing helix chain 'J' and resid 865 through 876 removed outlier: 3.675A pdb=" N ASN J 875 " --> pdb=" O LEU J 871 " (cutoff:3.500A) Processing helix chain 'J' and resid 895 through 900 removed outlier: 3.530A pdb=" N GLY J 900 " --> pdb=" O ALA J 896 " (cutoff:3.500A) Processing helix chain 'J' and resid 914 through 925 removed outlier: 3.683A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 930 Processing helix chain 'J' and resid 1137 through 1147 removed outlier: 4.114A pdb=" N VAL J1141 " --> pdb=" O GLY J1137 " (cutoff:3.500A) Processing helix chain 'J' and resid 1216 through 1225 removed outlier: 3.590A pdb=" N GLY J1225 " --> pdb=" O LEU J1221 " (cutoff:3.500A) Processing helix chain 'J' and resid 1225 through 1245 removed outlier: 4.052A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.071A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE J1256 " --> pdb=" O HIS J1252 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1293 Processing helix chain 'J' and resid 1308 through 1314 Processing helix chain 'J' and resid 1318 through 1323 removed outlier: 3.808A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 removed outlier: 3.658A pdb=" N ALA J1336 " --> pdb=" O LEU J1332 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL J1337 " --> pdb=" O THR J1333 " (cutoff:3.500A) Processing helix chain 'J' and resid 1346 through 1353 Processing helix chain 'J' and resid 1361 through 1374 removed outlier: 4.312A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 14 Processing helix chain 'K' and resid 17 through 32 removed outlier: 3.818A pdb=" N VAL K 32 " --> pdb=" O ARG K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 removed outlier: 3.626A pdb=" N GLU K 55 " --> pdb=" O LEU K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 80 removed outlier: 3.724A pdb=" N GLU K 76 " --> pdb=" O GLN K 72 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ALA K 77 " --> pdb=" O GLN K 73 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA K 78 " --> pdb=" O GLU K 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 106 removed outlier: 3.573A pdb=" N MET L 100 " --> pdb=" O ASP L 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 136 Processing helix chain 'L' and resid 137 through 153 Processing helix chain 'L' and resid 157 through 161 Processing helix chain 'L' and resid 215 through 233 Processing helix chain 'L' and resid 244 through 257 Processing helix chain 'L' and resid 262 through 290 Processing helix chain 'L' and resid 291 through 296 removed outlier: 3.812A pdb=" N CYS L 295 " --> pdb=" O CYS L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 307 Processing helix chain 'L' and resid 316 through 321 removed outlier: 3.636A pdb=" N ALA L 321 " --> pdb=" O ASN L 317 " (cutoff:3.500A) Processing helix chain 'L' and resid 333 through 352 Processing helix chain 'L' and resid 354 through 393 removed outlier: 4.046A pdb=" N ASN L 362 " --> pdb=" O VAL L 358 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ALA L 375 " --> pdb=" O LYS L 371 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLU L 378 " --> pdb=" O ARG L 374 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ARG L 385 " --> pdb=" O GLU L 381 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU L 386 " --> pdb=" O ALA L 382 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE L 390 " --> pdb=" O LEU L 386 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 419 Processing helix chain 'L' and resid 426 through 446 removed outlier: 3.884A pdb=" N TYR L 430 " --> pdb=" O LYS L 426 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N TRP L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TRP L 434 " --> pdb=" O TYR L 430 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 475 removed outlier: 4.925A pdb=" N GLN L 472 " --> pdb=" O ARG L 468 " (cutoff:3.500A) Processing helix chain 'L' and resid 482 through 487 removed outlier: 3.904A pdb=" N ARG L 486 " --> pdb=" O GLU L 482 " (cutoff:3.500A) Processing helix chain 'L' and resid 492 through 501 Processing helix chain 'L' and resid 511 through 515 removed outlier: 3.988A pdb=" N GLU L 515 " --> pdb=" O GLY L 512 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 523 removed outlier: 3.596A pdb=" N ILE L 523 " --> pdb=" O GLY L 520 " (cutoff:3.500A) Processing helix chain 'L' and resid 530 through 550 removed outlier: 3.572A pdb=" N GLY L 550 " --> pdb=" O ASP L 546 " (cutoff:3.500A) Processing helix chain 'L' and resid 552 through 563 removed outlier: 3.714A pdb=" N ALA L 556 " --> pdb=" O THR L 552 " (cutoff:3.500A) Processing helix chain 'L' and resid 572 through 580 Processing helix chain 'L' and resid 583 through 599 Processing helix chain 'L' and resid 604 through 611 Processing helix chain 'M' and resid 256 through 260 Processing helix chain 'M' and resid 263 through 273 removed outlier: 3.789A pdb=" N ALA M 267 " --> pdb=" O THR M 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 277 through 282 Processing helix chain 'M' and resid 285 through 291 removed outlier: 3.633A pdb=" N LEU M 289 " --> pdb=" O THR M 285 " (cutoff:3.500A) Processing helix chain 'M' and resid 296 through 310 removed outlier: 4.018A pdb=" N LEU M 300 " --> pdb=" O GLY M 296 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 27 removed outlier: 3.908A pdb=" N ALA N 8 " --> pdb=" O GLU N 4 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE N 27 " --> pdb=" O ILE N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 52 removed outlier: 3.547A pdb=" N PHE N 52 " --> pdb=" O ARG N 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 58 through 70 Processing sheet with id=AA1, first strand: chain 'G' and resid 24 through 31 removed outlier: 5.232A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG G 182 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'G' and resid 58 through 59 Processing sheet with id=AA4, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AA5, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.552A pdb=" N VAL G 146 " --> pdb=" O VAL G 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.685A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 16 through 17 removed outlier: 3.976A pdb=" N GLU H 17 " --> pdb=" O LYS H 25 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N HIS H 23 " --> pdb=" O THR H 207 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR H 207 " --> pdb=" O HIS H 23 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LYS H 25 " --> pdb=" O MET H 205 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N MET H 205 " --> pdb=" O LYS H 25 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N THR H 27 " --> pdb=" O ILE H 203 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE H 203 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N GLU H 29 " --> pdb=" O LEU H 201 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU H 201 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA H 184 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 50 through 60 removed outlier: 6.234A pdb=" N MET H 51 " --> pdb=" O GLY H 151 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY H 151 " --> pdb=" O MET H 51 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA H 55 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 50 through 60 removed outlier: 6.234A pdb=" N MET H 51 " --> pdb=" O GLY H 151 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY H 151 " --> pdb=" O MET H 51 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA H 55 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AB2, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AB3, first strand: chain 'H' and resid 110 through 111 removed outlier: 3.776A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.742A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'I' and resid 58 through 60 removed outlier: 7.105A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB7, first strand: chain 'I' and resid 451 through 453 removed outlier: 6.149A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 154 through 157 Processing sheet with id=AB9, first strand: chain 'I' and resid 284 through 286 removed outlier: 3.785A pdb=" N GLU I 240 " --> pdb=" O ILE I 229 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.958A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 296 through 297 removed outlier: 3.700A pdb=" N MET I 315 " --> pdb=" O VAL I 297 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 301 through 303 removed outlier: 5.339A pdb=" N ASP I 303 " --> pdb=" O LEU I 309 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEU I 309 " --> pdb=" O ASP I 303 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.599A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC6, first strand: chain 'I' and resid 633 through 636 Processing sheet with id=AC7, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.605A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 749 through 752 removed outlier: 6.951A 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 789 through 790 Processing sheet with id=AD2, first strand: chain 'I' and resid 1076 through 1080 removed outlier: 7.066A pdb=" N ILE I 816 " --> pdb=" O LYS I1078 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ASN I1080 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL I 818 " --> pdb=" O ASN I1080 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE I1096 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 834 through 840 removed outlier: 3.520A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 842 through 843 Processing sheet with id=AD5, first strand: chain 'I' and resid 882 through 884 Processing sheet with id=AD6, first strand: chain 'I' and resid 887 through 889 Processing sheet with id=AD7, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AD8, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AD9, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AE1, first strand: chain 'I' and resid 1336 through 1339 Processing sheet with id=AE2, first strand: chain 'J' and resid 104 through 112 removed outlier: 10.675A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.362A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 145 through 146 Processing sheet with id=AE4, first strand: chain 'J' and resid 252 through 254 removed outlier: 6.255A pdb=" N PHE J 260 " --> pdb=" O ILE L 505 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AE6, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE7, first strand: chain 'J' and resid 825 through 826 removed outlier: 6.833A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.734A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 956 through 957 removed outlier: 3.803A pdb=" N GLY J 956 " --> pdb=" O VAL J1011 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL J1011 " --> pdb=" O GLY J 956 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'J' and resid 959 through 961 Processing sheet with id=AF2, first strand: chain 'J' and resid 965 through 967 Processing sheet with id=AF3, first strand: chain 'J' and resid 1002 through 1003 Processing sheet with id=AF4, first strand: chain 'J' and resid 1024 through 1026 Processing sheet with id=AF5, first strand: chain 'J' and resid 1034 through 1038 removed outlier: 4.493A pdb=" N ALA J1097 " --> pdb=" O ILE J1080 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 1046 through 1051 Processing sheet with id=AF7, first strand: chain 'J' and resid 1156 through 1157 removed outlier: 3.986A pdb=" N ASP J1208 " --> pdb=" O ALA J1157 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 1187 through 1190 Processing sheet with id=AF9, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 7.085A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1293 hydrogen bonds defined for protein. 3636 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 113 hydrogen bonds 222 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 91 stacking parallelities Total time for adding SS restraints: 9.19 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10748 1.34 - 1.46: 7481 1.46 - 1.59: 14726 1.59 - 1.72: 251 1.72 - 1.84: 239 Bond restraints: 33445 Sorted by residual: bond pdb=" C19 1N7 J1504 " pdb=" C3 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.842 -0.310 2.00e-02 2.50e+03 2.40e+02 bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.820 -0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C3 1N7 J1504 " pdb=" C4 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.731 -0.199 2.00e-02 2.50e+03 9.93e+01 bond pdb=" C3 1N7 I1401 " pdb=" C4 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.712 -0.180 2.00e-02 2.50e+03 8.09e+01 bond pdb=" C7 1N7 I1401 " pdb=" C8 1N7 I1401 " ideal model delta sigma weight residual 1.542 1.694 -0.152 2.00e-02 2.50e+03 5.76e+01 ... (remaining 33440 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 43807 1.99 - 3.98: 1694 3.98 - 5.98: 168 5.98 - 7.97: 31 7.97 - 9.96: 9 Bond angle restraints: 45709 Sorted by residual: angle pdb=" N ILE N 27 " pdb=" CA ILE N 27 " pdb=" C ILE N 27 " ideal model delta sigma weight residual 106.21 113.68 -7.47 1.07e+00 8.73e-01 4.87e+01 angle pdb=" C THR L 94 " pdb=" N THR L 95 " pdb=" CA THR L 95 " ideal model delta sigma weight residual 122.56 113.32 9.24 1.50e+00 4.44e-01 3.79e+01 angle pdb=" N ILE J 490 " pdb=" CA ILE J 490 " pdb=" C ILE J 490 " ideal model delta sigma weight residual 113.20 108.82 4.38 9.60e-01 1.09e+00 2.08e+01 angle pdb=" N LEU I 237 " pdb=" CA LEU I 237 " pdb=" C LEU I 237 " ideal model delta sigma weight residual 110.91 116.10 -5.19 1.17e+00 7.31e-01 1.97e+01 angle pdb=" N ILE I1109 " pdb=" CA ILE I1109 " pdb=" C ILE I1109 " ideal model delta sigma weight residual 113.07 107.45 5.62 1.36e+00 5.41e-01 1.71e+01 ... (remaining 45704 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.36: 19187 32.36 - 64.71: 1134 64.71 - 97.07: 78 97.07 - 129.42: 5 129.42 - 161.78: 5 Dihedral angle restraints: 20409 sinusoidal: 9372 harmonic: 11037 Sorted by residual: dihedral pdb=" CA PHE I 545 " pdb=" C PHE I 545 " pdb=" N GLU I 546 " pdb=" CA GLU I 546 " ideal model delta harmonic sigma weight residual -180.00 -127.47 -52.53 0 5.00e+00 4.00e-02 1.10e+02 dihedral pdb=" CA PHE I 57 " pdb=" C PHE I 57 " pdb=" N PRO I 58 " pdb=" CA PRO I 58 " ideal model delta harmonic sigma weight residual 180.00 139.27 40.73 0 5.00e+00 4.00e-02 6.64e+01 dihedral pdb=" CA VAL I 442 " pdb=" C VAL I 442 " pdb=" N ASP I 443 " pdb=" CA ASP I 443 " ideal model delta harmonic sigma weight residual -180.00 -145.49 -34.51 0 5.00e+00 4.00e-02 4.76e+01 ... (remaining 20406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 4241 0.060 - 0.119: 896 0.119 - 0.179: 77 0.179 - 0.239: 7 0.239 - 0.298: 3 Chirality restraints: 5224 Sorted by residual: chirality pdb=" C19 1N7 I1401 " pdb=" C18 1N7 I1401 " pdb=" C2 1N7 I1401 " pdb=" C3 1N7 I1401 " both_signs ideal model delta sigma weight residual False -2.53 -2.83 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA ASP I 516 " pdb=" N ASP I 516 " pdb=" C ASP I 516 " pdb=" CB ASP I 516 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C19 1N7 J1504 " pdb=" C18 1N7 J1504 " pdb=" C2 1N7 J1504 " pdb=" C3 1N7 J1504 " both_signs ideal model delta sigma weight residual False -2.53 -2.78 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 5221 not shown) Planarity restraints: 5525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG I 974 " -0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C ARG I 974 " 0.063 2.00e-02 2.50e+03 pdb=" O ARG I 974 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE I 975 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA L 375 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.24e+00 pdb=" C ALA L 375 " 0.053 2.00e-02 2.50e+03 pdb=" O ALA L 375 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS L 376 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET H 51 " 0.050 5.00e-02 4.00e+02 7.54e-02 9.10e+00 pdb=" N PRO H 52 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO H 52 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO H 52 " 0.041 5.00e-02 4.00e+02 ... (remaining 5522 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 370 2.57 - 3.15: 30080 3.15 - 3.73: 51344 3.73 - 4.32: 73007 4.32 - 4.90: 115999 Nonbonded interactions: 270800 Sorted by model distance: nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG J1501 " model vdw 1.987 2.170 nonbonded pdb=" OH TYR I 346 " pdb=" OD1 ASN I 437 " model vdw 2.023 3.040 nonbonded pdb=" OG1 THR I 216 " pdb=" OE1 GLN I 219 " model vdw 2.026 3.040 nonbonded pdb=" O ASN J 962 " pdb=" OG1 THR J 980 " model vdw 2.059 3.040 nonbonded pdb=" OH TYR I 179 " pdb=" OE2 GLU I 458 " model vdw 2.063 3.040 ... (remaining 270795 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 6 through 7 and (name N or name CA or name C or name O or \ name CB )) or resid 8 through 158 or resid 171 through 233 or (resid 234 and (n \ ame N or name CA or name C or name O or name CB )))) selection = (chain 'H' and ((resid 6 through 7 and (name N or name CA or name C or name O or \ name CB )) or resid 8 through 121 or (resid 122 and (name N or name CA or name \ C or name O or name CB )) or resid 123 through 228 or (resid 229 through 230 and \ (name N or name CA or name C or name O or name CB )) or resid 231 through 232 o \ r (resid 233 through 234 and (name N or name CA or name C or name O or name CB ) \ ))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 40.780 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 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 : 0.008 0.310 33454 Z= 0.385 Angle : 0.954 64.649 45715 Z= 0.522 Chirality : 0.047 0.298 5224 Planarity : 0.005 0.075 5525 Dihedral : 18.871 161.776 13291 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 42.35 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.43 % Favored : 88.38 % Rotamer: Outliers : 0.40 % Allowed : 10.91 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -4.03 (0.11), residues: 3805 helix: -1.94 (0.11), residues: 1474 sheet: -3.31 (0.21), residues: 382 loop : -3.18 (0.12), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 842 TYR 0.024 0.002 TYR I 810 PHE 0.026 0.002 PHE J1325 TRP 0.034 0.002 TRP I 807 HIS 0.008 0.002 HIS J 430 Details of bonding type rmsd covalent geometry : bond 0.00811 (33445) covalent geometry : angle 0.88695 (45709) hydrogen bonds : bond 0.14986 ( 1396) hydrogen bonds : angle 7.41680 ( 3858) metal coordination : bond 0.09948 ( 9) metal coordination : angle 30.72869 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 597 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 145 LYS cc_start: 0.9053 (tmmt) cc_final: 0.8417 (tttt) REVERT: H 58 GLU cc_start: 0.6178 (tm-30) cc_final: 0.5874 (tt0) REVERT: H 74 VAL cc_start: 0.7236 (t) cc_final: 0.6382 (m) REVERT: H 83 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8128 (mt) REVERT: H 200 LYS cc_start: 0.8866 (tttt) cc_final: 0.8592 (tttp) REVERT: I 36 GLN cc_start: 0.8021 (tp40) cc_final: 0.7591 (tp40) REVERT: I 40 GLU cc_start: 0.7788 (tt0) cc_final: 0.7512 (tt0) REVERT: I 50 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6732 (tt0) REVERT: I 277 LEU cc_start: 0.3754 (mt) cc_final: 0.3483 (mp) REVERT: I 793 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7649 (mm-30) REVERT: I 1331 ARG cc_start: 0.8471 (ttm170) cc_final: 0.8079 (mtm180) REVERT: J 295 GLU cc_start: 0.8006 (tp30) cc_final: 0.7570 (tp30) REVERT: J 337 ARG cc_start: 0.8501 (mmt-90) cc_final: 0.8293 (mmt90) REVERT: J 555 TYR cc_start: 0.8271 (m-10) cc_final: 0.7846 (m-80) REVERT: J 707 ILE cc_start: 0.8006 (pt) cc_final: 0.7658 (tt) REVERT: J 715 LYS cc_start: 0.7556 (mtpp) cc_final: 0.7275 (mptt) REVERT: J 749 LYS cc_start: 0.8358 (ptmt) cc_final: 0.8148 (mtpt) REVERT: J 785 ASP cc_start: 0.8320 (t0) cc_final: 0.8088 (t0) REVERT: J 991 THR cc_start: 0.6370 (p) cc_final: 0.6088 (p) REVERT: J 1020 TRP cc_start: 0.5491 (p90) cc_final: 0.5276 (p90) REVERT: J 1132 LYS cc_start: 0.4773 (OUTLIER) cc_final: 0.1955 (mtpt) REVERT: J 1349 GLU cc_start: 0.7702 (mp0) cc_final: 0.7271 (mt-10) REVERT: K 55 GLU cc_start: 0.6775 (pp20) cc_final: 0.6409 (pp20) REVERT: K 56 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7701 (mm-30) REVERT: L 136 GLU cc_start: 0.5627 (mt-10) cc_final: 0.3996 (mm-30) REVERT: L 143 TYR cc_start: 0.5491 (t80) cc_final: 0.4630 (t80) REVERT: L 276 MET cc_start: 0.6904 (mpp) cc_final: 0.6510 (mpp) REVERT: L 277 MET cc_start: 0.6646 (tpt) cc_final: 0.6387 (tmm) REVERT: L 297 MET cc_start: 0.1451 (ttm) cc_final: 0.0500 (mtp) REVERT: L 576 VAL cc_start: 0.7664 (t) cc_final: 0.7462 (t) REVERT: M 316 MET cc_start: 0.3865 (tpt) cc_final: 0.1676 (tmm) REVERT: N 9 TYR cc_start: 0.7758 (t80) cc_final: 0.7463 (t80) REVERT: N 65 GLN cc_start: 0.6948 (tt0) cc_final: 0.6471 (tp40) outliers start: 13 outliers final: 9 residues processed: 609 average time/residue: 0.2551 time to fit residues: 236.7459 Evaluate side-chains 387 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 376 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1132 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.0770 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 overall best weight: 1.1740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 23 HIS H 84 ASN H 93 GLN ** I 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 760 ASN I 832 HIS I 834 GLN I 932 GLN I1116 HIS I1135 GLN I1220 GLN J 157 GLN ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 335 GLN ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 465 GLN J 560 ASN J 680 ASN J 720 ASN J 817 HIS J 875 ASN J 910 ASN J 951 GLN J1023 HIS J1249 ASN L 227 GLN L 242 HIS ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 472 GLN L 600 HIS N 30 HIS N 68 GLN N 71 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.152517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.116244 restraints weight = 55804.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.116808 restraints weight = 50044.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.117282 restraints weight = 37527.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.117737 restraints weight = 31504.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.117807 restraints weight = 28149.754| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 33454 Z= 0.155 Angle : 0.703 18.888 45715 Z= 0.365 Chirality : 0.045 0.297 5224 Planarity : 0.005 0.075 5525 Dihedral : 18.715 159.307 5749 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.46 % Favored : 92.43 % Rotamer: Outliers : 2.66 % Allowed : 15.67 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.05 % Twisted Proline : 0.66 % 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 aren not related in a simple way. whole: -2.69 (0.12), residues: 3805 helix: -0.58 (0.12), residues: 1512 sheet: -2.61 (0.24), residues: 361 loop : -2.68 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 67 TYR 0.018 0.002 TYR J 679 PHE 0.019 0.002 PHE H 8 TRP 0.014 0.001 TRP J 580 HIS 0.012 0.001 HIS N 30 Details of bonding type rmsd covalent geometry : bond 0.00353 (33445) covalent geometry : angle 0.69333 (45709) hydrogen bonds : bond 0.04531 ( 1396) hydrogen bonds : angle 5.35246 ( 3858) metal coordination : bond 0.00465 ( 9) metal coordination : angle 10.26808 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 524 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.8003 (OUTLIER) cc_final: 0.7620 (m-80) REVERT: G 68 TYR cc_start: 0.8809 (m-80) cc_final: 0.8141 (m-80) REVERT: G 145 LYS cc_start: 0.9025 (tmmt) cc_final: 0.8151 (tttt) REVERT: G 204 GLU cc_start: 0.7588 (tt0) cc_final: 0.7358 (tt0) REVERT: H 58 GLU cc_start: 0.6550 (tm-30) cc_final: 0.6331 (tt0) REVERT: H 83 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7923 (mt) REVERT: I 50 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6678 (tt0) REVERT: I 119 GLU cc_start: 0.7061 (tm-30) cc_final: 0.6255 (tt0) REVERT: I 219 GLN cc_start: 0.6873 (OUTLIER) cc_final: 0.6666 (pm20) REVERT: I 609 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7538 (tp) REVERT: I 704 MET cc_start: 0.8065 (mmm) cc_final: 0.7841 (tpp) REVERT: I 741 MET cc_start: 0.7855 (ttp) cc_final: 0.7170 (ttp) REVERT: I 974 ARG cc_start: 0.7639 (mmp80) cc_final: 0.7126 (mmp-170) REVERT: I 998 LEU cc_start: 0.5167 (mp) cc_final: 0.4948 (pp) REVERT: I 1137 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.6442 (mp0) REVERT: I 1296 ASP cc_start: 0.8023 (t70) cc_final: 0.7589 (t0) REVERT: I 1331 ARG cc_start: 0.8431 (ttm170) cc_final: 0.8015 (mtm180) REVERT: J 94 GLN cc_start: 0.8237 (mt0) cc_final: 0.8020 (pm20) REVERT: J 151 MET cc_start: 0.5598 (mpp) cc_final: 0.5353 (mpp) REVERT: J 165 TYR cc_start: 0.7992 (t80) cc_final: 0.7765 (t80) REVERT: J 466 MET cc_start: 0.8569 (mtp) cc_final: 0.8318 (mtt) REVERT: J 555 TYR cc_start: 0.8301 (m-10) cc_final: 0.7937 (m-80) REVERT: J 805 GLN cc_start: 0.8439 (pm20) cc_final: 0.8212 (pp30) REVERT: J 868 TRP cc_start: 0.7636 (m100) cc_final: 0.7322 (m100) REVERT: J 918 ILE cc_start: 0.8796 (pt) cc_final: 0.8296 (mt) REVERT: J 1132 LYS cc_start: 0.4085 (OUTLIER) cc_final: 0.3450 (mmtt) REVERT: J 1349 GLU cc_start: 0.7897 (mp0) cc_final: 0.7119 (mt-10) REVERT: J 1368 ASP cc_start: 0.7339 (OUTLIER) cc_final: 0.6037 (m-30) REVERT: J 1372 ARG cc_start: 0.6191 (mmp80) cc_final: 0.5827 (mtm-85) REVERT: K 56 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7816 (mm-30) REVERT: L 105 MET cc_start: 0.8401 (ppp) cc_final: 0.8172 (ppp) REVERT: L 161 LEU cc_start: 0.5671 (tt) cc_final: 0.5361 (tp) REVERT: L 268 TYR cc_start: 0.6638 (t80) cc_final: 0.6322 (t80) REVERT: L 273 MET cc_start: 0.7210 (mmm) cc_final: 0.6862 (mmm) REVERT: L 277 MET cc_start: 0.6978 (tpt) cc_final: 0.6356 (tmm) REVERT: L 297 MET cc_start: 0.0974 (ttm) cc_final: 0.0428 (mtp) REVERT: L 390 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8164 (tp) REVERT: M 316 MET cc_start: 0.3124 (tpt) cc_final: 0.1757 (tmm) REVERT: N 4 GLU cc_start: 0.7007 (mp0) cc_final: 0.6534 (mt-10) REVERT: N 9 TYR cc_start: 0.7667 (t80) cc_final: 0.7230 (t80) REVERT: N 17 MET cc_start: 0.6846 (OUTLIER) cc_final: 0.6407 (mmt) REVERT: N 65 GLN cc_start: 0.7236 (tt0) cc_final: 0.6584 (tp-100) outliers start: 87 outliers final: 43 residues processed: 589 average time/residue: 0.2023 time to fit residues: 188.6771 Evaluate side-chains 450 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 398 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 PHE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 857 VAL Chi-restraints excluded: chain I residue 870 ILE Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 1137 GLU Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1157 GLN Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1132 LYS Chi-restraints excluded: chain J residue 1149 ARG Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain L residue 244 THR Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain L residue 425 TYR Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain N residue 17 MET Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 37 CYS Chi-restraints excluded: chain N residue 58 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 348 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 chunk 226 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 chunk 118 optimal weight: 7.9990 chunk 299 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 chunk 366 optimal weight: 7.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 GLN H 128 HIS I 69 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 760 ASN J 158 GLN J 489 ASN J 954 ASN J1249 ASN ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.147192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.111427 restraints weight = 56311.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.112134 restraints weight = 51213.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.112219 restraints weight = 44721.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.112794 restraints weight = 35138.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.112873 restraints weight = 30335.738| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 33454 Z= 0.292 Angle : 0.777 16.599 45715 Z= 0.403 Chirality : 0.048 0.285 5224 Planarity : 0.006 0.095 5525 Dihedral : 18.767 155.135 5743 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.91 % Favored : 91.04 % Rotamer: Outliers : 5.13 % Allowed : 17.45 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -2.41 (0.13), residues: 3805 helix: -0.34 (0.13), residues: 1490 sheet: -2.45 (0.24), residues: 375 loop : -2.51 (0.13), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 67 TYR 0.021 0.002 TYR L 137 PHE 0.019 0.002 PHE G 231 TRP 0.012 0.002 TRP L 433 HIS 0.011 0.001 HIS N 30 Details of bonding type rmsd covalent geometry : bond 0.00685 (33445) covalent geometry : angle 0.76930 (45709) hydrogen bonds : bond 0.04950 ( 1396) hydrogen bonds : angle 5.43340 ( 3858) metal coordination : bond 0.01348 ( 9) metal coordination : angle 9.44768 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 401 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7642 (m-80) REVERT: H 32 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7302 (tp30) REVERT: H 58 GLU cc_start: 0.6614 (tm-30) cc_final: 0.6262 (tt0) REVERT: H 211 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8458 (pt) REVERT: I 50 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6678 (tt0) REVERT: I 119 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6656 (tt0) REVERT: I 704 MET cc_start: 0.8168 (mmm) cc_final: 0.7904 (tpp) REVERT: I 741 MET cc_start: 0.7733 (ttp) cc_final: 0.7493 (ttp) REVERT: I 1027 LYS cc_start: 0.6227 (mttt) cc_final: 0.6016 (mttt) REVERT: I 1072 ASN cc_start: 0.7845 (p0) cc_final: 0.7438 (p0) REVERT: I 1137 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6707 (mp0) REVERT: I 1331 ARG cc_start: 0.8420 (ttm170) cc_final: 0.8134 (mtm180) REVERT: J 368 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8819 (tt) REVERT: J 466 MET cc_start: 0.8762 (mtp) cc_final: 0.8445 (mtt) REVERT: J 555 TYR cc_start: 0.8409 (m-10) cc_final: 0.8007 (m-80) REVERT: J 785 ASP cc_start: 0.8738 (OUTLIER) cc_final: 0.8418 (m-30) REVERT: J 918 ILE cc_start: 0.8930 (pt) cc_final: 0.8345 (mt) REVERT: J 1040 MET cc_start: 0.4999 (mtp) cc_final: 0.4425 (ptp) REVERT: J 1132 LYS cc_start: 0.4492 (OUTLIER) cc_final: 0.2570 (mmtt) REVERT: J 1282 TYR cc_start: 0.8510 (t80) cc_final: 0.8265 (t80) REVERT: J 1349 GLU cc_start: 0.7791 (mp0) cc_final: 0.7133 (mt-10) REVERT: J 1368 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.5972 (m-30) REVERT: J 1372 ARG cc_start: 0.6416 (mmp80) cc_final: 0.5905 (mtm-85) REVERT: L 105 MET cc_start: 0.8398 (ppp) cc_final: 0.8118 (ppp) REVERT: L 277 MET cc_start: 0.6873 (tpt) cc_final: 0.6385 (tmm) REVERT: L 329 LYS cc_start: 0.6195 (mtpt) cc_final: 0.5054 (mmtp) REVERT: L 507 MET cc_start: 0.7829 (ttp) cc_final: 0.7613 (ttp) REVERT: M 316 MET cc_start: 0.3193 (tpt) cc_final: 0.1762 (tmm) REVERT: N 9 TYR cc_start: 0.7957 (t80) cc_final: 0.7331 (t80) REVERT: N 17 MET cc_start: 0.7024 (OUTLIER) cc_final: 0.6512 (mmt) REVERT: N 36 LEU cc_start: 0.4701 (OUTLIER) cc_final: 0.4428 (mp) REVERT: N 65 GLN cc_start: 0.7180 (tt0) cc_final: 0.6415 (tp-100) REVERT: N 66 GLU cc_start: 0.7789 (mm-30) cc_final: 0.6773 (pt0) outliers start: 168 outliers final: 105 residues processed: 524 average time/residue: 0.1906 time to fit residues: 163.0110 Evaluate side-chains 471 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 355 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 PHE Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 119 GLU Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 760 ASN Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 816 ILE Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 857 VAL Chi-restraints excluded: chain I residue 901 LEU Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 959 ASP Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1137 GLU Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1157 GLN Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 319 SER Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 485 MET Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 605 LEU Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1132 LYS Chi-restraints excluded: chain J residue 1149 ARG Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1328 THR Chi-restraints excluded: chain J residue 1337 VAL Chi-restraints excluded: chain J residue 1356 LEU Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 244 THR Chi-restraints excluded: chain L residue 359 LYS Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 17 MET Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 37 CYS Chi-restraints excluded: chain N residue 59 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 139 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 315 optimal weight: 4.9990 chunk 262 optimal weight: 9.9990 chunk 268 optimal weight: 0.2980 chunk 208 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 224 optimal weight: 0.1980 chunk 311 optimal weight: 0.0980 chunk 334 optimal weight: 9.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 238 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 725 GLN ** I 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1257 GLN ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 594 GLN ** J 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1108 GLN ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.153902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.117822 restraints weight = 56103.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.118730 restraints weight = 51484.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.119119 restraints weight = 37755.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.119468 restraints weight = 31465.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.119585 restraints weight = 28257.815| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33454 Z= 0.125 Angle : 0.632 12.068 45715 Z= 0.329 Chirality : 0.042 0.240 5224 Planarity : 0.004 0.073 5525 Dihedral : 18.191 156.573 5741 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.62 % Favored : 93.32 % Rotamer: Outliers : 4.16 % Allowed : 19.46 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.05 % Twisted Proline : 0.66 % 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 aren not related in a simple way. whole: -1.74 (0.13), residues: 3805 helix: 0.27 (0.13), residues: 1514 sheet: -2.04 (0.25), residues: 379 loop : -2.20 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 758 TYR 0.017 0.001 TYR J 679 PHE 0.021 0.001 PHE I 545 TRP 0.012 0.001 TRP I 807 HIS 0.012 0.001 HIS N 30 Details of bonding type rmsd covalent geometry : bond 0.00276 (33445) covalent geometry : angle 0.62849 (45709) hydrogen bonds : bond 0.03836 ( 1396) hydrogen bonds : angle 4.86909 ( 3858) metal coordination : bond 0.00396 ( 9) metal coordination : angle 5.80973 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 464 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.7663 (OUTLIER) cc_final: 0.7340 (m-10) REVERT: G 145 LYS cc_start: 0.8912 (tmmt) cc_final: 0.8460 (tmtt) REVERT: G 204 GLU cc_start: 0.7515 (tt0) cc_final: 0.7055 (pt0) REVERT: H 58 GLU cc_start: 0.6116 (tm-30) cc_final: 0.5743 (tt0) REVERT: H 83 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7857 (mt) REVERT: I 50 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6631 (tt0) REVERT: I 289 VAL cc_start: 0.3256 (OUTLIER) cc_final: 0.2946 (p) REVERT: I 515 MET cc_start: 0.8692 (ttp) cc_final: 0.8483 (ttt) REVERT: I 609 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7362 (tp) REVERT: I 741 MET cc_start: 0.7714 (ttp) cc_final: 0.7290 (ttp) REVERT: I 742 TYR cc_start: 0.4986 (m-80) cc_final: 0.4496 (m-80) REVERT: I 974 ARG cc_start: 0.7626 (mmp80) cc_final: 0.7209 (mmp-170) REVERT: I 987 GLU cc_start: 0.4672 (OUTLIER) cc_final: 0.3978 (pm20) REVERT: I 1047 LEU cc_start: 0.8584 (mt) cc_final: 0.8279 (mp) REVERT: I 1072 ASN cc_start: 0.7926 (p0) cc_final: 0.7714 (p0) REVERT: I 1240 ASP cc_start: 0.8659 (OUTLIER) cc_final: 0.8346 (m-30) REVERT: I 1319 MET cc_start: 0.6777 (ttm) cc_final: 0.6547 (tpp) REVERT: I 1331 ARG cc_start: 0.8437 (ttm170) cc_final: 0.7904 (mtm180) REVERT: J 78 LEU cc_start: 0.7809 (tp) cc_final: 0.7584 (tt) REVERT: J 94 GLN cc_start: 0.8288 (mt0) cc_final: 0.8045 (pm20) REVERT: J 130 MET cc_start: 0.7356 (ttt) cc_final: 0.7056 (ptm) REVERT: J 197 GLU cc_start: 0.6952 (tt0) cc_final: 0.6299 (tt0) REVERT: J 394 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8334 (mm) REVERT: J 443 GLU cc_start: 0.7286 (mm-30) cc_final: 0.7085 (mp0) REVERT: J 555 TYR cc_start: 0.8254 (m-10) cc_final: 0.7733 (m-80) REVERT: J 785 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.8139 (m-30) REVERT: J 805 GLN cc_start: 0.8448 (pm20) cc_final: 0.8076 (pp30) REVERT: J 918 ILE cc_start: 0.8815 (pt) cc_final: 0.8332 (mt) REVERT: J 1132 LYS cc_start: 0.3884 (OUTLIER) cc_final: 0.3475 (mmtt) REVERT: J 1158 GLU cc_start: 0.5891 (tp30) cc_final: 0.5691 (tp30) REVERT: J 1282 TYR cc_start: 0.8279 (t80) cc_final: 0.8039 (t80) REVERT: J 1341 ARG cc_start: 0.6731 (ttt-90) cc_final: 0.6498 (ttt-90) REVERT: J 1344 LEU cc_start: 0.8308 (mp) cc_final: 0.7359 (mt) REVERT: J 1349 GLU cc_start: 0.7810 (mp0) cc_final: 0.7205 (mt-10) REVERT: J 1368 ASP cc_start: 0.7279 (OUTLIER) cc_final: 0.6015 (m-30) REVERT: J 1372 ARG cc_start: 0.6079 (mmp80) cc_final: 0.5845 (mtm-85) REVERT: K 11 GLU cc_start: 0.6869 (tp30) cc_final: 0.6650 (tp30) REVERT: K 68 GLU cc_start: 0.7887 (tp30) cc_final: 0.7668 (tp30) REVERT: L 102 MET cc_start: 0.8430 (mmt) cc_final: 0.8114 (mmm) REVERT: L 105 MET cc_start: 0.8385 (ppp) cc_final: 0.8058 (ppp) REVERT: L 277 MET cc_start: 0.6724 (tpt) cc_final: 0.6255 (tmm) REVERT: L 297 MET cc_start: 0.1701 (mtp) cc_final: 0.1059 (ttm) REVERT: L 365 MET cc_start: 0.6105 (mmt) cc_final: 0.5492 (mmt) REVERT: L 425 TYR cc_start: 0.7288 (OUTLIER) cc_final: 0.6354 (m-80) REVERT: L 610 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.6820 (t80) REVERT: M 316 MET cc_start: 0.3138 (tpt) cc_final: 0.1748 (tmm) REVERT: N 4 GLU cc_start: 0.7072 (mp0) cc_final: 0.6532 (mt-10) REVERT: N 9 TYR cc_start: 0.7455 (t80) cc_final: 0.6947 (t80) REVERT: N 17 MET cc_start: 0.7010 (OUTLIER) cc_final: 0.6544 (mmt) REVERT: N 65 GLN cc_start: 0.7295 (tt0) cc_final: 0.6443 (tp-100) REVERT: N 66 GLU cc_start: 0.7812 (mm-30) cc_final: 0.6977 (pt0) outliers start: 136 outliers final: 67 residues processed: 562 average time/residue: 0.2098 time to fit residues: 190.8006 Evaluate side-chains 472 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 392 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 PHE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 238 GLN Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 987 GLU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 319 SER Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 394 ILE Chi-restraints excluded: chain J residue 485 MET Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 605 LEU Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1132 LYS Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 244 THR Chi-restraints excluded: chain L residue 402 LEU Chi-restraints excluded: chain L residue 425 TYR Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 610 PHE Chi-restraints excluded: chain M residue 252 ILE Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 17 MET Chi-restraints excluded: chain N residue 30 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 233 optimal weight: 2.9990 chunk 49 optimal weight: 20.0000 chunk 88 optimal weight: 8.9990 chunk 279 optimal weight: 20.0000 chunk 349 optimal weight: 4.9990 chunk 325 optimal weight: 6.9990 chunk 221 optimal weight: 6.9990 chunk 341 optimal weight: 3.9990 chunk 54 optimal weight: 0.1980 chunk 334 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.147995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.111949 restraints weight = 56197.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.113025 restraints weight = 51478.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.112871 restraints weight = 43707.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.113311 restraints weight = 37587.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.113714 restraints weight = 30628.485| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 33454 Z= 0.256 Angle : 0.731 12.737 45715 Z= 0.380 Chirality : 0.046 0.246 5224 Planarity : 0.005 0.083 5525 Dihedral : 18.371 149.927 5741 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.70 % Favored : 91.25 % Rotamer: Outliers : 4.67 % Allowed : 20.07 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: -1.75 (0.13), residues: 3805 helix: 0.20 (0.13), residues: 1499 sheet: -2.03 (0.25), residues: 377 loop : -2.13 (0.14), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I1034 TYR 0.017 0.002 TYR J 723 PHE 0.020 0.002 PHE N 52 TRP 0.013 0.002 TRP L 315 HIS 0.013 0.001 HIS N 30 Details of bonding type rmsd covalent geometry : bond 0.00596 (33445) covalent geometry : angle 0.72565 (45709) hydrogen bonds : bond 0.04548 ( 1396) hydrogen bonds : angle 5.13738 ( 3858) metal coordination : bond 0.01210 ( 9) metal coordination : angle 7.47745 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 377 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.7547 (m-10) REVERT: H 58 GLU cc_start: 0.6324 (tm-30) cc_final: 0.5965 (tt0) REVERT: I 50 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6662 (tt0) REVERT: I 369 MET cc_start: 0.7665 (tmm) cc_final: 0.7396 (tmm) REVERT: I 515 MET cc_start: 0.8722 (ttp) cc_final: 0.8229 (ttt) REVERT: I 741 MET cc_start: 0.7781 (ttp) cc_final: 0.7520 (ttp) REVERT: I 742 TYR cc_start: 0.5249 (m-80) cc_final: 0.4778 (m-80) REVERT: I 987 GLU cc_start: 0.5009 (OUTLIER) cc_final: 0.4311 (pm20) REVERT: I 1024 GLU cc_start: 0.8144 (pp20) cc_final: 0.6936 (mm-30) REVERT: I 1066 MET cc_start: 0.7893 (mtp) cc_final: 0.7549 (mtp) REVERT: I 1304 MET cc_start: 0.8480 (tpp) cc_final: 0.8083 (tpt) REVERT: I 1331 ARG cc_start: 0.8423 (ttm170) cc_final: 0.8123 (mtm180) REVERT: J 24 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8268 (mt) REVERT: J 78 LEU cc_start: 0.7945 (tp) cc_final: 0.7729 (tt) REVERT: J 368 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8763 (tt) REVERT: J 394 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8421 (mm) REVERT: J 555 TYR cc_start: 0.8355 (m-10) cc_final: 0.7837 (m-80) REVERT: J 785 ASP cc_start: 0.8625 (OUTLIER) cc_final: 0.8246 (m-30) REVERT: J 895 CYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8430 (p) REVERT: J 913 GLU cc_start: 0.7466 (tt0) cc_final: 0.7222 (tt0) REVERT: J 918 ILE cc_start: 0.8847 (pt) cc_final: 0.8331 (mt) REVERT: J 1040 MET cc_start: 0.5004 (mtp) cc_final: 0.4574 (ptp) REVERT: J 1132 LYS cc_start: 0.4146 (OUTLIER) cc_final: 0.3811 (mmtt) REVERT: J 1261 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8786 (pt) REVERT: J 1282 TYR cc_start: 0.8648 (t80) cc_final: 0.8329 (t80) REVERT: J 1349 GLU cc_start: 0.7891 (mp0) cc_final: 0.7268 (mt-10) REVERT: J 1368 ASP cc_start: 0.7417 (OUTLIER) cc_final: 0.6015 (m-30) REVERT: J 1372 ARG cc_start: 0.6255 (mmp80) cc_final: 0.5812 (mtm-85) REVERT: K 68 GLU cc_start: 0.7820 (tp30) cc_final: 0.7618 (tp30) REVERT: L 105 MET cc_start: 0.8422 (ppp) cc_final: 0.8082 (ppp) REVERT: L 277 MET cc_start: 0.6698 (tpt) cc_final: 0.6223 (tmm) REVERT: L 329 LYS cc_start: 0.6268 (mtpt) cc_final: 0.5085 (mmmm) REVERT: L 357 GLN cc_start: 0.6671 (mt0) cc_final: 0.6014 (mm-40) REVERT: L 425 TYR cc_start: 0.7494 (OUTLIER) cc_final: 0.6719 (m-80) REVERT: M 316 MET cc_start: 0.3036 (tpt) cc_final: 0.1572 (tmm) REVERT: N 9 TYR cc_start: 0.7944 (t80) cc_final: 0.7267 (t80) REVERT: N 65 GLN cc_start: 0.7347 (tt0) cc_final: 0.6548 (tp-100) REVERT: N 66 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7170 (pt0) outliers start: 153 outliers final: 109 residues processed: 493 average time/residue: 0.2011 time to fit residues: 161.9757 Evaluate side-chains 473 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 353 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 35 PHE Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 959 ASP Chi-restraints excluded: chain I residue 966 ILE Chi-restraints excluded: chain I residue 987 GLU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 319 SER Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 394 ILE Chi-restraints excluded: chain J residue 400 MET Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 485 MET Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 605 LEU Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1132 LYS Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1240 VAL Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1337 VAL Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 70 GLN Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 244 THR Chi-restraints excluded: chain L residue 359 LYS Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 402 LEU Chi-restraints excluded: chain L residue 425 TYR Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 610 PHE Chi-restraints excluded: chain M residue 300 LEU Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 30 HIS Chi-restraints excluded: chain N residue 37 CYS Chi-restraints excluded: chain N residue 40 CYS Chi-restraints excluded: chain N residue 59 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 182 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 209 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 284 optimal weight: 9.9990 chunk 153 optimal weight: 0.9990 chunk 352 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 296 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 219 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 824 GLN ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.149997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.113639 restraints weight = 55976.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115014 restraints weight = 52996.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.115133 restraints weight = 37221.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.115537 restraints weight = 31833.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.115638 restraints weight = 28390.498| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33454 Z= 0.181 Angle : 0.665 11.332 45715 Z= 0.346 Chirality : 0.044 0.235 5224 Planarity : 0.005 0.075 5525 Dihedral : 18.171 148.984 5741 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.52 % Favored : 92.43 % Rotamer: Outliers : 4.58 % Allowed : 21.30 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: -1.56 (0.13), residues: 3805 helix: 0.37 (0.13), residues: 1501 sheet: -1.97 (0.25), residues: 377 loop : -2.04 (0.14), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 67 TYR 0.017 0.001 TYR J 631 PHE 0.016 0.002 PHE N 52 TRP 0.010 0.001 TRP L 315 HIS 0.017 0.001 HIS N 30 Details of bonding type rmsd covalent geometry : bond 0.00419 (33445) covalent geometry : angle 0.66055 (45709) hydrogen bonds : bond 0.04094 ( 1396) hydrogen bonds : angle 4.94872 ( 3858) metal coordination : bond 0.00823 ( 9) metal coordination : angle 6.71333 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 384 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.7846 (OUTLIER) cc_final: 0.7560 (m-10) REVERT: H 58 GLU cc_start: 0.6217 (tm-30) cc_final: 0.5837 (tt0) REVERT: I 50 GLU cc_start: 0.7034 (mt-10) cc_final: 0.6666 (tt0) REVERT: I 515 MET cc_start: 0.8697 (ttp) cc_final: 0.8232 (ttt) REVERT: I 711 ASP cc_start: 0.6348 (m-30) cc_final: 0.6106 (m-30) REVERT: I 741 MET cc_start: 0.7777 (ttp) cc_final: 0.7490 (ttp) REVERT: I 742 TYR cc_start: 0.5308 (m-80) cc_final: 0.4788 (m-80) REVERT: I 1024 GLU cc_start: 0.8177 (pp20) cc_final: 0.7161 (mm-30) REVERT: I 1025 PHE cc_start: 0.7851 (t80) cc_final: 0.7618 (t80) REVERT: I 1066 MET cc_start: 0.8127 (mtp) cc_final: 0.7788 (mtp) REVERT: I 1304 MET cc_start: 0.8469 (tpp) cc_final: 0.8081 (tpt) REVERT: I 1319 MET cc_start: 0.6899 (ttm) cc_final: 0.6501 (tpp) REVERT: I 1331 ARG cc_start: 0.8509 (ttm170) cc_final: 0.7984 (mtm180) REVERT: J 24 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8231 (mt) REVERT: J 155 GLU cc_start: 0.6333 (mp0) cc_final: 0.5672 (pt0) REVERT: J 199 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6310 (mp0) REVERT: J 368 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8821 (tt) REVERT: J 394 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8372 (mm) REVERT: J 555 TYR cc_start: 0.8328 (m-10) cc_final: 0.7836 (m-80) REVERT: J 785 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.8118 (m-30) REVERT: J 807 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8776 (tt) REVERT: J 863 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7402 (tp) REVERT: J 895 CYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8543 (p) REVERT: J 913 GLU cc_start: 0.7493 (tt0) cc_final: 0.7243 (tt0) REVERT: J 918 ILE cc_start: 0.8868 (pt) cc_final: 0.8313 (mt) REVERT: J 1040 MET cc_start: 0.5233 (mtp) cc_final: 0.4846 (ptp) REVERT: J 1078 LEU cc_start: 0.6453 (OUTLIER) cc_final: 0.6134 (mt) REVERT: J 1132 LYS cc_start: 0.4093 (OUTLIER) cc_final: 0.3735 (mmtt) REVERT: J 1261 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8952 (pp) REVERT: J 1282 TYR cc_start: 0.8603 (t80) cc_final: 0.8265 (t80) REVERT: J 1344 LEU cc_start: 0.8483 (mp) cc_final: 0.7500 (mm) REVERT: J 1349 GLU cc_start: 0.7857 (mp0) cc_final: 0.7222 (mt-10) REVERT: J 1368 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.6119 (m-30) REVERT: J 1372 ARG cc_start: 0.6205 (mmp80) cc_final: 0.5796 (mtm-85) REVERT: L 105 MET cc_start: 0.8374 (ppp) cc_final: 0.8100 (ppp) REVERT: L 277 MET cc_start: 0.6656 (tpt) cc_final: 0.6211 (tmm) REVERT: L 329 LYS cc_start: 0.6147 (mtpt) cc_final: 0.5064 (mmtp) REVERT: L 357 GLN cc_start: 0.6958 (mt0) cc_final: 0.6101 (mm-40) REVERT: L 390 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8400 (tp) REVERT: L 425 TYR cc_start: 0.7610 (OUTLIER) cc_final: 0.6844 (m-80) REVERT: L 456 MET cc_start: 0.8289 (tpp) cc_final: 0.8001 (tpp) REVERT: L 610 PHE cc_start: 0.7359 (OUTLIER) cc_final: 0.6669 (t80) REVERT: M 316 MET cc_start: 0.3031 (tpt) cc_final: 0.1480 (tmm) REVERT: N 46 GLU cc_start: 0.5918 (tp30) cc_final: 0.5349 (pm20) REVERT: N 65 GLN cc_start: 0.7421 (tt0) cc_final: 0.6517 (tp-100) REVERT: N 66 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7236 (pt0) REVERT: N 72 TYR cc_start: 0.4528 (OUTLIER) cc_final: 0.3551 (m-10) outliers start: 150 outliers final: 107 residues processed: 494 average time/residue: 0.1784 time to fit residues: 144.1603 Evaluate side-chains 485 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 361 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 35 PHE Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 370 MET Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 966 ILE Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1145 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1177 ARG Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 319 SER Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 394 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 485 MET Chi-restraints excluded: chain J residue 605 LEU Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 679 TYR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 863 LEU Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1025 MET Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1078 LEU Chi-restraints excluded: chain J residue 1132 LYS Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 70 GLN Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 244 THR Chi-restraints excluded: chain L residue 359 LYS Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 425 TYR Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 610 PHE Chi-restraints excluded: chain M residue 300 LEU Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 30 HIS Chi-restraints excluded: chain N residue 35 TYR Chi-restraints excluded: chain N residue 40 CYS Chi-restraints excluded: chain N residue 72 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 290 optimal weight: 8.9990 chunk 291 optimal weight: 2.9990 chunk 255 optimal weight: 0.8980 chunk 49 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 281 optimal weight: 20.0000 chunk 8 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 212 optimal weight: 0.9990 chunk 276 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1023 HIS ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1220 GLN L 227 GLN L 362 ASN ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.149764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.113863 restraints weight = 56300.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.115454 restraints weight = 50493.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.115181 restraints weight = 40608.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.115569 restraints weight = 36096.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.115863 restraints weight = 29584.811| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 33454 Z= 0.190 Angle : 0.668 13.414 45715 Z= 0.347 Chirality : 0.044 0.238 5224 Planarity : 0.005 0.075 5525 Dihedral : 18.075 147.015 5739 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.30 % Favored : 91.64 % Rotamer: Outliers : 4.80 % Allowed : 21.78 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: -1.50 (0.13), residues: 3805 helix: 0.44 (0.13), residues: 1497 sheet: -2.06 (0.24), residues: 405 loop : -1.97 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 67 TYR 0.017 0.002 TYR J 631 PHE 0.019 0.002 PHE I 545 TRP 0.010 0.001 TRP L 315 HIS 0.017 0.001 HIS N 30 Details of bonding type rmsd covalent geometry : bond 0.00440 (33445) covalent geometry : angle 0.66294 (45709) hydrogen bonds : bond 0.04109 ( 1396) hydrogen bonds : angle 4.94661 ( 3858) metal coordination : bond 0.01087 ( 9) metal coordination : angle 7.14082 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 367 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.7821 (OUTLIER) cc_final: 0.7510 (m-10) REVERT: G 145 LYS cc_start: 0.8917 (tmmt) cc_final: 0.8537 (tmtt) REVERT: G 177 TYR cc_start: 0.8845 (OUTLIER) cc_final: 0.7109 (p90) REVERT: H 58 GLU cc_start: 0.6320 (tm-30) cc_final: 0.5964 (tt0) REVERT: H 147 GLN cc_start: 0.7621 (tt0) cc_final: 0.7177 (mt0) REVERT: I 50 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6668 (tt0) REVERT: I 119 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6548 (tt0) REVERT: I 515 MET cc_start: 0.8708 (ttp) cc_final: 0.8262 (ttt) REVERT: I 711 ASP cc_start: 0.6274 (m-30) cc_final: 0.6040 (m-30) REVERT: I 741 MET cc_start: 0.7766 (ttp) cc_final: 0.7466 (ttp) REVERT: I 742 TYR cc_start: 0.5328 (m-80) cc_final: 0.4804 (m-80) REVERT: I 1024 GLU cc_start: 0.8153 (pp20) cc_final: 0.7166 (mm-30) REVERT: I 1066 MET cc_start: 0.8255 (mtp) cc_final: 0.7954 (mtp) REVERT: I 1304 MET cc_start: 0.8474 (tpp) cc_final: 0.8082 (tpt) REVERT: I 1319 MET cc_start: 0.6856 (ttm) cc_final: 0.6383 (tpp) REVERT: I 1331 ARG cc_start: 0.8401 (ttm170) cc_final: 0.7939 (mtm180) REVERT: J 24 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8099 (mt) REVERT: J 130 MET cc_start: 0.7467 (ttt) cc_final: 0.7189 (ptm) REVERT: J 155 GLU cc_start: 0.6361 (mp0) cc_final: 0.5604 (pt0) REVERT: J 199 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6290 (mp0) REVERT: J 334 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8074 (tttm) REVERT: J 394 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8388 (mm) REVERT: J 555 TYR cc_start: 0.8315 (m-10) cc_final: 0.7829 (m-80) REVERT: J 785 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8184 (m-30) REVERT: J 803 VAL cc_start: 0.9480 (OUTLIER) cc_final: 0.9208 (p) REVERT: J 863 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7375 (tp) REVERT: J 895 CYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8556 (p) REVERT: J 918 ILE cc_start: 0.8800 (pt) cc_final: 0.8282 (mt) REVERT: J 1078 LEU cc_start: 0.6458 (OUTLIER) cc_final: 0.6083 (mt) REVERT: J 1132 LYS cc_start: 0.4086 (OUTLIER) cc_final: 0.3724 (mmtt) REVERT: J 1261 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8972 (pp) REVERT: J 1282 TYR cc_start: 0.8641 (t80) cc_final: 0.8358 (t80) REVERT: J 1344 LEU cc_start: 0.8467 (mp) cc_final: 0.7398 (mm) REVERT: J 1349 GLU cc_start: 0.7887 (mp0) cc_final: 0.7223 (mt-10) REVERT: J 1368 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.6116 (m-30) REVERT: J 1372 ARG cc_start: 0.6213 (mmp80) cc_final: 0.5798 (mtm-85) REVERT: L 105 MET cc_start: 0.8386 (ppp) cc_final: 0.8099 (ppp) REVERT: L 277 MET cc_start: 0.6628 (tpt) cc_final: 0.6165 (tmm) REVERT: L 329 LYS cc_start: 0.6032 (mtpt) cc_final: 0.5054 (tptp) REVERT: L 390 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8407 (tp) REVERT: L 425 TYR cc_start: 0.7662 (OUTLIER) cc_final: 0.6894 (m-80) REVERT: L 456 MET cc_start: 0.8304 (tpp) cc_final: 0.8020 (tpp) REVERT: M 316 MET cc_start: 0.2831 (tpt) cc_final: 0.1595 (tmm) REVERT: N 9 TYR cc_start: 0.7750 (t80) cc_final: 0.7306 (t80) REVERT: N 46 GLU cc_start: 0.5971 (tp30) cc_final: 0.5471 (pm20) REVERT: N 65 GLN cc_start: 0.7413 (tt0) cc_final: 0.6671 (tp-100) REVERT: N 66 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7255 (pt0) REVERT: N 72 TYR cc_start: 0.4385 (OUTLIER) cc_final: 0.3600 (m-10) outliers start: 157 outliers final: 116 residues processed: 483 average time/residue: 0.1886 time to fit residues: 149.2536 Evaluate side-chains 492 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 358 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 35 PHE Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 119 GLU Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 370 MET Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 966 ILE Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1145 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1177 ARG Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 334 LYS Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 394 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 485 MET Chi-restraints excluded: chain J residue 605 LEU Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 679 TYR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 863 LEU Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1025 MET Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1078 LEU Chi-restraints excluded: chain J residue 1132 LYS Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 244 THR Chi-restraints excluded: chain L residue 359 LYS Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 402 LEU Chi-restraints excluded: chain L residue 425 TYR Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 610 PHE Chi-restraints excluded: chain M residue 252 ILE Chi-restraints excluded: chain M residue 300 LEU Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 30 HIS Chi-restraints excluded: chain N residue 35 TYR Chi-restraints excluded: chain N residue 37 CYS Chi-restraints excluded: chain N residue 72 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 302 optimal weight: 2.9990 chunk 273 optimal weight: 9.9990 chunk 361 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 240 optimal weight: 0.6980 chunk 298 optimal weight: 6.9990 chunk 299 optimal weight: 0.8980 chunk 235 optimal weight: 0.8980 chunk 117 optimal weight: 0.0370 chunk 189 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1279 GLN ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.154175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.117544 restraints weight = 55937.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.118265 restraints weight = 51688.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.118751 restraints weight = 37164.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.119157 restraints weight = 31919.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.119239 restraints weight = 28414.502| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33454 Z= 0.121 Angle : 0.614 15.172 45715 Z= 0.319 Chirality : 0.042 0.218 5224 Planarity : 0.004 0.069 5525 Dihedral : 17.716 149.323 5739 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.23 % Favored : 93.72 % Rotamer: Outliers : 3.70 % Allowed : 23.13 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.03 % Twisted Proline : 0.66 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -1.20 (0.14), residues: 3805 helix: 0.63 (0.13), residues: 1525 sheet: -1.76 (0.25), residues: 382 loop : -1.82 (0.14), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 436 TYR 0.017 0.001 TYR J 679 PHE 0.012 0.001 PHE I 253 TRP 0.011 0.001 TRP J1020 HIS 0.014 0.001 HIS N 30 Details of bonding type rmsd covalent geometry : bond 0.00267 (33445) covalent geometry : angle 0.61128 (45709) hydrogen bonds : bond 0.03603 ( 1396) hydrogen bonds : angle 4.69426 ( 3858) metal coordination : bond 0.00592 ( 9) metal coordination : angle 5.23436 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 421 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 145 LYS cc_start: 0.8917 (tmmt) cc_final: 0.8619 (tmtt) REVERT: G 177 TYR cc_start: 0.8812 (OUTLIER) cc_final: 0.7036 (p90) REVERT: H 58 GLU cc_start: 0.6091 (tm-30) cc_final: 0.5853 (tt0) REVERT: H 83 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7888 (mt) REVERT: H 133 LEU cc_start: 0.5243 (mt) cc_final: 0.4905 (mt) REVERT: H 147 GLN cc_start: 0.7597 (tt0) cc_final: 0.7182 (mt0) REVERT: H 194 GLN cc_start: 0.7566 (mp10) cc_final: 0.7353 (mp-120) REVERT: I 119 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6631 (tt0) REVERT: I 192 ASP cc_start: 0.6093 (t70) cc_final: 0.5767 (t70) REVERT: I 458 GLU cc_start: 0.7527 (tt0) cc_final: 0.7237 (tt0) REVERT: I 515 MET cc_start: 0.8643 (ttp) cc_final: 0.8112 (ttt) REVERT: I 681 MET cc_start: 0.8144 (mmt) cc_final: 0.7857 (mmt) REVERT: I 711 ASP cc_start: 0.5935 (m-30) cc_final: 0.5700 (m-30) REVERT: I 741 MET cc_start: 0.7863 (ttp) cc_final: 0.7508 (ttp) REVERT: I 742 TYR cc_start: 0.5093 (m-80) cc_final: 0.4470 (m-80) REVERT: I 1024 GLU cc_start: 0.8122 (pp20) cc_final: 0.6881 (mm-30) REVERT: I 1025 PHE cc_start: 0.7650 (t80) cc_final: 0.7444 (t80) REVERT: I 1066 MET cc_start: 0.8012 (mtp) cc_final: 0.7609 (mtp) REVERT: I 1246 ARG cc_start: 0.8648 (ttt180) cc_final: 0.8352 (ttt180) REVERT: I 1296 ASP cc_start: 0.7590 (t70) cc_final: 0.7218 (t0) REVERT: I 1304 MET cc_start: 0.8345 (tpp) cc_final: 0.7929 (tpt) REVERT: I 1319 MET cc_start: 0.6655 (ttm) cc_final: 0.6420 (tpp) REVERT: I 1331 ARG cc_start: 0.8478 (ttm170) cc_final: 0.7980 (mtm180) REVERT: J 24 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.7956 (mt) REVERT: J 155 GLU cc_start: 0.6185 (mp0) cc_final: 0.5694 (pt0) REVERT: J 199 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6213 (mp0) REVERT: J 334 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7990 (tttm) REVERT: J 349 TYR cc_start: 0.8668 (m-80) cc_final: 0.8458 (m-80) REVERT: J 394 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8325 (mm) REVERT: J 555 TYR cc_start: 0.8244 (m-10) cc_final: 0.7760 (m-80) REVERT: J 698 MET cc_start: 0.7840 (mmp) cc_final: 0.7620 (mmt) REVERT: J 785 ASP cc_start: 0.8531 (t0) cc_final: 0.8082 (m-30) REVERT: J 918 ILE cc_start: 0.8828 (pt) cc_final: 0.8303 (mt) REVERT: J 932 MET cc_start: 0.6315 (OUTLIER) cc_final: 0.6115 (ptm) REVERT: J 1040 MET cc_start: 0.5240 (mtp) cc_final: 0.4740 (ptp) REVERT: J 1078 LEU cc_start: 0.6672 (OUTLIER) cc_final: 0.6385 (mt) REVERT: J 1132 LYS cc_start: 0.3993 (OUTLIER) cc_final: 0.3605 (mmtt) REVERT: J 1248 ILE cc_start: 0.8347 (mt) cc_final: 0.8127 (mm) REVERT: J 1282 TYR cc_start: 0.8361 (t80) cc_final: 0.8045 (t80) REVERT: J 1292 LEU cc_start: 0.7944 (mm) cc_final: 0.7659 (mp) REVERT: J 1328 THR cc_start: 0.9019 (p) cc_final: 0.8713 (m) REVERT: J 1344 LEU cc_start: 0.8362 (mp) cc_final: 0.7462 (mt) REVERT: J 1349 GLU cc_start: 0.7915 (mp0) cc_final: 0.7333 (mt-10) REVERT: J 1368 ASP cc_start: 0.7480 (OUTLIER) cc_final: 0.6183 (m-30) REVERT: K 67 ARG cc_start: 0.6476 (mtt-85) cc_final: 0.5737 (ttm-80) REVERT: L 105 MET cc_start: 0.8410 (ppp) cc_final: 0.8118 (ppp) REVERT: L 329 LYS cc_start: 0.5902 (mtpt) cc_final: 0.4934 (tptp) REVERT: L 390 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8361 (tp) REVERT: L 425 TYR cc_start: 0.7612 (OUTLIER) cc_final: 0.6949 (m-80) REVERT: L 456 MET cc_start: 0.8239 (tpp) cc_final: 0.7929 (tpp) REVERT: L 610 PHE cc_start: 0.6909 (OUTLIER) cc_final: 0.6611 (t80) REVERT: M 316 MET cc_start: 0.2809 (tpt) cc_final: 0.1569 (tmm) REVERT: N 46 GLU cc_start: 0.5778 (tp30) cc_final: 0.5446 (pm20) REVERT: N 65 GLN cc_start: 0.7246 (tt0) cc_final: 0.6598 (tp-100) REVERT: N 66 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7117 (pt0) REVERT: N 72 TYR cc_start: 0.4486 (OUTLIER) cc_final: 0.3554 (m-10) outliers start: 121 outliers final: 73 residues processed: 509 average time/residue: 0.1960 time to fit residues: 162.9211 Evaluate side-chains 468 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 380 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain I residue 119 GLU Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 370 MET Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 966 ILE Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1145 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 334 LYS Chi-restraints excluded: chain J residue 394 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 485 MET Chi-restraints excluded: chain J residue 605 LEU Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 679 TYR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1078 LEU Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1132 LYS Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1327 GLU Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 425 TYR Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 610 PHE Chi-restraints excluded: chain M residue 252 ILE Chi-restraints excluded: chain M residue 300 LEU Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 30 HIS Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 40 CYS Chi-restraints excluded: chain N residue 72 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 28 optimal weight: 0.0040 chunk 243 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 278 optimal weight: 30.0000 chunk 209 optimal weight: 4.9990 chunk 72 optimal weight: 0.0170 chunk 49 optimal weight: 10.0000 chunk 210 optimal weight: 5.9990 chunk 198 optimal weight: 0.2980 chunk 60 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.6634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 139 ASN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.154727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.118131 restraints weight = 55874.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.118554 restraints weight = 52853.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.119079 restraints weight = 38855.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.119483 restraints weight = 32833.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.119612 restraints weight = 29525.531| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33454 Z= 0.122 Angle : 0.621 15.038 45715 Z= 0.321 Chirality : 0.041 0.203 5224 Planarity : 0.004 0.070 5525 Dihedral : 17.550 148.833 5737 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.41 % Favored : 93.53 % Rotamer: Outliers : 2.93 % Allowed : 24.01 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: -1.01 (0.14), residues: 3805 helix: 0.78 (0.13), residues: 1520 sheet: -1.60 (0.26), residues: 376 loop : -1.72 (0.14), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J1149 TYR 0.017 0.001 TYR J 679 PHE 0.017 0.001 PHE L 302 TRP 0.013 0.001 TRP J1020 HIS 0.012 0.001 HIS N 30 Details of bonding type rmsd covalent geometry : bond 0.00272 (33445) covalent geometry : angle 0.61871 (45709) hydrogen bonds : bond 0.03533 ( 1396) hydrogen bonds : angle 4.60445 ( 3858) metal coordination : bond 0.00541 ( 9) metal coordination : angle 4.30149 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 404 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 145 LYS cc_start: 0.8909 (tmmt) cc_final: 0.8640 (tmtt) REVERT: H 58 GLU cc_start: 0.6105 (tm-30) cc_final: 0.5856 (tt0) REVERT: H 83 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7913 (mt) REVERT: H 147 GLN cc_start: 0.7579 (tt0) cc_final: 0.7208 (mt0) REVERT: I 50 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6708 (tt0) REVERT: I 119 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6674 (tt0) REVERT: I 192 ASP cc_start: 0.5664 (t70) cc_final: 0.5140 (m-30) REVERT: I 486 THR cc_start: 0.7229 (p) cc_final: 0.6814 (m) REVERT: I 515 MET cc_start: 0.8623 (ttp) cc_final: 0.8107 (ttt) REVERT: I 681 MET cc_start: 0.8137 (mmt) cc_final: 0.7858 (mmt) REVERT: I 741 MET cc_start: 0.7754 (ttp) cc_final: 0.7449 (ttp) REVERT: I 1024 GLU cc_start: 0.7975 (pp20) cc_final: 0.7074 (mm-30) REVERT: I 1066 MET cc_start: 0.8015 (mtp) cc_final: 0.7670 (mtp) REVERT: I 1296 ASP cc_start: 0.7646 (t70) cc_final: 0.7232 (t0) REVERT: I 1319 MET cc_start: 0.6646 (ttm) cc_final: 0.6417 (tpp) REVERT: I 1331 ARG cc_start: 0.8450 (ttm170) cc_final: 0.7924 (mtm180) REVERT: J 24 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.7971 (mt) REVERT: J 199 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6264 (mp0) REVERT: J 394 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8341 (mm) REVERT: J 555 TYR cc_start: 0.8097 (m-10) cc_final: 0.7664 (m-80) REVERT: J 709 ARG cc_start: 0.6389 (tpt170) cc_final: 0.6177 (tpt170) REVERT: J 785 ASP cc_start: 0.8479 (t0) cc_final: 0.8029 (m-30) REVERT: J 918 ILE cc_start: 0.8883 (pt) cc_final: 0.8330 (mt) REVERT: J 1040 MET cc_start: 0.4998 (mtp) cc_final: 0.4469 (ptp) REVERT: J 1132 LYS cc_start: 0.3932 (OUTLIER) cc_final: 0.3600 (mmtt) REVERT: J 1188 GLU cc_start: 0.6432 (pm20) cc_final: 0.5985 (pm20) REVERT: J 1248 ILE cc_start: 0.8380 (mt) cc_final: 0.8133 (mm) REVERT: J 1282 TYR cc_start: 0.8401 (t80) cc_final: 0.8112 (t80) REVERT: J 1328 THR cc_start: 0.8953 (p) cc_final: 0.8652 (m) REVERT: J 1341 ARG cc_start: 0.6692 (ttt-90) cc_final: 0.6481 (tmt170) REVERT: J 1344 LEU cc_start: 0.8349 (mp) cc_final: 0.7507 (mm) REVERT: J 1349 GLU cc_start: 0.7850 (mp0) cc_final: 0.7276 (mt-10) REVERT: J 1368 ASP cc_start: 0.7071 (OUTLIER) cc_final: 0.5834 (m-30) REVERT: K 55 GLU cc_start: 0.6472 (pp20) cc_final: 0.6141 (pp20) REVERT: K 67 ARG cc_start: 0.6467 (mtt-85) cc_final: 0.5754 (ttm-80) REVERT: L 96 ASP cc_start: 0.7612 (t0) cc_final: 0.7272 (t0) REVERT: L 105 MET cc_start: 0.8356 (ppp) cc_final: 0.8085 (ppp) REVERT: L 329 LYS cc_start: 0.5762 (mtpt) cc_final: 0.4958 (tptp) REVERT: L 390 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8404 (tp) REVERT: L 425 TYR cc_start: 0.7586 (OUTLIER) cc_final: 0.6881 (m-80) REVERT: L 456 MET cc_start: 0.8272 (tpp) cc_final: 0.7937 (tpp) REVERT: L 508 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7181 (mm-30) REVERT: L 610 PHE cc_start: 0.6832 (OUTLIER) cc_final: 0.6531 (t80) REVERT: M 316 MET cc_start: 0.2827 (tpt) cc_final: 0.1563 (tmm) REVERT: N 9 TYR cc_start: 0.7552 (t80) cc_final: 0.7140 (t80) REVERT: N 25 GLN cc_start: 0.6930 (mt0) cc_final: 0.6558 (pp30) REVERT: N 46 GLU cc_start: 0.5753 (tp30) cc_final: 0.5434 (pm20) REVERT: N 65 GLN cc_start: 0.7219 (tt0) cc_final: 0.6574 (tp-100) REVERT: N 66 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7135 (pt0) REVERT: N 72 TYR cc_start: 0.4336 (OUTLIER) cc_final: 0.3346 (m-10) outliers start: 96 outliers final: 71 residues processed: 475 average time/residue: 0.1911 time to fit residues: 147.8215 Evaluate side-chains 460 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 378 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 119 GLU Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 370 MET Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 959 ASP Chi-restraints excluded: chain I residue 966 ILE Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1079 ILE Chi-restraints excluded: chain I residue 1145 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 394 ILE Chi-restraints excluded: chain J residue 605 LEU Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 679 TYR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1132 LYS Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 425 TYR Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 610 PHE Chi-restraints excluded: chain M residue 300 LEU Chi-restraints excluded: chain N residue 30 HIS Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 40 CYS Chi-restraints excluded: chain N residue 72 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.4617 > 50: distance: 67 - 70: 26.530 distance: 70 - 71: 27.409 distance: 71 - 72: 23.435 distance: 71 - 74: 25.203 distance: 72 - 73: 25.850 distance: 72 - 78: 26.481 distance: 74 - 75: 25.714 distance: 75 - 76: 18.447 distance: 75 - 77: 7.795 distance: 78 - 79: 22.777 distance: 79 - 80: 44.620 distance: 80 - 81: 44.069 distance: 80 - 82: 23.716 distance: 82 - 83: 32.893 distance: 83 - 84: 37.963 distance: 83 - 86: 37.871 distance: 84 - 85: 26.623 distance: 84 - 91: 22.813 distance: 86 - 87: 4.944 distance: 87 - 88: 17.370 distance: 88 - 89: 30.199 distance: 88 - 90: 18.179 distance: 91 - 92: 42.601 distance: 91 - 97: 65.462 distance: 92 - 93: 30.908 distance: 92 - 95: 20.680 distance: 93 - 94: 27.848 distance: 93 - 98: 6.084 distance: 95 - 96: 12.850 distance: 96 - 97: 39.916 distance: 98 - 99: 29.596 distance: 99 - 100: 31.004 distance: 99 - 102: 37.014 distance: 100 - 101: 20.351 distance: 100 - 106: 21.817 distance: 102 - 103: 12.529 distance: 102 - 104: 21.548 distance: 103 - 105: 21.803 distance: 106 - 107: 19.506 distance: 107 - 108: 7.393 distance: 107 - 110: 17.883 distance: 108 - 109: 13.748 distance: 108 - 114: 19.575 distance: 110 - 111: 23.630 distance: 110 - 112: 10.810 distance: 111 - 113: 5.454 distance: 114 - 115: 40.309 distance: 115 - 116: 38.265 distance: 115 - 118: 28.070 distance: 116 - 117: 8.850 distance: 116 - 121: 10.673 distance: 118 - 119: 36.190 distance: 118 - 120: 20.023 distance: 121 - 122: 42.243 distance: 121 - 127: 49.836 distance: 122 - 123: 41.967 distance: 122 - 125: 11.013 distance: 123 - 128: 40.455 distance: 125 - 126: 10.003 distance: 126 - 127: 18.420 distance: 128 - 129: 18.287 distance: 129 - 130: 12.429 distance: 129 - 132: 14.706 distance: 130 - 131: 44.825 distance: 130 - 134: 23.275 distance: 132 - 133: 35.017 distance: 134 - 135: 25.831 distance: 135 - 136: 44.995 distance: 135 - 138: 24.345 distance: 136 - 137: 39.759 distance: 136 - 143: 34.135 distance: 137 - 163: 33.158 distance: 138 - 139: 12.395 distance: 139 - 140: 39.395 distance: 140 - 141: 23.777 distance: 140 - 142: 16.208