Starting phenix.real_space_refine on Tue Jul 7 05:29:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c9s_45369/07_2026/9c9s_45369_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c9s_45369/07_2026/9c9s_45369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c9s_45369/07_2026/9c9s_45369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c9s_45369/07_2026/9c9s_45369.map" model { file = "/net/cci-nas-00/data/ceres_data/9c9s_45369/07_2026/9c9s_45369_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c9s_45369/07_2026/9c9s_45369_neut.cif" } resolution = 3.09 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= 0.004 sd= 0.039 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: 5 Type Number sf(0) Gaussians P 306 5.49 5 S 107 5.16 5 C 26227 2.51 5 N 7650 2.21 5 O 8873 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 43163 Number of models: 1 Model: "" Number of chains: 26 Chain: "Q" Number of atoms: 5277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5277 Classifications: {'peptide': 660} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 30, 'TRANS': 629} Chain breaks: 3 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 9, 'ASN:plan1': 1, 'GLN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 72 Chain: "R" Number of atoms: 4067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4067 Classifications: {'peptide': 550} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 28, 'TRANS': 521} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 432 Unresolved non-hydrogen angles: 538 Unresolved non-hydrogen dihedrals: 363 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 20, 'ARG:plan': 9, 'GLN:plan1': 5, 'TRP:plan': 3, 'ASP:plan': 9, 'ASN:plan1': 6, 'TYR:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 255 Chain: "S" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1014 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 9, 'TRANS': 115} Chain breaks: 1 Chain: "T" Number of atoms: 3339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3339 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 417} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 3421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3421 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 434} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "V" Number of atoms: 3397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3397 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 18, 'TRANS': 423} Chain: "W" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3394 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 431} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3404 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 18, 'TRANS': 424} Chain: "Y" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3350 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 425} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "Z" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 367 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain breaks: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 41 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "B" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 624 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "F" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 620 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3030 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2997 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "T" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.73, per 1000 atoms: 0.23 Number of scatterers: 43163 At special positions: 0 Unit cell: (131.93, 177.855, 218.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 107 16.00 P 306 15.00 O 8873 8.00 N 7650 7.00 C 26227 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.60 Conformation dependent library (CDL) restraints added in 1.6 seconds 9452 Ramachandran restraints generated. 4726 Oldfield, 0 Emsley, 4726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8944 Finding SS restraints... Secondary structure from input PDB file: 202 helices and 39 sheets defined 50.4% alpha, 9.6% beta 138 base pairs and 250 stacking pairs defined. Time for finding SS restraints: 5.19 Creating SS restraints... Processing helix chain 'Q' and resid 709 through 724 removed outlier: 3.854A pdb=" N GLY Q 713 " --> pdb=" O TYR Q 709 " (cutoff:3.500A) Processing helix chain 'Q' and resid 736 through 753 removed outlier: 3.691A pdb=" N GLN Q 740 " --> pdb=" O GLY Q 736 " (cutoff:3.500A) Processing helix chain 'Q' and resid 766 through 778 Processing helix chain 'Q' and resid 789 through 800 Processing helix chain 'Q' and resid 819 through 826 Processing helix chain 'Q' and resid 843 through 847 removed outlier: 4.222A pdb=" N LYS Q 847 " --> pdb=" O GLN Q 844 " (cutoff:3.500A) Processing helix chain 'Q' and resid 851 through 859 Processing helix chain 'Q' and resid 878 through 888 Processing helix chain 'Q' and resid 894 through 901 removed outlier: 3.548A pdb=" N PHE Q 898 " --> pdb=" O SER Q 894 " (cutoff:3.500A) Processing helix chain 'Q' and resid 921 through 928 removed outlier: 4.196A pdb=" N LEU Q 928 " --> pdb=" O LEU Q 924 " (cutoff:3.500A) Processing helix chain 'Q' and resid 957 through 971 Processing helix chain 'Q' and resid 1004 through 1013 removed outlier: 3.980A pdb=" N HIS Q1013 " --> pdb=" O LYS Q1009 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1014 through 1017 removed outlier: 3.625A pdb=" N PHE Q1017 " --> pdb=" O PRO Q1014 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 1014 through 1017' Processing helix chain 'Q' and resid 1086 through 1094 removed outlier: 3.729A pdb=" N TYR Q1090 " --> pdb=" O PRO Q1086 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1101 through 1111 Processing helix chain 'Q' and resid 1121 through 1133 Processing helix chain 'Q' and resid 1138 through 1144 Processing helix chain 'Q' and resid 1147 through 1155 Processing helix chain 'Q' and resid 1169 through 1178 removed outlier: 3.788A pdb=" N THR Q1178 " --> pdb=" O LEU Q1174 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1185 through 1191 Processing helix chain 'Q' and resid 1192 through 1201 Processing helix chain 'Q' and resid 1202 through 1206 removed outlier: 3.580A pdb=" N CYS Q1205 " --> pdb=" O TYR Q1202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1227 through 1238 Processing helix chain 'Q' and resid 1239 through 1246 Processing helix chain 'Q' and resid 1250 through 1259 Processing helix chain 'Q' and resid 1264 through 1268 Processing helix chain 'Q' and resid 1280 through 1284 removed outlier: 3.608A pdb=" N SER Q1283 " --> pdb=" O LYS Q1280 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER Q1284 " --> pdb=" O ASN Q1281 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 1280 through 1284' Processing helix chain 'Q' and resid 1291 through 1297 Processing helix chain 'Q' and resid 1298 through 1315 removed outlier: 3.827A pdb=" N LYS Q1310 " --> pdb=" O GLU Q1306 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1324 through 1339 removed outlier: 3.708A pdb=" N MET Q1328 " --> pdb=" O MET Q1324 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET Q1331 " --> pdb=" O MET Q1327 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1352 through 1364 removed outlier: 3.616A pdb=" N ASP Q1356 " --> pdb=" O GLU Q1352 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N VAL Q1358 " --> pdb=" O ARG Q1354 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1397 through 1403 Processing helix chain 'Q' and resid 1428 through 1446 removed outlier: 3.618A pdb=" N MET Q1432 " --> pdb=" O ILE Q1428 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP Q1434 " --> pdb=" O GLU Q1430 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG Q1435 " --> pdb=" O ARG Q1431 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 34 removed outlier: 3.526A pdb=" N ALA R 33 " --> pdb=" O GLU R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 87 Processing helix chain 'R' and resid 89 through 95 removed outlier: 3.795A pdb=" N GLN R 95 " --> pdb=" O ALA R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 122 Processing helix chain 'R' and resid 143 through 157 Processing helix chain 'R' and resid 167 through 177 Processing helix chain 'R' and resid 215 through 231 Processing helix chain 'R' and resid 239 through 250 removed outlier: 3.606A pdb=" N TYR R 243 " --> pdb=" O SER R 239 " (cutoff:3.500A) Processing helix chain 'R' and resid 256 through 261 Processing helix chain 'R' and resid 266 through 271 removed outlier: 3.601A pdb=" N ASP R 271 " --> pdb=" O LEU R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 435 through 456 Processing helix chain 'R' and resid 456 through 486 removed outlier: 3.611A pdb=" N LYS R 486 " --> pdb=" O ARG R 482 " (cutoff:3.500A) Processing helix chain 'R' and resid 490 through 506 Processing helix chain 'R' and resid 533 through 542 Processing helix chain 'R' and resid 545 through 570 Processing helix chain 'R' and resid 589 through 597 Processing helix chain 'R' and resid 607 through 611 removed outlier: 3.705A pdb=" N HIS R 610 " --> pdb=" O HIS R 607 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN R 611 " --> pdb=" O GLU R 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 607 through 611' Processing helix chain 'R' and resid 616 through 621 Processing helix chain 'R' and resid 622 through 626 removed outlier: 4.051A pdb=" N ILE R 625 " --> pdb=" O PRO R 622 " (cutoff:3.500A) Processing helix chain 'R' and resid 627 through 632 Processing helix chain 'R' and resid 637 through 647 Processing helix chain 'R' and resid 658 through 666 Processing helix chain 'R' and resid 672 through 677 removed outlier: 3.591A pdb=" N ALA R 675 " --> pdb=" O GLY R 672 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS R 676 " --> pdb=" O GLY R 673 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL R 677 " --> pdb=" O ASN R 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 672 through 677' Processing helix chain 'R' and resid 679 through 692 Processing helix chain 'R' and resid 708 through 720 Processing helix chain 'R' and resid 721 through 728 removed outlier: 3.844A pdb=" N TYR R 724 " --> pdb=" O GLU R 721 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL R 728 " --> pdb=" O ARG R 725 " (cutoff:3.500A) Processing helix chain 'R' and resid 730 through 738 removed outlier: 3.532A pdb=" N TYR R 734 " --> pdb=" O SER R 730 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 40 removed outlier: 4.290A pdb=" N LEU S 33 " --> pdb=" O ARG S 29 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG S 34 " --> pdb=" O LEU S 30 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN S 40 " --> pdb=" O VAL S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 83 removed outlier: 3.567A pdb=" N LEU S 66 " --> pdb=" O SER S 62 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ILE S 67 " --> pdb=" O ALA S 63 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER S 68 " --> pdb=" O ARG S 64 " (cutoff:3.500A) Processing helix chain 'S' and resid 136 through 143 Processing helix chain 'S' and resid 150 through 157 removed outlier: 3.682A pdb=" N GLU S 154 " --> pdb=" O GLY S 150 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 68 removed outlier: 3.842A pdb=" N LYS T 68 " --> pdb=" O LEU T 64 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 97 removed outlier: 3.544A pdb=" N GLY T 97 " --> pdb=" O SER T 93 " (cutoff:3.500A) Processing helix chain 'T' and resid 108 through 111 removed outlier: 3.801A pdb=" N TYR T 111 " --> pdb=" O SER T 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 108 through 111' Processing helix chain 'T' and resid 116 through 127 Processing helix chain 'T' and resid 182 through 192 Processing helix chain 'T' and resid 217 through 219 No H-bonds generated for 'chain 'T' and resid 217 through 219' Processing helix chain 'T' and resid 249 through 257 Processing helix chain 'T' and resid 281 through 298 removed outlier: 3.732A pdb=" N ARG T 285 " --> pdb=" O THR T 281 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP T 297 " --> pdb=" O ALA T 293 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN T 298 " --> pdb=" O LYS T 294 " (cutoff:3.500A) Processing helix chain 'T' and resid 312 through 316 removed outlier: 3.552A pdb=" N LEU T 316 " --> pdb=" O VAL T 313 " (cutoff:3.500A) Processing helix chain 'T' and resid 317 through 328 removed outlier: 3.696A pdb=" N ASN T 325 " --> pdb=" O PHE T 321 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS T 326 " --> pdb=" O THR T 322 " (cutoff:3.500A) Processing helix chain 'T' and resid 360 through 365 Processing helix chain 'T' and resid 376 through 391 Processing helix chain 'T' and resid 396 through 410 removed outlier: 3.751A pdb=" N ASP T 401 " --> pdb=" O SER T 397 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU T 402 " --> pdb=" O SER T 398 " (cutoff:3.500A) Processing helix chain 'T' and resid 411 through 418 Processing helix chain 'T' and resid 418 through 429 removed outlier: 3.683A pdb=" N SER T 429 " --> pdb=" O LEU T 425 " (cutoff:3.500A) Processing helix chain 'T' and resid 435 through 446 removed outlier: 3.520A pdb=" N VAL T 439 " --> pdb=" O VAL T 435 " (cutoff:3.500A) Processing helix chain 'T' and resid 448 through 458 Processing helix chain 'U' and resid 47 through 64 Processing helix chain 'U' and resid 80 through 93 removed outlier: 3.883A pdb=" N GLY U 93 " --> pdb=" O SER U 89 " (cutoff:3.500A) Processing helix chain 'U' and resid 104 through 107 removed outlier: 3.834A pdb=" N PHE U 107 " --> pdb=" O SER U 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 104 through 107' Processing helix chain 'U' and resid 112 through 123 Processing helix chain 'U' and resid 172 through 181 removed outlier: 3.565A pdb=" N LYS U 181 " --> pdb=" O ASP U 177 " (cutoff:3.500A) Processing helix chain 'U' and resid 207 through 209 No H-bonds generated for 'chain 'U' and resid 207 through 209' Processing helix chain 'U' and resid 241 through 250 removed outlier: 3.917A pdb=" N ARG U 250 " --> pdb=" O VAL U 246 " (cutoff:3.500A) Processing helix chain 'U' and resid 253 through 260 Processing helix chain 'U' and resid 266 through 284 removed outlier: 3.956A pdb=" N ARG U 270 " --> pdb=" O ARG U 266 " (cutoff:3.500A) Processing helix chain 'U' and resid 302 through 313 Processing helix chain 'U' and resid 344 through 350 removed outlier: 3.707A pdb=" N ARG U 350 " --> pdb=" O ASP U 346 " (cutoff:3.500A) Processing helix chain 'U' and resid 360 through 375 Processing helix chain 'U' and resid 380 through 394 Processing helix chain 'U' and resid 395 through 413 removed outlier: 4.159A pdb=" N SER U 399 " --> pdb=" O SER U 395 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER U 404 " --> pdb=" O SER U 400 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN U 408 " --> pdb=" O SER U 404 " (cutoff:3.500A) Processing helix chain 'U' and resid 419 through 430 Processing helix chain 'U' and resid 432 through 443 removed outlier: 3.517A pdb=" N SER U 436 " --> pdb=" O ASP U 432 " (cutoff:3.500A) Processing helix chain 'U' and resid 444 through 447 Processing helix chain 'V' and resid 51 through 68 removed outlier: 3.674A pdb=" N LYS V 68 " --> pdb=" O LEU V 64 " (cutoff:3.500A) Processing helix chain 'V' and resid 84 through 97 removed outlier: 3.573A pdb=" N GLY V 97 " --> pdb=" O SER V 93 " (cutoff:3.500A) Processing helix chain 'V' and resid 108 through 111 removed outlier: 3.676A pdb=" N TYR V 111 " --> pdb=" O SER V 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 108 through 111' Processing helix chain 'V' and resid 116 through 127 Processing helix chain 'V' and resid 184 through 192 removed outlier: 3.892A pdb=" N SER V 188 " --> pdb=" O THR V 184 " (cutoff:3.500A) Processing helix chain 'V' and resid 216 through 219 removed outlier: 3.670A pdb=" N ALA V 219 " --> pdb=" O ASP V 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 216 through 219' Processing helix chain 'V' and resid 249 through 258 removed outlier: 3.655A pdb=" N ARG V 258 " --> pdb=" O VAL V 254 " (cutoff:3.500A) Processing helix chain 'V' and resid 264 through 272 removed outlier: 3.507A pdb=" N MET V 268 " --> pdb=" O ASP V 264 " (cutoff:3.500A) Processing helix chain 'V' and resid 281 through 298 removed outlier: 3.790A pdb=" N ARG V 285 " --> pdb=" O THR V 281 " (cutoff:3.500A) Processing helix chain 'V' and resid 313 through 316 Processing helix chain 'V' and resid 317 through 328 Processing helix chain 'V' and resid 360 through 365 Processing helix chain 'V' and resid 376 through 391 Processing helix chain 'V' and resid 396 through 410 Processing helix chain 'V' and resid 411 through 418 Processing helix chain 'V' and resid 418 through 429 Processing helix chain 'V' and resid 435 through 446 Processing helix chain 'V' and resid 448 through 458 Processing helix chain 'W' and resid 47 through 64 removed outlier: 3.522A pdb=" N GLY W 64 " --> pdb=" O MET W 60 " (cutoff:3.500A) Processing helix chain 'W' and resid 80 through 93 removed outlier: 3.857A pdb=" N GLY W 93 " --> pdb=" O SER W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 104 through 106 No H-bonds generated for 'chain 'W' and resid 104 through 106' Processing helix chain 'W' and resid 112 through 123 Processing helix chain 'W' and resid 172 through 181 Processing helix chain 'W' and resid 241 through 250 removed outlier: 4.223A pdb=" N ARG W 250 " --> pdb=" O VAL W 246 " (cutoff:3.500A) Processing helix chain 'W' and resid 252 through 260 removed outlier: 4.092A pdb=" N PHE W 258 " --> pdb=" O PHE W 254 " (cutoff:3.500A) Processing helix chain 'W' and resid 266 through 283 removed outlier: 3.678A pdb=" N ARG W 270 " --> pdb=" O ARG W 266 " (cutoff:3.500A) Processing helix chain 'W' and resid 302 through 313 removed outlier: 3.753A pdb=" N ARG W 311 " --> pdb=" O SER W 307 " (cutoff:3.500A) Processing helix chain 'W' and resid 344 through 350 removed outlier: 3.669A pdb=" N ARG W 350 " --> pdb=" O ASP W 346 " (cutoff:3.500A) Processing helix chain 'W' and resid 360 through 375 Processing helix chain 'W' and resid 380 through 394 Processing helix chain 'W' and resid 395 through 413 removed outlier: 3.759A pdb=" N SER W 399 " --> pdb=" O SER W 395 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE W 403 " --> pdb=" O SER W 399 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N SER W 404 " --> pdb=" O SER W 400 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL W 405 " --> pdb=" O ASN W 401 " (cutoff:3.500A) Processing helix chain 'W' and resid 419 through 430 removed outlier: 3.506A pdb=" N VAL W 423 " --> pdb=" O GLU W 419 " (cutoff:3.500A) Processing helix chain 'W' and resid 432 through 443 removed outlier: 3.961A pdb=" N SER W 436 " --> pdb=" O ASP W 432 " (cutoff:3.500A) Processing helix chain 'W' and resid 444 through 447 Processing helix chain 'X' and resid 51 through 68 removed outlier: 3.821A pdb=" N LYS X 68 " --> pdb=" O LEU X 64 " (cutoff:3.500A) Processing helix chain 'X' and resid 84 through 97 removed outlier: 3.613A pdb=" N LEU X 88 " --> pdb=" O GLY X 84 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY X 97 " --> pdb=" O SER X 93 " (cutoff:3.500A) Processing helix chain 'X' and resid 108 through 111 removed outlier: 3.836A pdb=" N TYR X 111 " --> pdb=" O SER X 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 108 through 111' Processing helix chain 'X' and resid 116 through 127 Processing helix chain 'X' and resid 182 through 192 removed outlier: 3.829A pdb=" N SER X 188 " --> pdb=" O THR X 184 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU X 192 " --> pdb=" O SER X 188 " (cutoff:3.500A) Processing helix chain 'X' and resid 249 through 258 Processing helix chain 'X' and resid 264 through 271 removed outlier: 3.892A pdb=" N GLN X 271 " --> pdb=" O SER X 267 " (cutoff:3.500A) Processing helix chain 'X' and resid 281 through 298 removed outlier: 3.656A pdb=" N ARG X 285 " --> pdb=" O THR X 281 " (cutoff:3.500A) Processing helix chain 'X' and resid 312 through 316 Processing helix chain 'X' and resid 317 through 328 removed outlier: 3.630A pdb=" N LYS X 326 " --> pdb=" O THR X 322 " (cutoff:3.500A) Processing helix chain 'X' and resid 360 through 365 Processing helix chain 'X' and resid 376 through 391 Processing helix chain 'X' and resid 396 through 410 Processing helix chain 'X' and resid 411 through 418 Processing helix chain 'X' and resid 418 through 429 removed outlier: 3.523A pdb=" N SER X 429 " --> pdb=" O LEU X 425 " (cutoff:3.500A) Processing helix chain 'X' and resid 435 through 446 Processing helix chain 'X' and resid 448 through 458 Processing helix chain 'Y' and resid 47 through 64 Processing helix chain 'Y' and resid 80 through 93 removed outlier: 3.601A pdb=" N ALA Y 85 " --> pdb=" O LYS Y 81 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY Y 93 " --> pdb=" O SER Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 104 through 107 removed outlier: 3.810A pdb=" N PHE Y 107 " --> pdb=" O SER Y 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 104 through 107' Processing helix chain 'Y' and resid 112 through 122 Processing helix chain 'Y' and resid 172 through 181 Processing helix chain 'Y' and resid 241 through 249 Processing helix chain 'Y' and resid 255 through 260 Processing helix chain 'Y' and resid 266 through 283 removed outlier: 4.130A pdb=" N ARG Y 270 " --> pdb=" O ARG Y 266 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU Y 282 " --> pdb=" O ALA Y 278 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU Y 283 " --> pdb=" O GLU Y 279 " (cutoff:3.500A) Processing helix chain 'Y' and resid 298 through 301 Processing helix chain 'Y' and resid 302 through 313 removed outlier: 3.744A pdb=" N ARG Y 311 " --> pdb=" O SER Y 307 " (cutoff:3.500A) Processing helix chain 'Y' and resid 340 through 343 Processing helix chain 'Y' and resid 344 through 350 removed outlier: 3.545A pdb=" N ARG Y 350 " --> pdb=" O ASP Y 346 " (cutoff:3.500A) Processing helix chain 'Y' and resid 360 through 375 Processing helix chain 'Y' and resid 380 through 394 Processing helix chain 'Y' and resid 395 through 413 removed outlier: 3.812A pdb=" N SER Y 399 " --> pdb=" O SER Y 395 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE Y 403 " --> pdb=" O SER Y 399 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N SER Y 404 " --> pdb=" O SER Y 400 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL Y 405 " --> pdb=" O ASN Y 401 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN Y 408 " --> pdb=" O SER Y 404 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE Y 409 " --> pdb=" O VAL Y 405 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG Y 413 " --> pdb=" O ILE Y 409 " (cutoff:3.500A) Processing helix chain 'Y' and resid 419 through 430 removed outlier: 3.533A pdb=" N VAL Y 423 " --> pdb=" O GLU Y 419 " (cutoff:3.500A) Processing helix chain 'Y' and resid 432 through 443 removed outlier: 3.574A pdb=" N ASN Y 443 " --> pdb=" O TYR Y 439 " (cutoff:3.500A) Processing helix chain 'Y' and resid 444 through 447 removed outlier: 3.556A pdb=" N TYR Y 447 " --> pdb=" O GLU Y 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 444 through 447' Processing helix chain 'Z' and resid 255 through 277 Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.648A pdb=" N ILE A 124 " --> pdb=" O GLN A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 42 removed outlier: 3.825A pdb=" N ILE B 35 " --> pdb=" O THR B 31 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 77 removed outlier: 4.174A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASN B 65 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP B 69 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA B 77 " --> pdb=" O TYR B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 95 removed outlier: 4.242A pdb=" N VAL B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLN B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 4.212A pdb=" N VAL C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 removed outlier: 3.811A pdb=" N ASN C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'D' and resid 40 through 52 Processing helix chain 'D' and resid 58 through 87 Processing helix chain 'D' and resid 93 through 104 removed outlier: 3.795A pdb=" N ILE D 97 " --> pdb=" O SER D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 127 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.598A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.885A pdb=" N ILE E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP E 106 " --> pdb=" O SER E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 26 through 30 removed outlier: 4.170A pdb=" N ILE F 30 " --> pdb=" O ILE F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 50 through 77 removed outlier: 3.828A pdb=" N VAL F 61 " --> pdb=" O GLY F 57 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU F 64 " --> pdb=" O LYS F 60 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL F 66 " --> pdb=" O PHE F 62 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP F 69 " --> pdb=" O ASN F 65 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR F 72 " --> pdb=" O ARG F 68 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR F 73 " --> pdb=" O ASP F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 95 removed outlier: 3.976A pdb=" N VAL F 87 " --> pdb=" O THR F 83 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL F 88 " --> pdb=" O ALA F 84 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR F 89 " --> pdb=" O MET F 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 22 removed outlier: 3.645A pdb=" N LYS G 21 " --> pdb=" O SER G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 4.656A pdb=" N VAL G 50 " --> pdb=" O SER G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 91 removed outlier: 3.805A pdb=" N ASP G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 98 Processing helix chain 'G' and resid 113 through 117 Processing helix chain 'H' and resid 40 through 52 removed outlier: 3.715A pdb=" N THR H 51 " --> pdb=" O VAL H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 87 Processing helix chain 'H' and resid 93 through 105 removed outlier: 3.864A pdb=" N ILE H 97 " --> pdb=" O SER H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 125 Processing sheet with id=AA1, first strand: chain 'Q' and resid 728 through 729 removed outlier: 6.390A pdb=" N MET Q 838 " --> pdb=" O LEU Q 866 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N LEU Q 868 " --> pdb=" O MET Q 838 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU Q 840 " --> pdb=" O LEU Q 868 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LEU Q 759 " --> pdb=" O ILE Q 839 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ASP Q 841 " --> pdb=" O LEU Q 759 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL Q 761 " --> pdb=" O ASP Q 841 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Q' and resid 783 through 784 Processing sheet with id=AA3, first strand: chain 'Q' and resid 948 through 954 removed outlier: 5.854A pdb=" N ILE Q 948 " --> pdb=" O VAL Q1419 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ARG Q1421 " --> pdb=" O ILE Q 948 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE Q 950 " --> pdb=" O ARG Q1421 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LEU Q1423 " --> pdb=" O ILE Q 950 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N VAL Q 952 " --> pdb=" O LEU Q1423 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU Q1422 " --> pdb=" O PHE Q1391 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL Q1318 " --> pdb=" O PHE Q1370 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N LEU Q1372 " --> pdb=" O VAL Q1318 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE Q1320 " --> pdb=" O LEU Q1372 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Q' and resid 1026 through 1027 removed outlier: 6.038A pdb=" N PHE Q1026 " --> pdb=" O SER Q1215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'Q' and resid 1071 through 1073 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 1071 through 1073 current: chain 'X' and resid 163 through 172 removed outlier: 3.685A pdb=" N GLY X 175 " --> pdb=" O SER X 172 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 175 through 181 current: chain 'X' and resid 209 through 215 removed outlier: 6.596A pdb=" N VAL X 230 " --> pdb=" O VAL X 212 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ARG X 214 " --> pdb=" O VAL X 230 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Q' and resid 1082 through 1084 Processing sheet with id=AA7, first strand: chain 'R' and resid 14 through 15 removed outlier: 3.647A pdb=" N VAL R 275 " --> pdb=" O LEU R 614 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 61 through 64 removed outlier: 3.524A pdb=" N PHE R 63 " --> pdb=" O LEU R 49 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE R 40 " --> pdb=" O LEU R 135 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 67 through 68 removed outlier: 3.942A pdb=" N PHE R 81 " --> pdb=" O THR R 68 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 100 through 101 removed outlier: 3.821A pdb=" N PHE R 104 " --> pdb=" O ASP R 101 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 184 through 189 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 203 through 204 current: chain 'R' and resid 700 through 701 Processing sheet with id=AB3, first strand: chain 'S' and resid 125 through 126 Processing sheet with id=AB4, first strand: chain 'T' and resid 44 through 45 Processing sheet with id=AB5, first strand: chain 'T' and resid 102 through 106 removed outlier: 6.226A pdb=" N CYS T 103 " --> pdb=" O PHE T 309 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ASP T 311 " --> pdb=" O CYS T 103 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU T 105 " --> pdb=" O ASP T 311 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER T 340 " --> pdb=" O LEU T 77 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY T 79 " --> pdb=" O SER T 340 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ALA T 74 " --> pdb=" O LEU T 368 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N VAL T 370 " --> pdb=" O ALA T 74 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU T 76 " --> pdb=" O VAL T 370 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N THR T 372 " --> pdb=" O LEU T 76 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA T 78 " --> pdb=" O THR T 372 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'T' and resid 129 through 151 removed outlier: 5.608A pdb=" N VAL T 144 " --> pdb=" O LYS T 171 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS T 171 " --> pdb=" O VAL T 144 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU T 146 " --> pdb=" O GLY T 169 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 175 through 181 current: chain 'T' and resid 209 through 215 removed outlier: 6.509A pdb=" N VAL T 230 " --> pdb=" O VAL T 212 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ARG T 214 " --> pdb=" O VAL T 230 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'T' and resid 344 through 346 removed outlier: 3.598A pdb=" N SER T 355 " --> pdb=" O THR T 345 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'U' and resid 40 through 41 removed outlier: 3.507A pdb=" N SER U 41 " --> pdb=" O MET U 44 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'U' and resid 98 through 102 removed outlier: 6.247A pdb=" N THR U 99 " --> pdb=" O PHE U 294 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ASP U 296 " --> pdb=" O THR U 99 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE U 101 " --> pdb=" O ASP U 296 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU U 293 " --> pdb=" O MET U 322 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ALA U 324 " --> pdb=" O LEU U 293 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE U 295 " --> pdb=" O ALA U 324 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ALA U 70 " --> pdb=" O ILE U 352 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ILE U 354 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU U 72 " --> pdb=" O ILE U 354 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'U' and resid 126 through 147 removed outlier: 5.307A pdb=" N VAL U 140 " --> pdb=" O LYS U 161 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LYS U 161 " --> pdb=" O VAL U 140 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY U 156 " --> pdb=" O LEU U 171 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 166 through 171 current: chain 'U' and resid 199 through 205 removed outlier: 6.116A pdb=" N VAL U 222 " --> pdb=" O LEU U 202 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ARG U 204 " --> pdb=" O VAL U 222 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'U' and resid 329 through 331 Processing sheet with id=AC3, first strand: chain 'V' and resid 44 through 45 Processing sheet with id=AC4, first strand: chain 'V' and resid 102 through 106 removed outlier: 6.238A pdb=" N CYS V 103 " --> pdb=" O PHE V 309 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ASP V 311 " --> pdb=" O CYS V 103 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU V 105 " --> pdb=" O ASP V 311 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE V 75 " --> pdb=" O LEU V 338 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N SER V 340 " --> pdb=" O ILE V 75 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU V 77 " --> pdb=" O SER V 340 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'V' and resid 129 through 151 removed outlier: 6.194A pdb=" N GLY V 169 " --> pdb=" O THR V 145 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU V 147 " --> pdb=" O ILE V 167 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE V 167 " --> pdb=" O LEU V 147 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N HIS V 165 " --> pdb=" O PRO V 149 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASP V 151 " --> pdb=" O ILE V 163 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE V 163 " --> pdb=" O ASP V 151 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY V 175 " --> pdb=" O SER V 172 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 175 through 178 current: chain 'V' and resid 207 through 214 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 207 through 214 current: chain 'W' and resid 154 through 161 removed outlier: 3.809A pdb=" N GLY W 156 " --> pdb=" O LEU W 171 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 166 through 171 current: chain 'W' and resid 198 through 204 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 198 through 204 current: chain 'Z' and resid 315 through 319 Processing sheet with id=AC6, first strand: chain 'V' and resid 344 through 346 Processing sheet with id=AC7, first strand: chain 'W' and resid 40 through 41 removed outlier: 3.517A pdb=" N SER W 41 " --> pdb=" O MET W 44 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'W' and resid 98 through 102 removed outlier: 6.397A pdb=" N THR W 99 " --> pdb=" O PHE W 294 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ASP W 296 " --> pdb=" O THR W 99 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE W 101 " --> pdb=" O ASP W 296 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU W 293 " --> pdb=" O MET W 322 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ALA W 324 " --> pdb=" O LEU W 293 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE W 295 " --> pdb=" O ALA W 324 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL W 71 " --> pdb=" O MET W 323 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N THR W 325 " --> pdb=" O VAL W 71 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL W 73 " --> pdb=" O THR W 325 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA W 70 " --> pdb=" O ILE W 352 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE W 354 " --> pdb=" O ALA W 70 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU W 72 " --> pdb=" O ILE W 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'W' and resid 329 through 331 Processing sheet with id=AD1, first strand: chain 'X' and resid 44 through 45 removed outlier: 3.513A pdb=" N GLU X 45 " --> pdb=" O PHE X 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'X' and resid 102 through 106 removed outlier: 3.533A pdb=" N ALA X 339 " --> pdb=" O ILE X 310 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE X 75 " --> pdb=" O LEU X 338 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N SER X 340 " --> pdb=" O ILE X 75 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU X 77 " --> pdb=" O SER X 340 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N VAL X 370 " --> pdb=" O ALA X 74 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU X 76 " --> pdb=" O VAL X 370 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'X' and resid 344 through 345 removed outlier: 3.518A pdb=" N SER X 355 " --> pdb=" O THR X 345 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'X' and resid 394 through 395 removed outlier: 7.466A pdb=" N GLN X 394 " --> pdb=" O ILE X 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'Y' and resid 40 through 41 Processing sheet with id=AD6, first strand: chain 'Y' and resid 98 through 102 removed outlier: 6.313A pdb=" N THR Y 99 " --> pdb=" O PHE Y 294 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ASP Y 296 " --> pdb=" O THR Y 99 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE Y 101 " --> pdb=" O ASP Y 296 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ALA Y 70 " --> pdb=" O ILE Y 352 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ILE Y 354 " --> pdb=" O ALA Y 70 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU Y 72 " --> pdb=" O ILE Y 354 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Y' and resid 125 through 147 removed outlier: 5.323A pdb=" N VAL Y 140 " --> pdb=" O LYS Y 161 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS Y 161 " --> pdb=" O VAL Y 140 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY Y 156 " --> pdb=" O LEU Y 171 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 166 through 171 current: chain 'Y' and resid 199 through 204 Processing sheet with id=AD8, first strand: chain 'Y' and resid 330 through 331 Processing sheet with id=AD9, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.745A pdb=" N ARG C 43 " --> pdb=" O ILE D 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AE2, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.278A pdb=" N ARG G 43 " --> pdb=" O ILE H 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'G' and resid 78 through 79 1632 hydrogen bonds defined for protein. 4782 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 352 hydrogen bonds 692 hydrogen bond angles 0 basepair planarities 138 basepair parallelities 250 stacking parallelities Total time for adding SS restraints: 14.59 Time building geometry restraints manager: 4.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10688 1.33 - 1.46: 11366 1.46 - 1.58: 21602 1.58 - 1.71: 607 1.71 - 1.83: 189 Bond restraints: 44452 Sorted by residual: bond pdb=" C1' DC I 37 " pdb=" N1 DC I 37 " ideal model delta sigma weight residual 1.468 1.527 -0.059 1.40e-02 5.10e+03 1.80e+01 bond pdb=" C3' DT I -17 " pdb=" O3' DT I -17 " ideal model delta sigma weight residual 1.435 1.486 -0.051 1.30e-02 5.92e+03 1.52e+01 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.435 1.481 -0.046 1.30e-02 5.92e+03 1.28e+01 bond pdb=" C5' DC I -25 " pdb=" C4' DC I -25 " ideal model delta sigma weight residual 1.512 1.536 -0.024 7.00e-03 2.04e+04 1.18e+01 bond pdb=" C3' DA I -60 " pdb=" O3' DA I -60 " ideal model delta sigma weight residual 1.435 1.391 0.044 1.30e-02 5.92e+03 1.15e+01 ... (remaining 44447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.86: 60994 3.86 - 7.72: 347 7.72 - 11.58: 57 11.58 - 15.44: 10 15.44 - 19.30: 4 Bond angle restraints: 61412 Sorted by residual: angle pdb=" CA GLU A 105 " pdb=" CB GLU A 105 " pdb=" CG GLU A 105 " ideal model delta sigma weight residual 114.10 128.36 -14.26 2.00e+00 2.50e-01 5.08e+01 angle pdb=" O4' DC I -58 " pdb=" C1' DC I -58 " pdb=" N1 DC I -58 " ideal model delta sigma weight residual 108.00 112.78 -4.78 7.00e-01 2.04e+00 4.66e+01 angle pdb=" CA LYS E 56 " pdb=" CB LYS E 56 " pdb=" CG LYS E 56 " ideal model delta sigma weight residual 114.10 126.62 -12.52 2.00e+00 2.50e-01 3.92e+01 angle pdb=" N GLU A 105 " pdb=" CA GLU A 105 " pdb=" CB GLU A 105 " ideal model delta sigma weight residual 110.40 120.22 -9.82 1.63e+00 3.76e-01 3.63e+01 angle pdb=" O4' DA I -38 " pdb=" C4' DA I -38 " pdb=" C3' DA I -38 " ideal model delta sigma weight residual 106.00 102.44 3.56 6.00e-01 2.78e+00 3.53e+01 ... (remaining 61407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.55: 24118 35.55 - 71.10: 2111 71.10 - 106.65: 84 106.65 - 142.20: 1 142.20 - 177.75: 3 Dihedral angle restraints: 26317 sinusoidal: 12480 harmonic: 13837 Sorted by residual: dihedral pdb=" O2A ADP T1001 " pdb=" O3A ADP T1001 " pdb=" PA ADP T1001 " pdb=" PB ADP T1001 " ideal model delta sinusoidal sigma weight residual -60.00 53.18 -113.18 1 2.00e+01 2.50e-03 3.34e+01 dihedral pdb=" O2A ADP W1001 " pdb=" O3A ADP W1001 " pdb=" PA ADP W1001 " pdb=" PB ADP W1001 " ideal model delta sinusoidal sigma weight residual -60.00 -165.01 105.01 1 2.00e+01 2.50e-03 3.02e+01 dihedral pdb=" C5' ADP X1001 " pdb=" O5' ADP X1001 " pdb=" PA ADP X1001 " pdb=" O2A ADP X1001 " ideal model delta sinusoidal sigma weight residual -60.00 -164.36 104.36 1 2.00e+01 2.50e-03 3.00e+01 ... (remaining 26314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 6578 0.092 - 0.184: 545 0.184 - 0.276: 17 0.276 - 0.368: 3 0.368 - 0.460: 1 Chirality restraints: 7144 Sorted by residual: chirality pdb=" CG LEU A 100 " pdb=" CB LEU A 100 " pdb=" CD1 LEU A 100 " pdb=" CD2 LEU A 100 " both_signs ideal model delta sigma weight residual False -2.59 -2.13 -0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" CB ILE Q 873 " pdb=" CA ILE Q 873 " pdb=" CG1 ILE Q 873 " pdb=" CG2 ILE Q 873 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CG LEU B 63 " pdb=" CB LEU B 63 " pdb=" CD1 LEU B 63 " pdb=" CD2 LEU B 63 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 7141 not shown) Planarity restraints: 6830 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 96 " 0.314 9.50e-02 1.11e+02 1.41e-01 1.28e+01 pdb=" NE ARG F 96 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG F 96 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG F 96 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG F 96 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP H 71 " 0.017 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" CG ASP H 71 " -0.058 2.00e-02 2.50e+03 pdb=" OD1 ASP H 71 " 0.022 2.00e-02 2.50e+03 pdb=" OD2 ASP H 71 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE Q1017 " -0.017 2.00e-02 2.50e+03 2.34e-02 9.57e+00 pdb=" CG PHE Q1017 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE Q1017 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE Q1017 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE Q1017 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE Q1017 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE Q1017 " -0.000 2.00e-02 2.50e+03 ... (remaining 6827 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.20: 1 2.20 - 2.87: 15103 2.87 - 3.55: 59516 3.55 - 4.22: 102754 4.22 - 4.90: 169858 Nonbonded interactions: 347232 Sorted by model distance: nonbonded pdb=" CD LYS A 79 " pdb=" OE2 GLU B 75 " model vdw 1.521 3.440 nonbonded pdb=" CG LYS A 79 " pdb=" OE2 GLU B 75 " model vdw 2.198 3.440 nonbonded pdb=" N2 DG I 29 " pdb=" O2 DC J -29 " model vdw 2.261 2.496 nonbonded pdb=" O GLY Q1185 " pdb=" OG SER Q1189 " model vdw 2.284 3.040 nonbonded pdb=" O2 DC I 41 " pdb=" N2 DG J -41 " model vdw 2.286 2.496 ... (remaining 347227 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 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 25 through 91 or (resid 92 and (name N or name CA or name \ C or name O or name CB )) or resid 93 through 103)) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 16 through 62 or (resid 63 and (name N or name CA or name \ C or name O or name CB )) or resid 64 through 87 or (resid 88 and (name N or nam \ e CA or name C or name O or name CB )) or resid 89 through 120)) selection = (chain 'G' and resid 16 through 120) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'T' and resid 22 through 1001) selection = (chain 'V' and (resid 22 through 152 or (resid 161 through 163 and (name N or na \ me CA or name C or name O or name CB )) or resid 164 through 1001)) selection = (chain 'X' and (resid 22 through 152 or (resid 161 through 163 and (name N or na \ me CA or name C or name O or name CB )) or resid 164 through 1001)) } ncs_group { reference = (chain 'U' and (resid 18 through 181 or (resid 182 through 183 and (name N or na \ me CA or name C or name O or name CB )) or resid 184 through 210 or resid 221 th \ rough 459 or resid 1001)) selection = (chain 'W' and (resid 18 through 181 or (resid 182 through 183 and (name N or na \ me CA or name C or name O or name CB )) or resid 184 through 210 or resid 221 th \ rough 1001)) selection = (chain 'Y' and (resid 18 through 182 or (resid 183 and (name N or name CA or nam \ e C or name O or name CB )) or resid 184 through 459 or resid 1001)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 0.780 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 48.130 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.100 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 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 : 0.005 0.074 44453 Z= 0.335 Angle : 0.883 19.301 61412 Z= 0.557 Chirality : 0.050 0.460 7144 Planarity : 0.006 0.141 6830 Dihedral : 22.067 177.752 17373 Min Nonbonded Distance : 1.521 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 25.50 % Favored : 74.50 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.11), residues: 4726 helix: -1.31 (0.09), residues: 2278 sheet: 0.35 (0.20), residues: 654 loop : -1.50 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 37 TYR 0.030 0.002 TYR G 58 PHE 0.053 0.002 PHE Q1017 TRP 0.033 0.002 TRP Q 755 HIS 0.030 0.001 HIS Q 885 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.34 (44452) covalent geometry : angle 0.88333 / 0.56 (61412) hydrogen bonds : bond 0.15132 / 9.73 ( 1984) hydrogen bonds : angle 5.86798 / 4.16 ( 5474) Misc. bond : bond 0.01237 / 0.65 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9452 Ramachandran restraints generated. 4726 Oldfield, 0 Emsley, 4726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9452 Ramachandran restraints generated. 4726 Oldfield, 0 Emsley, 4726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 4141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1091 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8541 (mp0) REVERT: R 643 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8663 (tm-30) REVERT: Y 177 ASP cc_start: 0.8889 (m-30) cc_final: 0.8618 (m-30) REVERT: B 68 ARG cc_start: 0.9463 (ptp90) cc_final: 0.9171 (ptp90) REVERT: C 92 ASP cc_start: 0.9412 (m-30) cc_final: 0.9156 (p0) REVERT: D 102 ARG cc_start: 0.8843 (ttm-80) cc_final: 0.8268 (ttp-170) REVERT: E 79 LYS cc_start: 0.8869 (ttpp) cc_final: 0.8665 (tmmt) REVERT: F 69 ASP cc_start: 0.8865 (m-30) cc_final: 0.7923 (p0) REVERT: F 89 TYR cc_start: 0.8147 (m-80) cc_final: 0.7808 (m-80) REVERT: G 37 ARG cc_start: 0.9172 (ptp90) cc_final: 0.8768 (mtm110) REVERT: G 91 ASP cc_start: 0.8435 (t0) cc_final: 0.8152 (t0) REVERT: H 86 TYR cc_start: 0.8155 (t80) cc_final: 0.7612 (t80) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.2961 time to fit residues: 123.6300 Evaluate side-chains 245 residues out of total 4141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.6980 chunk 494 optimal weight: 30.0000 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.0980 chunk 207 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.074644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.046162 restraints weight = 174609.744| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 3.31 r_work: 0.2767 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 44453 Z= 0.149 Angle : 0.591 8.490 61412 Z= 0.318 Chirality : 0.043 0.254 7144 Planarity : 0.004 0.053 6830 Dihedral : 22.692 179.267 8431 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.31 % Allowed : 23.76 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.12), residues: 4726 helix: 0.38 (0.10), residues: 2290 sheet: 0.46 (0.21), residues: 639 loop : -1.26 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 134 TYR 0.024 0.001 TYR X 462 PHE 0.020 0.001 PHE R 691 TRP 0.016 0.001 TRP Q 755 HIS 0.008 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (44452) covalent geometry : angle 0.59081 / 0.32 (61412) hydrogen bonds : bond 0.04868 / 3.17 ( 1984) hydrogen bonds : angle 4.10016 / 2.90 ( 5474) Misc. bond : bond 0.00404 / 0.21 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9452 Ramachandran restraints generated. 4726 Oldfield, 0 Emsley, 4726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9452 Ramachandran restraints generated. 4726 Oldfield, 0 Emsley, 4726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 4141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 247 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 733 MET cc_start: 0.5225 (mmm) cc_final: 0.4827 (mmm) REVERT: V 268 MET cc_start: 0.8364 (mtt) cc_final: 0.8131 (mtt) REVERT: Y 60 MET cc_start: 0.9246 (mtp) cc_final: 0.9038 (mtp) REVERT: A 94 GLU cc_start: 0.9361 (mm-30) cc_final: 0.9075 (tp30) REVERT: A 97 GLU cc_start: 0.9529 (tt0) cc_final: 0.9262 (tm-30) REVERT: B 68 ARG cc_start: 0.9555 (ptp90) cc_final: 0.9242 (ptt-90) REVERT: C 85 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8848 (tm-30) REVERT: C 96 LYS cc_start: 0.9604 (mmtt) cc_final: 0.9121 (pptt) REVERT: D 36 ARG cc_start: 0.7948 (tpt-90) cc_final: 0.7180 (tpp80) REVERT: E 97 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8543 (pp20) REVERT: F 28 GLN cc_start: 0.9033 (mm-40) cc_final: 0.8644 (mm-40) REVERT: F 69 ASP cc_start: 0.8989 (m-30) cc_final: 0.8025 (p0) REVERT: F 85 MET cc_start: 0.8964 (tpp) cc_final: 0.8661 (tpp) REVERT: G 91 ASP cc_start: 0.8224 (t0) cc_final: 0.8008 (t0) outliers start: 52 outliers final: 24 residues processed: 291 average time/residue: 0.2920 time to fit residues: 136.3194 Evaluate side-chains 250 residues out of total 4141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 225 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 948 ILE Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1318 VAL Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 367 LEU Chi-restraints excluded: chain U residue 175 MET Chi-restraints excluded: chain U residue 300 MET Chi-restraints excluded: chain V residue 42 LYS Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 373 LEU Chi-restraints excluded: chain X residue 44 VAL Chi-restraints excluded: chain X residue 326 LYS Chi-restraints excluded: chain Y residue 95 ASP Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain H residue 51 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 169 optimal weight: 6.9990 chunk 324 optimal weight: 0.8980 chunk 201 optimal weight: 4.9990 chunk 320 optimal weight: 20.0000 chunk 257 optimal weight: 3.9990 chunk 455 optimal weight: 0.9980 chunk 338 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 424 optimal weight: 7.9990 chunk 383 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q1359 HIS R 132 ASN R 659 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 GLN C 42 GLN C 85 GLN ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.074940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.046601 restraints weight = 174625.525| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 3.36 r_work: 0.2776 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 44453 Z= 0.115 Angle : 0.542 8.540 61412 Z= 0.292 Chirality : 0.041 0.243 7144 Planarity : 0.003 0.063 6830 Dihedral : 22.618 176.558 8431 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.69 % Allowed : 23.05 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.12), residues: 4726 helix: 1.06 (0.11), residues: 2296 sheet: 0.50 (0.21), residues: 639 loop : -1.12 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG V 191 TYR 0.020 0.001 TYR X 462 PHE 0.020 0.001 PHE R 691 TRP 0.020 0.001 TRP Q 755 HIS 0.007 0.001 HIS Q 885 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.12 (44452) covalent geometry : angle 0.54180 / 0.29 (61412) hydrogen bonds : bond 0.04139 / 2.72 ( 1984) hydrogen bonds : angle 3.78337 / 2.69 ( 5474) Misc. bond : bond 0.00744 / 0.39 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9452 Ramachandran restraints generated. 4726 Oldfield, 0 Emsley, 4726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9452 Ramachandran restraints generated. 4726 Oldfield, 0 Emsley, 4726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 4141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 244 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 733 MET cc_start: 0.5189 (mmm) cc_final: 0.4821 (mmm) REVERT: Q 1291 MET cc_start: 0.7682 (tpt) cc_final: 0.7414 (tpt) REVERT: S 154 GLU cc_start: 0.8948 (tp30) cc_final: 0.8732 (tp30) REVERT: Y 60 MET cc_start: 0.9216 (mtp) cc_final: 0.8893 (mtp) REVERT: A 94 GLU cc_start: 0.9366 (mm-30) cc_final: 0.9072 (tp30) REVERT: A 97 GLU cc_start: 0.9529 (tt0) cc_final: 0.9235 (tm-30) REVERT: B 68 ARG cc_start: 0.9562 (ptp90) cc_final: 0.9212 (ptp90) REVERT: C 85 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8787 (tm-30) REVERT: C 96 LYS cc_start: 0.9591 (mmtt) cc_final: 0.9133 (pptt) REVERT: D 36 ARG cc_start: 0.7925 (tpt-90) cc_final: 0.7246 (tpp80) REVERT: E 79 LYS cc_start: 0.8987 (ttpp) cc_final: 0.8562 (pptt) REVERT: E 97 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8573 (pp20) REVERT: F 28 GLN cc_start: 0.9040 (mm-40) cc_final: 0.8660 (mm-40) REVERT: F 69 ASP cc_start: 0.8942 (m-30) cc_final: 0.8031 (p0) REVERT: G 72 ARG cc_start: 0.8190 (ttp-110) cc_final: 0.7940 (ttp-110) REVERT: G 91 ASP cc_start: 0.8265 (t0) cc_final: 0.7744 (t0) REVERT: H 50 GLN cc_start: 0.9260 (mm-40) cc_final: 0.9032 (mm-40) REVERT: H 96 GLU cc_start: 0.8863 (mp0) cc_final: 0.8501 (mp0) outliers start: 67 outliers final: 29 residues processed: 297 average time/residue: 0.2660 time to fit residues: 128.5572 Evaluate side-chains 254 residues out of total 4141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 224 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 901 TRP Chi-restraints excluded: chain Q residue 1284 SER Chi-restraints excluded: chain Q residue 1307 LEU Chi-restraints excluded: chain Q residue 1419 VAL Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 367 LEU Chi-restraints excluded: chain U residue 175 MET Chi-restraints excluded: chain U residue 300 MET Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 226 THR Chi-restraints excluded: chain V residue 373 LEU Chi-restraints excluded: chain W residue 29 LEU Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain H residue 40 TYR Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 58 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 488 optimal weight: 40.0000 chunk 485 optimal weight: 50.0000 chunk 175 optimal weight: 2.9990 chunk 385 optimal weight: 0.9990 chunk 324 optimal weight: 4.9990 chunk 446 optimal weight: 7.9990 chunk 215 optimal weight: 1.9990 chunk 224 optimal weight: 0.9980 chunk 197 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1409 HIS T 357 HIS Y 415 ASN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN C 85 GLN ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.074164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.045772 restraints weight = 176246.314| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 3.36 r_work: 0.2753 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 44453 Z= 0.159 Angle : 0.563 9.041 61412 Z= 0.299 Chirality : 0.041 0.240 7144 Planarity : 0.003 0.042 6830 Dihedral : 22.611 176.569 8431 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.91 % Allowed : 22.85 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.13), residues: 4726 helix: 1.42 (0.11), residues: 2298 sheet: 0.47 (0.21), residues: 639 loop : -1.04 (0.15), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 56 TYR 0.030 0.001 TYR D 86 PHE 0.019 0.001 PHE R 691 TRP 0.017 0.001 TRP Q 755 HIS 0.005 0.001 HIS Q 885 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (44452) covalent geometry : angle 0.56262 / 0.30 (61412) hydrogen bonds : bond 0.04216 / 2.78 ( 1984) hydrogen bonds : angle 3.69636 / 2.63 ( 5474) Misc. bond : bond 0.00080 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9452 Ramachandran restraints generated. 4726 Oldfield, 0 Emsley, 4726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9452 Ramachandran restraints generated. 4726 Oldfield, 0 Emsley, 4726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 4141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 234 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 733 MET cc_start: 0.5346 (mmm) cc_final: 0.4971 (mmm) REVERT: Q 1291 MET cc_start: 0.7887 (tpt) cc_final: 0.7656 (tpt) REVERT: T 269 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.7397 (mpp) REVERT: U 378 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8040 (tm-30) REVERT: V 182 ASP cc_start: 0.9069 (OUTLIER) cc_final: 0.8856 (t0) REVERT: Y 60 MET cc_start: 0.9256 (mtp) cc_final: 0.8997 (mtp) REVERT: A 68 GLN cc_start: 0.9328 (OUTLIER) cc_final: 0.8927 (pp30) REVERT: A 94 GLU cc_start: 0.9376 (mm-30) cc_final: 0.9120 (tp30) REVERT: A 97 GLU cc_start: 0.9535 (tt0) cc_final: 0.9249 (tm-30) REVERT: B 68 ARG cc_start: 0.9558 (ptp90) cc_final: 0.9141 (ptp90) REVERT: B 96 ARG cc_start: 0.8201 (ttm-80) cc_final: 0.7889 (ttm-80) REVERT: C 96 LYS cc_start: 0.9579 (mmtt) cc_final: 0.9113 (pptt) REVERT: D 102 ARG cc_start: 0.8894 (ttm-80) cc_final: 0.8162 (ttm110) REVERT: E 97 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8586 (pp20) REVERT: F 28 GLN cc_start: 0.9070 (mm-40) cc_final: 0.8674 (mm-40) REVERT: F 69 ASP cc_start: 0.8985 (m-30) cc_final: 0.8139 (p0) REVERT: F 85 MET cc_start: 0.8848 (tpp) cc_final: 0.8587 (tpp) REVERT: G 91 ASP cc_start: 0.8133 (t0) cc_final: 0.7558 (t0) REVERT: H 96 GLU cc_start: 0.8904 (mp0) cc_final: 0.8552 (mp0) outliers start: 76 outliers final: 43 residues processed: 296 average time/residue: 0.2800 time to fit residues: 135.8287 Evaluate side-chains 270 residues out of total 4141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 223 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 769 ASN Chi-restraints excluded: chain Q residue 901 TRP Chi-restraints excluded: chain Q residue 948 ILE Chi-restraints excluded: chain Q residue 1119 SER Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1284 SER Chi-restraints excluded: chain Q residue 1307 LEU Chi-restraints excluded: chain Q residue 1318 VAL Chi-restraints excluded: chain Q residue 1419 VAL Chi-restraints excluded: chain R residue 21 LEU Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 269 MET Chi-restraints excluded: chain T residue 313 VAL Chi-restraints excluded: chain T residue 367 LEU Chi-restraints excluded: chain U residue 23 HIS Chi-restraints excluded: chain U residue 175 MET Chi-restraints excluded: chain U residue 300 MET Chi-restraints excluded: chain U residue 378 GLU Chi-restraints excluded: chain V residue 42 LYS Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 182 ASP Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 226 THR Chi-restraints excluded: chain W residue 29 LEU Chi-restraints excluded: chain W residue 432 ASP Chi-restraints excluded: chain X residue 44 VAL Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain X residue 326 LYS Chi-restraints excluded: chain Y residue 95 ASP Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 58 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 421 optimal weight: 20.0000 chunk 307 optimal weight: 7.9990 chunk 275 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 347 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 407 optimal weight: 9.9990 chunk 208 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q1254 GLN ** Q1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 190 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.073072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.044607 restraints weight = 174913.685| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 3.34 r_work: 0.2717 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 44453 Z= 0.227 Angle : 0.606 9.451 61412 Z= 0.317 Chirality : 0.042 0.247 7144 Planarity : 0.003 0.042 6830 Dihedral : 22.700 176.799 8431 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.34 % Allowed : 22.68 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.13), residues: 4726 helix: 1.58 (0.11), residues: 2308 sheet: 0.25 (0.20), residues: 653 loop : -0.98 (0.15), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG V 191 TYR 0.030 0.001 TYR X 462 PHE 0.019 0.001 PHE R 691 TRP 0.019 0.001 TRP Q 755 HIS 0.004 0.001 HIS V 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.23 (44452) covalent geometry : angle 0.60596 / 0.32 (61412) hydrogen bonds : bond 0.04692 / 3.11 ( 1984) hydrogen bonds : angle 3.75372 / 2.67 ( 5474) Misc. bond : bond 0.01019 / 0.54 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9452 Ramachandran restraints generated. 4726 Oldfield, 0 Emsley, 4726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9452 Ramachandran restraints generated. 4726 Oldfield, 0 Emsley, 4726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 4141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 236 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 932 MET cc_start: 0.6080 (mmm) cc_final: 0.5850 (mmm) REVERT: Q 1410 ARG cc_start: 0.7190 (OUTLIER) cc_final: 0.6034 (ttt-90) REVERT: T 269 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.7540 (mpp) REVERT: T 317 ASP cc_start: 0.9215 (t70) cc_final: 0.8925 (t70) REVERT: U 165 MET cc_start: 0.8994 (pmm) cc_final: 0.8468 (pmm) REVERT: U 378 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8052 (tm-30) REVERT: A 94 GLU cc_start: 0.9375 (mm-30) cc_final: 0.9113 (tp30) REVERT: A 97 GLU cc_start: 0.9540 (tt0) cc_final: 0.9206 (tm-30) REVERT: B 68 ARG cc_start: 0.9576 (ptp90) cc_final: 0.9121 (ptp90) REVERT: B 85 MET cc_start: 0.8744 (mmp) cc_final: 0.8507 (mmt) REVERT: B 96 ARG cc_start: 0.8323 (ttm-80) cc_final: 0.7854 (ttm-80) REVERT: D 102 ARG cc_start: 0.8923 (ttm-80) cc_final: 0.8224 (ttm110) REVERT: E 97 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8590 (pp20) REVERT: F 85 MET cc_start: 0.8726 (tpp) cc_final: 0.8169 (tpp) REVERT: F 89 TYR cc_start: 0.8532 (m-80) cc_final: 0.7567 (m-10) REVERT: G 91 ASP cc_start: 0.8164 (t0) cc_final: 0.7788 (t0) REVERT: G 93 GLU cc_start: 0.8512 (pm20) cc_final: 0.8218 (pm20) REVERT: H 96 GLU cc_start: 0.8939 (mp0) cc_final: 0.8555 (mp0) outliers start: 93 outliers final: 59 residues processed: 314 average time/residue: 0.2782 time to fit residues: 143.5851 Evaluate side-chains 291 residues out of total 4141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 229 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 769 ASN Chi-restraints excluded: chain Q residue 901 TRP Chi-restraints excluded: chain Q residue 948 ILE Chi-restraints excluded: chain Q residue 1119 SER Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1249 ILE Chi-restraints excluded: chain Q residue 1284 SER Chi-restraints excluded: chain Q residue 1307 LEU Chi-restraints excluded: chain Q residue 1316 HIS Chi-restraints excluded: chain Q residue 1318 VAL Chi-restraints excluded: chain Q residue 1410 ARG Chi-restraints excluded: chain Q residue 1419 VAL Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 21 LEU Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 177 ASN Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 246 MET Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 265 VAL Chi-restraints excluded: chain T residue 269 MET Chi-restraints excluded: chain T residue 367 LEU Chi-restraints excluded: chain U residue 23 HIS Chi-restraints excluded: chain U residue 175 MET Chi-restraints excluded: chain U residue 247 ILE Chi-restraints excluded: chain U residue 300 MET Chi-restraints excluded: chain U residue 378 GLU Chi-restraints excluded: chain V residue 42 LYS Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 226 THR Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 373 LEU Chi-restraints excluded: chain W residue 29 LEU Chi-restraints excluded: chain W residue 82 THR Chi-restraints excluded: chain W residue 432 ASP Chi-restraints excluded: chain W residue 450 ASP Chi-restraints excluded: chain X residue 44 VAL Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain X residue 326 LYS Chi-restraints excluded: chain Y residue 95 ASP Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 360 ASN Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 58 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 440 optimal weight: 10.0000 chunk 139 optimal weight: 1.9990 chunk 458 optimal weight: 2.9990 chunk 210 optimal weight: 8.9990 chunk 293 optimal weight: 0.2980 chunk 88 optimal weight: 1.9990 chunk 290 optimal weight: 0.9980 chunk 169 optimal weight: 0.7980 chunk 396 optimal weight: 8.9990 chunk 341 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... W 407 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.074069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.045644 restraints weight = 175987.822| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 3.36 r_work: 0.2749 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 44453 Z= 0.116 Angle : 0.549 11.138 61412 Z= 0.290 Chirality : 0.041 0.284 7144 Planarity : 0.003 0.044 6830 Dihedral : 22.644 176.577 8431 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.79 % Allowed : 23.48 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.13), residues: 4726 helix: 1.69 (0.11), residues: 2298 sheet: 0.40 (0.21), residues: 629 loop : -0.93 (0.15), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG V 191 TYR 0.022 0.001 TYR D 86 PHE 0.017 0.001 PHE R 691 TRP 0.018 0.001 TRP Q 755 HIS 0.003 0.001 HIS S 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (44452) covalent geometry : angle 0.54924 / 0.29 (61412) hydrogen bonds : bond 0.03876 / 2.54 ( 1984) hydrogen bonds : angle 3.56647 / 2.53 ( 5474) Misc. bond : bond 0.00272 / 0.14 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9452 Ramachandran restraints generated. 4726 Oldfield, 0 Emsley, 4726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9452 Ramachandran restraints generated. 4726 Oldfield, 0 Emsley, 4726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 4141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 240 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 838 MET cc_start: -0.1540 (ptm) cc_final: -0.1751 (ptm) REVERT: Q 871 THR cc_start: 0.8863 (OUTLIER) cc_final: 0.8478 (p) REVERT: Q 1410 ARG cc_start: 0.7063 (OUTLIER) cc_final: 0.5968 (ttt-90) REVERT: R 262 GLU cc_start: 0.8731 (mp0) cc_final: 0.8365 (mp0) REVERT: S 104 GLU cc_start: 0.9032 (tt0) cc_final: 0.8816 (tp30) REVERT: T 269 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.7548 (mpp) REVERT: T 317 ASP cc_start: 0.9197 (t70) cc_final: 0.8897 (t70) REVERT: U 165 MET cc_start: 0.9029 (pmm) cc_final: 0.8488 (pmm) REVERT: U 351 SER cc_start: 0.9579 (OUTLIER) cc_final: 0.9377 (p) REVERT: V 418 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8968 (mp) REVERT: A 94 GLU cc_start: 0.9383 (mm-30) cc_final: 0.9107 (tp30) REVERT: A 97 GLU cc_start: 0.9542 (tt0) cc_final: 0.9159 (tm-30) REVERT: B 96 ARG cc_start: 0.8253 (ttm-80) cc_final: 0.7841 (ttm-80) REVERT: D 86 TYR cc_start: 0.8259 (t80) cc_final: 0.8056 (t80) REVERT: D 102 ARG cc_start: 0.8927 (ttm-80) cc_final: 0.8196 (ttm110) REVERT: E 50 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7902 (pp20) REVERT: E 97 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8569 (pp20) REVERT: F 28 GLN cc_start: 0.9095 (mm-40) cc_final: 0.8714 (mm-40) REVERT: G 91 ASP cc_start: 0.8218 (t0) cc_final: 0.7836 (t0) REVERT: G 93 GLU cc_start: 0.8422 (pm20) cc_final: 0.8121 (pm20) REVERT: H 96 GLU cc_start: 0.8899 (mp0) cc_final: 0.8507 (mp0) outliers start: 71 outliers final: 47 residues processed: 299 average time/residue: 0.2596 time to fit residues: 127.3710 Evaluate side-chains 283 residues out of total 4141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 231 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 769 ASN Chi-restraints excluded: chain Q residue 871 THR Chi-restraints excluded: chain Q residue 885 HIS Chi-restraints excluded: chain Q residue 901 TRP Chi-restraints excluded: chain Q residue 948 ILE Chi-restraints excluded: chain Q residue 1119 SER Chi-restraints excluded: chain Q residue 1234 ASN Chi-restraints excluded: chain Q residue 1284 SER Chi-restraints excluded: chain Q residue 1316 HIS Chi-restraints excluded: chain Q residue 1410 ARG Chi-restraints excluded: chain Q residue 1419 VAL Chi-restraints excluded: chain R residue 21 LEU Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 177 ASN Chi-restraints excluded: chain R residue 707 SER Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 269 MET Chi-restraints excluded: chain T residue 367 LEU Chi-restraints excluded: chain U residue 23 HIS Chi-restraints excluded: chain U residue 44 MET Chi-restraints excluded: chain U residue 175 MET Chi-restraints excluded: chain U residue 300 MET Chi-restraints excluded: chain U residue 351 SER Chi-restraints excluded: chain V residue 42 LYS Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 226 THR Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 418 LEU Chi-restraints excluded: chain V residue 433 GLU Chi-restraints excluded: chain W residue 29 LEU Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 82 THR Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 432 ASP Chi-restraints excluded: chain X residue 44 VAL Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain X residue 326 LYS Chi-restraints excluded: chain Y residue 95 ASP Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain H residue 51 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 3 optimal weight: 9.9990 chunk 442 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 286 optimal weight: 4.9990 chunk 438 optimal weight: 9.9990 chunk 396 optimal weight: 8.9990 chunk 228 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 486 optimal weight: 50.0000 chunk 244 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 23 GLN V 286 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.072583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.044258 restraints weight = 176022.434| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 3.32 r_work: 0.2706 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 44453 Z= 0.252 Angle : 0.612 9.941 61412 Z= 0.321 Chirality : 0.043 0.255 7144 Planarity : 0.003 0.042 6830 Dihedral : 22.705 177.349 8431 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.97 % Allowed : 23.58 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.13), residues: 4726 helix: 1.69 (0.11), residues: 2310 sheet: 0.15 (0.20), residues: 652 loop : -0.95 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 37 TYR 0.030 0.001 TYR X 462 PHE 0.020 0.001 PHE A 67 TRP 0.016 0.001 TRP Q 755 HIS 0.009 0.001 HIS Q 895 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.25 (44452) covalent geometry : angle 0.61215 / 0.32 (61412) hydrogen bonds : bond 0.04778 / 3.17 ( 1984) hydrogen bonds : angle 3.71368 / 2.63 ( 5474) Misc. bond : bond 0.00787 / 0.41 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9452 Ramachandran restraints generated. 4726 Oldfield, 0 Emsley, 4726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9452 Ramachandran restraints generated. 4726 Oldfield, 0 Emsley, 4726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 4141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 236 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 871 THR cc_start: 0.8867 (OUTLIER) cc_final: 0.8496 (p) REVERT: Q 932 MET cc_start: 0.5969 (mmm) cc_final: 0.5620 (mmm) REVERT: Q 1410 ARG cc_start: 0.7084 (OUTLIER) cc_final: 0.5934 (ttt-90) REVERT: R 262 GLU cc_start: 0.8753 (mp0) cc_final: 0.8412 (mp0) REVERT: S 104 GLU cc_start: 0.9047 (tt0) cc_final: 0.8840 (tp30) REVERT: T 269 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.7544 (mpp) REVERT: T 317 ASP cc_start: 0.9239 (t70) cc_final: 0.8959 (t70) REVERT: U 165 MET cc_start: 0.8889 (pmm) cc_final: 0.8408 (pmm) REVERT: U 351 SER cc_start: 0.9588 (OUTLIER) cc_final: 0.9377 (p) REVERT: U 378 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8029 (tm-30) REVERT: V 418 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8997 (mp) REVERT: A 94 GLU cc_start: 0.9389 (mm-30) cc_final: 0.9134 (tp30) REVERT: A 97 GLU cc_start: 0.9544 (tt0) cc_final: 0.9133 (tm-30) REVERT: B 96 ARG cc_start: 0.8329 (ttm-80) cc_final: 0.7916 (ttm-80) REVERT: D 102 ARG cc_start: 0.8955 (ttm-80) cc_final: 0.8266 (ttm110) REVERT: E 50 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7974 (pp20) REVERT: E 97 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8592 (pp20) REVERT: F 28 GLN cc_start: 0.9141 (mm-40) cc_final: 0.8747 (mm-40) REVERT: F 30 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8516 (mm) REVERT: G 91 ASP cc_start: 0.8223 (t0) cc_final: 0.7711 (t0) outliers start: 78 outliers final: 56 residues processed: 300 average time/residue: 0.2633 time to fit residues: 128.8241 Evaluate side-chains 294 residues out of total 4141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 231 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 769 ASN Chi-restraints excluded: chain Q residue 871 THR Chi-restraints excluded: chain Q residue 901 TRP Chi-restraints excluded: chain Q residue 948 ILE Chi-restraints excluded: chain Q residue 1119 SER Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1234 ASN Chi-restraints excluded: chain Q residue 1284 SER Chi-restraints excluded: chain Q residue 1316 HIS Chi-restraints excluded: chain Q residue 1318 VAL Chi-restraints excluded: chain Q residue 1410 ARG Chi-restraints excluded: chain Q residue 1419 VAL Chi-restraints excluded: chain R residue 21 LEU Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 177 ASN Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 246 MET Chi-restraints excluded: chain R residue 707 SER Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 265 VAL Chi-restraints excluded: chain T residue 269 MET Chi-restraints excluded: chain T residue 367 LEU Chi-restraints excluded: chain U residue 23 HIS Chi-restraints excluded: chain U residue 175 MET Chi-restraints excluded: chain U residue 300 MET Chi-restraints excluded: chain U residue 351 SER Chi-restraints excluded: chain U residue 378 GLU Chi-restraints excluded: chain U residue 392 VAL Chi-restraints excluded: chain V residue 42 LYS Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 226 THR Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 418 LEU Chi-restraints excluded: chain V residue 433 GLU Chi-restraints excluded: chain W residue 29 LEU Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 82 THR Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain W residue 432 ASP Chi-restraints excluded: chain X residue 44 VAL Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain X residue 326 LYS Chi-restraints excluded: chain Y residue 95 ASP Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 417 THR Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 58 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 114 optimal weight: 3.9990 chunk 195 optimal weight: 9.9990 chunk 455 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 203 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 379 optimal weight: 0.9990 chunk 409 optimal weight: 4.9990 chunk 249 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 154 ASN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.073206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.044862 restraints weight = 175736.387| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 3.32 r_work: 0.2725 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 44453 Z= 0.160 Angle : 0.567 11.535 61412 Z= 0.298 Chirality : 0.042 0.286 7144 Planarity : 0.003 0.043 6830 Dihedral : 22.682 177.021 8431 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.61 % Allowed : 24.01 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.13), residues: 4726 helix: 1.77 (0.11), residues: 2301 sheet: 0.19 (0.20), residues: 650 loop : -0.92 (0.15), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG V 191 TYR 0.045 0.001 TYR D 86 PHE 0.017 0.001 PHE R 691 TRP 0.015 0.001 TRP Q 755 HIS 0.002 0.001 HIS R 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (44452) covalent geometry : angle 0.56664 / 0.30 (61412) hydrogen bonds : bond 0.04123 / 2.71 ( 1984) hydrogen bonds : angle 3.60712 / 2.56 ( 5474) Misc. bond : bond 0.00294 / 0.15 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9452 Ramachandran restraints generated. 4726 Oldfield, 0 Emsley, 4726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9452 Ramachandran restraints generated. 4726 Oldfield, 0 Emsley, 4726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 4141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 238 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 770 TRP cc_start: 0.7192 (t60) cc_final: 0.6991 (t60) REVERT: Q 871 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8521 (p) REVERT: Q 932 MET cc_start: 0.5909 (mmm) cc_final: 0.5671 (mmm) REVERT: Q 1410 ARG cc_start: 0.6980 (OUTLIER) cc_final: 0.5818 (ttt-90) REVERT: R 262 GLU cc_start: 0.8749 (mp0) cc_final: 0.8407 (mp0) REVERT: S 104 GLU cc_start: 0.9036 (tt0) cc_final: 0.8831 (tp30) REVERT: T 269 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.7559 (mpp) REVERT: T 317 ASP cc_start: 0.9226 (t70) cc_final: 0.8946 (t70) REVERT: U 165 MET cc_start: 0.8894 (pmm) cc_final: 0.8423 (pmm) REVERT: U 378 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8013 (tm-30) REVERT: W 411 MET cc_start: 0.8782 (mpp) cc_final: 0.8346 (mpp) REVERT: X 154 ASN cc_start: 0.9409 (OUTLIER) cc_final: 0.9167 (p0) REVERT: X 355 SER cc_start: 0.9003 (OUTLIER) cc_final: 0.8656 (t) REVERT: A 94 GLU cc_start: 0.9383 (mm-30) cc_final: 0.9134 (tp30) REVERT: A 97 GLU cc_start: 0.9551 (tt0) cc_final: 0.9124 (tm-30) REVERT: B 96 ARG cc_start: 0.8342 (ttm-80) cc_final: 0.7915 (ttm-80) REVERT: D 102 ARG cc_start: 0.8959 (ttm-80) cc_final: 0.8228 (ttm110) REVERT: E 50 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7934 (pp20) REVERT: E 97 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8565 (pp20) REVERT: F 28 GLN cc_start: 0.9153 (mm-40) cc_final: 0.8763 (mm-40) REVERT: G 91 ASP cc_start: 0.8243 (t0) cc_final: 0.7940 (t0) REVERT: G 93 GLU cc_start: 0.8436 (pm20) cc_final: 0.8100 (pm20) REVERT: H 62 MET cc_start: 0.8606 (tpp) cc_final: 0.8254 (tpp) outliers start: 64 outliers final: 51 residues processed: 289 average time/residue: 0.2536 time to fit residues: 119.7931 Evaluate side-chains 289 residues out of total 4141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 232 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 769 ASN Chi-restraints excluded: chain Q residue 871 THR Chi-restraints excluded: chain Q residue 901 TRP Chi-restraints excluded: chain Q residue 948 ILE Chi-restraints excluded: chain Q residue 1119 SER Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1234 ASN Chi-restraints excluded: chain Q residue 1249 ILE Chi-restraints excluded: chain Q residue 1281 ASN Chi-restraints excluded: chain Q residue 1284 SER Chi-restraints excluded: chain Q residue 1316 HIS Chi-restraints excluded: chain Q residue 1410 ARG Chi-restraints excluded: chain Q residue 1419 VAL Chi-restraints excluded: chain R residue 21 LEU Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 177 ASN Chi-restraints excluded: chain R residue 707 SER Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 269 MET Chi-restraints excluded: chain T residue 367 LEU Chi-restraints excluded: chain U residue 23 HIS Chi-restraints excluded: chain U residue 175 MET Chi-restraints excluded: chain U residue 247 ILE Chi-restraints excluded: chain U residue 300 MET Chi-restraints excluded: chain U residue 378 GLU Chi-restraints excluded: chain V residue 42 LYS Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 226 THR Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 433 GLU Chi-restraints excluded: chain W residue 29 LEU Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 82 THR Chi-restraints excluded: chain W residue 432 ASP Chi-restraints excluded: chain W residue 450 ASP Chi-restraints excluded: chain X residue 44 VAL Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain X residue 154 ASN Chi-restraints excluded: chain X residue 326 LYS Chi-restraints excluded: chain X residue 355 SER Chi-restraints excluded: chain Y residue 95 ASP Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 58 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 213 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 183 optimal weight: 3.9990 chunk 14 optimal weight: 20.0000 chunk 324 optimal weight: 3.9990 chunk 184 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 chunk 488 optimal weight: 50.0000 chunk 10 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 119 optimal weight: 0.0970 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 752 HIS Q 899 ASN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.074092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.045799 restraints weight = 174538.903| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 3.33 r_work: 0.2754 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 44453 Z= 0.110 Angle : 0.548 11.619 61412 Z= 0.289 Chirality : 0.041 0.258 7144 Planarity : 0.003 0.044 6830 Dihedral : 22.564 176.634 8431 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.44 % Allowed : 24.19 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.13), residues: 4726 helix: 1.83 (0.11), residues: 2294 sheet: 0.35 (0.21), residues: 628 loop : -0.86 (0.15), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG V 191 TYR 0.032 0.001 TYR D 86 PHE 0.019 0.001 PHE A 67 TRP 0.015 0.001 TRP Q 755 HIS 0.002 0.001 HIS R 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (44452) covalent geometry : angle 0.54826 / 0.29 (61412) hydrogen bonds : bond 0.03685 / 2.41 ( 1984) hydrogen bonds : angle 3.46673 / 2.45 ( 5474) Misc. bond : bond 0.00370 / 0.19 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9452 Ramachandran restraints generated. 4726 Oldfield, 0 Emsley, 4726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9452 Ramachandran restraints generated. 4726 Oldfield, 0 Emsley, 4726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 4141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 244 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 770 TRP cc_start: 0.7188 (t60) cc_final: 0.6974 (t60) REVERT: Q 871 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8451 (p) REVERT: Q 932 MET cc_start: 0.6000 (mmm) cc_final: 0.5725 (mmm) REVERT: Q 1355 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8394 (ptt180) REVERT: R 262 GLU cc_start: 0.8753 (mp0) cc_final: 0.8415 (mp0) REVERT: S 104 GLU cc_start: 0.9036 (tt0) cc_final: 0.8829 (tp30) REVERT: T 317 ASP cc_start: 0.9191 (t70) cc_final: 0.8902 (t70) REVERT: U 165 MET cc_start: 0.8944 (pmm) cc_final: 0.8459 (pmm) REVERT: U 378 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8007 (tm-30) REVERT: W 411 MET cc_start: 0.8637 (mpp) cc_final: 0.8290 (mpp) REVERT: X 355 SER cc_start: 0.8923 (OUTLIER) cc_final: 0.8593 (t) REVERT: A 68 GLN cc_start: 0.9364 (OUTLIER) cc_final: 0.8958 (pp30) REVERT: A 94 GLU cc_start: 0.9352 (mm-30) cc_final: 0.9087 (tp30) REVERT: A 97 GLU cc_start: 0.9556 (tt0) cc_final: 0.9105 (tm-30) REVERT: B 73 TYR cc_start: 0.8981 (m-80) cc_final: 0.8615 (m-80) REVERT: B 96 ARG cc_start: 0.8343 (ttm-80) cc_final: 0.7922 (ttm-80) REVERT: D 102 ARG cc_start: 0.8905 (ttm-80) cc_final: 0.8204 (ttm110) REVERT: E 50 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7983 (pp20) REVERT: E 97 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8549 (pp20) REVERT: F 28 GLN cc_start: 0.9143 (mm-40) cc_final: 0.8769 (mm-40) REVERT: F 89 TYR cc_start: 0.8381 (m-80) cc_final: 0.7603 (m-10) REVERT: G 57 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8439 (mm-30) REVERT: G 91 ASP cc_start: 0.8224 (t0) cc_final: 0.7967 (t0) REVERT: G 93 GLU cc_start: 0.8399 (pm20) cc_final: 0.8025 (pm20) REVERT: H 96 GLU cc_start: 0.8961 (mp0) cc_final: 0.8614 (mp0) outliers start: 57 outliers final: 47 residues processed: 290 average time/residue: 0.2507 time to fit residues: 118.6285 Evaluate side-chains 289 residues out of total 4141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 237 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 769 ASN Chi-restraints excluded: chain Q residue 871 THR Chi-restraints excluded: chain Q residue 901 TRP Chi-restraints excluded: chain Q residue 948 ILE Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1234 ASN Chi-restraints excluded: chain Q residue 1281 ASN Chi-restraints excluded: chain Q residue 1284 SER Chi-restraints excluded: chain Q residue 1316 HIS Chi-restraints excluded: chain Q residue 1355 ARG Chi-restraints excluded: chain Q residue 1419 VAL Chi-restraints excluded: chain R residue 21 LEU Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 177 ASN Chi-restraints excluded: chain R residue 707 SER Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 367 LEU Chi-restraints excluded: chain U residue 23 HIS Chi-restraints excluded: chain U residue 175 MET Chi-restraints excluded: chain U residue 300 MET Chi-restraints excluded: chain U residue 378 GLU Chi-restraints excluded: chain V residue 42 LYS Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 226 THR Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 433 GLU Chi-restraints excluded: chain W residue 29 LEU Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 82 THR Chi-restraints excluded: chain W residue 432 ASP Chi-restraints excluded: chain X residue 44 VAL Chi-restraints excluded: chain X residue 105 LEU Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain X residue 355 SER Chi-restraints excluded: chain Y residue 95 ASP Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain H residue 51 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 200 optimal weight: 0.5980 chunk 384 optimal weight: 3.9990 chunk 176 optimal weight: 0.5980 chunk 179 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 chunk 157 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 386 optimal weight: 1.9990 chunk 268 optimal weight: 4.9990 chunk 119 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q1254 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.074455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.046965 restraints weight = 175741.994| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 3.62 r_work: 0.2753 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 44453 Z= 0.105 Angle : 0.550 14.808 61412 Z= 0.288 Chirality : 0.041 0.260 7144 Planarity : 0.003 0.066 6830 Dihedral : 22.460 175.794 8431 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.31 % Allowed : 24.34 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.13), residues: 4726 helix: 1.84 (0.11), residues: 2303 sheet: 0.37 (0.21), residues: 630 loop : -0.83 (0.15), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG W 397 TYR 0.029 0.001 TYR D 86 PHE 0.016 0.001 PHE R 691 TRP 0.015 0.001 TRP Q 755 HIS 0.002 0.000 HIS R 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (44452) covalent geometry : angle 0.54981 / 0.29 (61412) hydrogen bonds : bond 0.03578 / 2.34 ( 1984) hydrogen bonds : angle 3.40534 / 2.41 ( 5474) Misc. bond : bond 0.00280 / 0.15 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9452 Ramachandran restraints generated. 4726 Oldfield, 0 Emsley, 4726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9452 Ramachandran restraints generated. 4726 Oldfield, 0 Emsley, 4726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 4141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 244 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 770 TRP cc_start: 0.7207 (t60) cc_final: 0.6987 (t60) REVERT: Q 871 THR cc_start: 0.8766 (OUTLIER) cc_final: 0.8392 (p) REVERT: Q 932 MET cc_start: 0.6173 (mmm) cc_final: 0.5876 (mmm) REVERT: Q 1331 MET cc_start: 0.9199 (tmm) cc_final: 0.8918 (tpp) REVERT: Q 1355 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8508 (ptt180) REVERT: Q 1432 MET cc_start: 0.8111 (pmm) cc_final: 0.7473 (ptp) REVERT: R 262 GLU cc_start: 0.8776 (mp0) cc_final: 0.8380 (mp0) REVERT: U 165 MET cc_start: 0.9011 (pmm) cc_final: 0.8532 (pmm) REVERT: U 378 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7999 (tm-30) REVERT: X 148 THR cc_start: 0.9510 (m) cc_final: 0.9281 (p) REVERT: X 355 SER cc_start: 0.8865 (OUTLIER) cc_final: 0.8534 (t) REVERT: Y 86 MET cc_start: 0.9133 (tpp) cc_final: 0.8917 (tpp) REVERT: Y 166 GLU cc_start: 0.9164 (tt0) cc_final: 0.8831 (tt0) REVERT: A 68 GLN cc_start: 0.9355 (OUTLIER) cc_final: 0.8941 (pp30) REVERT: A 94 GLU cc_start: 0.9343 (mm-30) cc_final: 0.9071 (tp30) REVERT: A 97 GLU cc_start: 0.9561 (tt0) cc_final: 0.9091 (tm-30) REVERT: B 64 GLU cc_start: 0.9418 (mm-30) cc_final: 0.9202 (mm-30) REVERT: B 73 TYR cc_start: 0.8944 (m-80) cc_final: 0.8528 (m-80) REVERT: B 96 ARG cc_start: 0.8352 (ttm-80) cc_final: 0.7940 (ttm-80) REVERT: D 102 ARG cc_start: 0.8953 (ttm-80) cc_final: 0.8225 (ttm110) REVERT: E 50 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7986 (pp20) REVERT: E 97 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8535 (pp20) REVERT: F 28 GLN cc_start: 0.9144 (mm-40) cc_final: 0.8791 (mm-40) REVERT: F 89 TYR cc_start: 0.8235 (m-80) cc_final: 0.7863 (m-80) REVERT: G 57 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8440 (mm-30) REVERT: G 91 ASP cc_start: 0.8200 (t0) cc_final: 0.7890 (t0) REVERT: G 93 GLU cc_start: 0.8468 (pm20) cc_final: 0.8102 (pm20) REVERT: H 96 GLU cc_start: 0.8951 (mp0) cc_final: 0.8602 (mp0) outliers start: 52 outliers final: 41 residues processed: 286 average time/residue: 0.2306 time to fit residues: 108.5143 Evaluate side-chains 281 residues out of total 4141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 235 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 871 THR Chi-restraints excluded: chain Q residue 901 TRP Chi-restraints excluded: chain Q residue 948 ILE Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1234 ASN Chi-restraints excluded: chain Q residue 1281 ASN Chi-restraints excluded: chain Q residue 1316 HIS Chi-restraints excluded: chain Q residue 1355 ARG Chi-restraints excluded: chain Q residue 1419 VAL Chi-restraints excluded: chain R residue 177 ASN Chi-restraints excluded: chain R residue 707 SER Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 367 LEU Chi-restraints excluded: chain U residue 23 HIS Chi-restraints excluded: chain U residue 175 MET Chi-restraints excluded: chain U residue 300 MET Chi-restraints excluded: chain U residue 378 GLU Chi-restraints excluded: chain V residue 42 LYS Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 226 THR Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 433 GLU Chi-restraints excluded: chain W residue 29 LEU Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 82 THR Chi-restraints excluded: chain W residue 432 ASP Chi-restraints excluded: chain X residue 44 VAL Chi-restraints excluded: chain X residue 105 LEU Chi-restraints excluded: chain X residue 355 SER Chi-restraints excluded: chain Y residue 95 ASP Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain H residue 51 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 210 optimal weight: 6.9990 chunk 225 optimal weight: 2.9990 chunk 350 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 360 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 238 optimal weight: 0.6980 chunk 128 optimal weight: 0.0010 chunk 98 optimal weight: 30.0000 chunk 148 optimal weight: 4.9990 overall best weight: 1.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.074257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.046019 restraints weight = 175951.538| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.35 r_work: 0.2762 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 44453 Z= 0.116 Angle : 0.545 12.358 61412 Z= 0.285 Chirality : 0.041 0.261 7144 Planarity : 0.003 0.060 6830 Dihedral : 22.437 175.460 8431 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.28 % Allowed : 24.21 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.13), residues: 4726 helix: 1.89 (0.11), residues: 2303 sheet: 0.33 (0.21), residues: 636 loop : -0.80 (0.15), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG V 191 TYR 0.026 0.001 TYR D 86 PHE 0.031 0.001 PHE E 67 TRP 0.015 0.001 TRP Q 755 HIS 0.002 0.000 HIS R 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (44452) covalent geometry : angle 0.54544 / 0.29 (61412) hydrogen bonds : bond 0.03642 / 2.39 ( 1984) hydrogen bonds : angle 3.39055 / 2.40 ( 5474) Misc. bond : bond 0.00370 / 0.19 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12092.42 seconds wall clock time: 207 minutes 9.19 seconds (12429.19 seconds total)