Starting phenix.real_space_refine on Mon Sep 14 12:57:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sba_24974/09_2026/7sba_24974.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sba_24974/09_2026/7sba_24974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7sba_24974/09_2026/7sba_24974.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sba_24974/09_2026/7sba_24974.cif" model { file = "/net/cci-nas-00/data/ceres_data/7sba_24974/09_2026/7sba_24974.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sba_24974/09_2026/7sba_24974.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sba_24974/09_2026/7sba_24974.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sba_24974/09_2026/7sba_24974.map" } resolution = 2.9 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= 0.001 sd= 0.015 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 69 5.49 5 S 117 5.16 5 C 19153 2.51 5 N 5247 2.21 5 O 6065 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30651 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2503 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 10, 'TRANS': 309} Chain: "B" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2503 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 10, 'TRANS': 309} Chain: "C" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2503 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 10, 'TRANS': 309} Chain: "D" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2503 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 10, 'TRANS': 309} Chain: "E" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2503 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 10, 'TRANS': 309} Chain: "F" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2503 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 10, 'TRANS': 309} Chain: "G" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2503 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 10, 'TRANS': 309} Chain: "H" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1929 Classifications: {'peptide': 238} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 223} Chain: "I" Number of atoms: 7323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7323 Classifications: {'peptide': 899} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 39, 'TRANS': 859} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "J" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1194 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain: "K" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1194 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain: "X" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 325 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "Y" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 261 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "Z" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 904 Classifications: {'RNAv2': 43} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 12, 'rna3p_pur': 10, 'rna3p_pyr': 13} Link IDs: {'rna2p': 19, 'rna3p': 23} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.01, per 1000 atoms: 0.23 Number of scatterers: 30651 At special positions: 0 Unit cell: (135.85, 127.49, 230.945, 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 117 16.00 P 69 15.00 O 6065 8.00 N 5247 7.00 C 19153 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 1.4 seconds 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6852 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 40 sheets defined 46.5% alpha, 15.1% beta 12 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 3.54 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 Processing helix chain 'A' and resid 64 through 83 Proline residue: A 71 - end of helix removed outlier: 3.590A pdb=" N ALA A 75 " --> pdb=" O PRO A 71 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 113 Processing helix chain 'A' and resid 137 through 141 Processing helix chain 'A' and resid 188 through 202 Processing helix chain 'A' and resid 231 through 244 Processing helix chain 'A' and resid 250 through 267 Processing helix chain 'A' and resid 279 through 294 removed outlier: 3.689A pdb=" N ILE A 292 " --> pdb=" O GLU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 317 Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 7 through 9 No H-bonds generated for 'chain 'B' and resid 7 through 9' Processing helix chain 'B' and resid 64 through 68 removed outlier: 3.595A pdb=" N GLN B 68 " --> pdb=" O LYS B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 83 Processing helix chain 'B' and resid 107 through 113 Processing helix chain 'B' and resid 137 through 140 Processing helix chain 'B' and resid 188 through 202 Processing helix chain 'B' and resid 231 through 243 Processing helix chain 'B' and resid 250 through 267 removed outlier: 3.568A pdb=" N THR B 260 " --> pdb=" O GLU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 294 removed outlier: 3.942A pdb=" N GLN B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE B 292 " --> pdb=" O GLU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 317 Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 64 through 68 removed outlier: 4.087A pdb=" N GLN C 68 " --> pdb=" O LYS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 83 Processing helix chain 'C' and resid 107 through 113 Processing helix chain 'C' and resid 137 through 140 Processing helix chain 'C' and resid 188 through 202 Processing helix chain 'C' and resid 231 through 243 Processing helix chain 'C' and resid 250 through 267 removed outlier: 3.703A pdb=" N ASP C 264 " --> pdb=" O THR C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 294 removed outlier: 3.612A pdb=" N GLU C 288 " --> pdb=" O THR C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 317 removed outlier: 3.689A pdb=" N LYS C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 6 Processing helix chain 'D' and resid 7 through 9 No H-bonds generated for 'chain 'D' and resid 7 through 9' Processing helix chain 'D' and resid 65 through 83 removed outlier: 3.779A pdb=" N THR D 69 " --> pdb=" O LYS D 65 " (cutoff:3.500A) Proline residue: D 71 - end of helix Processing helix chain 'D' and resid 107 through 113 Processing helix chain 'D' and resid 137 through 140 Processing helix chain 'D' and resid 188 through 202 Processing helix chain 'D' and resid 231 through 243 Processing helix chain 'D' and resid 250 through 267 Processing helix chain 'D' and resid 279 through 295 removed outlier: 3.567A pdb=" N ILE D 292 " --> pdb=" O GLU D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 317 Processing helix chain 'E' and resid 2 through 6 Processing helix chain 'E' and resid 64 through 83 removed outlier: 4.091A pdb=" N GLN E 68 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N THR E 69 " --> pdb=" O LYS E 65 " (cutoff:3.500A) Proline residue: E 71 - end of helix Processing helix chain 'E' and resid 107 through 113 Processing helix chain 'E' and resid 137 through 140 Processing helix chain 'E' and resid 188 through 202 Processing helix chain 'E' and resid 231 through 244 Processing helix chain 'E' and resid 250 through 267 Processing helix chain 'E' and resid 279 through 294 removed outlier: 3.952A pdb=" N GLN E 287 " --> pdb=" O ASP E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 317 Processing helix chain 'F' and resid 2 through 6 Processing helix chain 'F' and resid 7 through 9 No H-bonds generated for 'chain 'F' and resid 7 through 9' Processing helix chain 'F' and resid 69 through 83 removed outlier: 3.511A pdb=" N ALA F 75 " --> pdb=" O PRO F 71 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU F 79 " --> pdb=" O ALA F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 113 Processing helix chain 'F' and resid 137 through 140 Processing helix chain 'F' and resid 188 through 202 Processing helix chain 'F' and resid 231 through 242 Processing helix chain 'F' and resid 250 through 267 Processing helix chain 'F' and resid 279 through 290 Processing helix chain 'F' and resid 295 through 317 removed outlier: 3.638A pdb=" N LEU F 299 " --> pdb=" O ASN F 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 6 removed outlier: 3.513A pdb=" N LYS G 6 " --> pdb=" O LEU G 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2 through 6' Processing helix chain 'G' and resid 7 through 9 No H-bonds generated for 'chain 'G' and resid 7 through 9' Processing helix chain 'G' and resid 69 through 83 removed outlier: 3.602A pdb=" N LEU G 79 " --> pdb=" O ALA G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 113 Processing helix chain 'G' and resid 188 through 202 removed outlier: 3.632A pdb=" N THR G 202 " --> pdb=" O ASN G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 244 removed outlier: 3.935A pdb=" N THR G 236 " --> pdb=" O ASN G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 266 removed outlier: 3.519A pdb=" N LEU G 254 " --> pdb=" O PRO G 250 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA G 259 " --> pdb=" O CYS G 255 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR G 260 " --> pdb=" O GLU G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 293 removed outlier: 3.940A pdb=" N THR G 284 " --> pdb=" O ALA G 280 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU G 288 " --> pdb=" O THR G 284 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE G 292 " --> pdb=" O GLU G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 317 removed outlier: 4.514A pdb=" N LYS G 301 " --> pdb=" O ALA G 297 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 43 Processing helix chain 'H' and resid 55 through 59 Processing helix chain 'H' and resid 73 through 79 Processing helix chain 'H' and resid 187 through 191 Processing helix chain 'I' and resid 3 through 13 removed outlier: 4.113A pdb=" N ARG I 11 " --> pdb=" O THR I 7 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR I 12 " --> pdb=" O LEU I 8 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU I 13 " --> pdb=" O LEU I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 17 removed outlier: 3.568A pdb=" N LYS I 17 " --> pdb=" O SER I 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 14 through 17' Processing helix chain 'I' and resid 18 through 36 removed outlier: 3.612A pdb=" N LEU I 22 " --> pdb=" O ASP I 18 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LEU I 29 " --> pdb=" O PHE I 25 " (cutoff:3.500A) Proline residue: I 30 - end of helix removed outlier: 3.789A pdb=" N GLU I 34 " --> pdb=" O PRO I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 94 Processing helix chain 'I' and resid 101 through 115 removed outlier: 3.829A pdb=" N ARG I 106 " --> pdb=" O ASP I 102 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR I 113 " --> pdb=" O CYS I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 148 removed outlier: 3.526A pdb=" N ASN I 139 " --> pdb=" O GLN I 135 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ILE I 140 " --> pdb=" O GLU I 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 154 removed outlier: 4.011A pdb=" N PHE I 153 " --> pdb=" O ASN I 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 159 removed outlier: 4.193A pdb=" N ARG I 158 " --> pdb=" O ALA I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 167 Processing helix chain 'I' and resid 195 through 213 removed outlier: 3.880A pdb=" N ASP I 199 " --> pdb=" O GLU I 195 " (cutoff:3.500A) Proline residue: I 201 - end of helix removed outlier: 3.807A pdb=" N VAL I 211 " --> pdb=" O THR I 207 " (cutoff:3.500A) Processing helix chain 'I' and resid 217 through 222 removed outlier: 3.784A pdb=" N LEU I 221 " --> pdb=" O PRO I 218 " (cutoff:3.500A) Processing helix chain 'I' and resid 223 through 237 removed outlier: 3.850A pdb=" N GLY I 227 " --> pdb=" O SER I 223 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP I 228 " --> pdb=" O SER I 224 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ARG I 229 " --> pdb=" O THR I 225 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU I 230 " --> pdb=" O MET I 226 " (cutoff:3.500A) Processing helix chain 'I' and resid 252 through 268 Processing helix chain 'I' and resid 269 through 271 No H-bonds generated for 'chain 'I' and resid 269 through 271' Processing helix chain 'I' and resid 294 through 317 removed outlier: 3.723A pdb=" N GLN I 300 " --> pdb=" O ASN I 296 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS I 313 " --> pdb=" O GLU I 309 " (cutoff:3.500A) Processing helix chain 'I' and resid 333 through 338 Processing helix chain 'I' and resid 339 through 355 removed outlier: 3.802A pdb=" N VAL I 344 " --> pdb=" O ALA I 340 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG I 345 " --> pdb=" O ALA I 341 " (cutoff:3.500A) Proline residue: I 348 - end of helix removed outlier: 3.605A pdb=" N SER I 352 " --> pdb=" O PRO I 348 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL I 353 " --> pdb=" O GLN I 349 " (cutoff:3.500A) Processing helix chain 'I' and resid 361 through 371 removed outlier: 4.683A pdb=" N LYS I 365 " --> pdb=" O PRO I 361 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS I 369 " --> pdb=" O LYS I 365 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU I 371 " --> pdb=" O LEU I 367 " (cutoff:3.500A) Processing helix chain 'I' and resid 376 through 382 removed outlier: 3.659A pdb=" N LEU I 380 " --> pdb=" O GLU I 376 " (cutoff:3.500A) Processing helix chain 'I' and resid 385 through 402 removed outlier: 3.622A pdb=" N ASP I 389 " --> pdb=" O ASP I 385 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU I 391 " --> pdb=" O ARG I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 406 through 417 removed outlier: 4.069A pdb=" N TRP I 412 " --> pdb=" O PRO I 408 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS I 415 " --> pdb=" O GLU I 411 " (cutoff:3.500A) Processing helix chain 'I' and resid 425 through 429 Processing helix chain 'I' and resid 436 through 450 removed outlier: 4.393A pdb=" N TYR I 440 " --> pdb=" O ASN I 436 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG I 441 " --> pdb=" O TYR I 437 " (cutoff:3.500A) Processing helix chain 'I' and resid 454 through 477 removed outlier: 3.688A pdb=" N GLY I 464 " --> pdb=" O GLU I 460 " (cutoff:3.500A) Processing helix chain 'I' and resid 484 through 497 removed outlier: 4.020A pdb=" N GLN I 488 " --> pdb=" O SER I 484 " (cutoff:3.500A) Processing helix chain 'I' and resid 510 through 519 Processing helix chain 'I' and resid 571 through 585 Processing helix chain 'I' and resid 591 through 595 Processing helix chain 'I' and resid 608 through 620 Processing helix chain 'I' and resid 626 through 636 removed outlier: 3.819A pdb=" N VAL I 630 " --> pdb=" O ASN I 626 " (cutoff:3.500A) Processing helix chain 'I' and resid 640 through 647 Processing helix chain 'I' and resid 683 through 703 removed outlier: 5.399A pdb=" N LYS I 690 " --> pdb=" O ASP I 686 " (cutoff:3.500A) Proline residue: I 691 - end of helix Proline residue: I 699 - end of helix Processing helix chain 'I' and resid 720 through 724 removed outlier: 3.720A pdb=" N GLU I 724 " --> pdb=" O ASP I 721 " (cutoff:3.500A) Processing helix chain 'I' and resid 733 through 738 Processing helix chain 'I' and resid 745 through 747 No H-bonds generated for 'chain 'I' and resid 745 through 747' Processing helix chain 'I' and resid 748 through 764 Processing helix chain 'I' and resid 774 through 776 No H-bonds generated for 'chain 'I' and resid 774 through 776' Processing helix chain 'I' and resid 777 through 788 Processing helix chain 'I' and resid 790 through 803 Processing helix chain 'I' and resid 809 through 824 removed outlier: 3.694A pdb=" N THR I 814 " --> pdb=" O GLU I 810 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TRP I 817 " --> pdb=" O VAL I 813 " (cutoff:3.500A) Processing helix chain 'I' and resid 827 through 845 removed outlier: 3.668A pdb=" N VAL I 841 " --> pdb=" O THR I 837 " (cutoff:3.500A) Processing helix chain 'I' and resid 851 through 855 Processing helix chain 'I' and resid 857 through 862 Processing helix chain 'I' and resid 862 through 875 removed outlier: 3.640A pdb=" N GLN I 871 " --> pdb=" O LYS I 867 " (cutoff:3.500A) Processing helix chain 'I' and resid 880 through 897 removed outlier: 4.063A pdb=" N LEU I 886 " --> pdb=" O GLU I 882 " (cutoff:3.500A) Processing helix chain 'I' and resid 898 through 899 No H-bonds generated for 'chain 'I' and resid 898 through 899' Processing helix chain 'I' and resid 900 through 904 Processing helix chain 'I' and resid 913 through 935 Processing helix chain 'I' and resid 944 through 974 removed outlier: 3.582A pdb=" N GLN I 951 " --> pdb=" O ILE I 947 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ASN I 953 " --> pdb=" O GLN I 949 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ARG I 954 " --> pdb=" O GLU I 950 " (cutoff:3.500A) Processing helix chain 'J' and resid 1 through 5 removed outlier: 3.641A pdb=" N LEU J 5 " --> pdb=" O THR J 2 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 17 removed outlier: 3.652A pdb=" N TYR J 15 " --> pdb=" O LEU J 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 26 Processing helix chain 'J' and resid 28 through 33 removed outlier: 3.511A pdb=" N LEU J 33 " --> pdb=" O THR J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 33 through 46 Processing helix chain 'J' and resid 51 through 68 removed outlier: 3.527A pdb=" N GLN J 58 " --> pdb=" O GLU J 54 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ALA J 66 " --> pdb=" O GLN J 62 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP J 68 " --> pdb=" O GLN J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 70 No H-bonds generated for 'chain 'J' and resid 69 through 70' Processing helix chain 'J' and resid 71 through 75 Processing helix chain 'J' and resid 84 through 106 removed outlier: 3.516A pdb=" N GLN J 89 " --> pdb=" O TYR J 85 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU J 90 " --> pdb=" O GLU J 86 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU J 94 " --> pdb=" O LEU J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 145 removed outlier: 5.331A pdb=" N ASN J 124 " --> pdb=" O GLN J 120 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ARG J 125 " --> pdb=" O GLU J 121 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA J 130 " --> pdb=" O ILE J 126 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN J 142 " --> pdb=" O ALA J 138 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLN J 143 " --> pdb=" O LEU J 139 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN J 144 " --> pdb=" O GLU J 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 17 removed outlier: 4.620A pdb=" N LEU K 7 " --> pdb=" O GLU K 3 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N VAL K 12 " --> pdb=" O THR K 8 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N TYR K 15 " --> pdb=" O LEU K 11 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG K 17 " --> pdb=" O GLU K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 26 Processing helix chain 'K' and resid 28 through 33 Processing helix chain 'K' and resid 33 through 45 Processing helix chain 'K' and resid 51 through 67 Processing helix chain 'K' and resid 71 through 74 Processing helix chain 'K' and resid 75 through 80 Processing helix chain 'K' and resid 84 through 106 removed outlier: 3.617A pdb=" N LEU K 90 " --> pdb=" O GLU K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 115 through 121 Processing helix chain 'K' and resid 122 through 144 removed outlier: 3.547A pdb=" N ARG K 135 " --> pdb=" O GLU K 131 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU K 140 " --> pdb=" O LEU K 136 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 127 through 129 removed outlier: 6.808A pdb=" N TYR A 21 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N PHE A 224 " --> pdb=" O TYR A 21 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N HIS A 23 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE A 222 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU A 25 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR A 214 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU A 275 " --> pdb=" O PHE A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 38 removed outlier: 3.601A pdb=" N THR A 38 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 41 " --> pdb=" O THR A 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 44 through 48 Processing sheet with id=AA4, first strand: chain 'A' and resid 115 through 118 removed outlier: 6.224A pdb=" N GLY A 121 " --> pdb=" O ILE A 117 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 142 through 148 Processing sheet with id=AA6, first strand: chain 'A' and resid 157 through 158 Processing sheet with id=AA7, first strand: chain 'B' and resid 127 through 128 removed outlier: 6.918A pdb=" N TYR B 21 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N PHE B 224 " --> pdb=" O TYR B 21 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N HIS B 23 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE B 222 " --> pdb=" O HIS B 23 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU B 25 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU B 275 " --> pdb=" O PHE B 224 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 37 through 38 removed outlier: 3.970A pdb=" N THR B 38 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL B 41 " --> pdb=" O THR B 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 44 through 48 Processing sheet with id=AB1, first strand: chain 'B' and resid 122 through 123 Processing sheet with id=AB2, first strand: chain 'B' and resid 142 through 148 Processing sheet with id=AB3, first strand: chain 'C' and resid 127 through 128 removed outlier: 6.867A pdb=" N TYR C 21 " --> pdb=" O PHE C 224 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N PHE C 224 " --> pdb=" O TYR C 21 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N HIS C 23 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE C 222 " --> pdb=" O HIS C 23 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU C 25 " --> pdb=" O VAL C 220 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR C 214 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU C 275 " --> pdb=" O PHE C 224 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 37 through 38 removed outlier: 4.242A pdb=" N THR C 38 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL C 41 " --> pdb=" O THR C 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 44 through 48 Processing sheet with id=AB6, first strand: chain 'C' and resid 142 through 147 Processing sheet with id=AB7, first strand: chain 'D' and resid 127 through 128 removed outlier: 6.964A pdb=" N TYR D 21 " --> pdb=" O PHE D 224 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N PHE D 224 " --> pdb=" O TYR D 21 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N HIS D 23 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE D 222 " --> pdb=" O HIS D 23 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU D 25 " --> pdb=" O VAL D 220 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU D 275 " --> pdb=" O PHE D 224 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 44 through 48 Processing sheet with id=AB9, first strand: chain 'D' and resid 115 through 116 Processing sheet with id=AC1, first strand: chain 'D' and resid 142 through 148 Processing sheet with id=AC2, first strand: chain 'E' and resid 127 through 128 removed outlier: 6.898A pdb=" N TYR E 21 " --> pdb=" O PHE E 224 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE E 224 " --> pdb=" O TYR E 21 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N HIS E 23 " --> pdb=" O ILE E 222 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ILE E 222 " --> pdb=" O HIS E 23 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU E 25 " --> pdb=" O VAL E 220 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 44 through 47 Processing sheet with id=AC4, first strand: chain 'E' and resid 115 through 116 Processing sheet with id=AC5, first strand: chain 'E' and resid 142 through 148 Processing sheet with id=AC6, first strand: chain 'F' and resid 127 through 128 removed outlier: 6.914A pdb=" N TYR F 21 " --> pdb=" O PHE F 224 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE F 224 " --> pdb=" O TYR F 21 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N HIS F 23 " --> pdb=" O ILE F 222 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE F 222 " --> pdb=" O HIS F 23 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU F 25 " --> pdb=" O VAL F 220 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU F 275 " --> pdb=" O PHE F 224 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 44 through 48 Processing sheet with id=AC8, first strand: chain 'F' and resid 115 through 118 removed outlier: 6.834A pdb=" N GLY F 121 " --> pdb=" O ILE F 117 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 142 through 146 Processing sheet with id=AD1, first strand: chain 'G' and resid 127 through 129 removed outlier: 6.534A pdb=" N LEU G 27 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N LEU G 219 " --> pdb=" O LEU G 27 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N HIS G 29 " --> pdb=" O ASN G 217 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ASN G 217 " --> pdb=" O HIS G 29 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU G 275 " --> pdb=" O PHE G 224 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 44 through 47 removed outlier: 6.550A pdb=" N SER G 59 " --> pdb=" O GLY G 136 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLY G 136 " --> pdb=" O SER G 59 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N LEU G 61 " --> pdb=" O SER G 134 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 115 through 116 Processing sheet with id=AD4, first strand: chain 'G' and resid 142 through 146 Processing sheet with id=AD5, first strand: chain 'H' and resid 80 through 82 removed outlier: 6.448A pdb=" N LEU H 137 " --> pdb=" O PRO H 87 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 80 through 82 Processing sheet with id=AD7, first strand: chain 'H' and resid 20 through 22 Processing sheet with id=AD8, first strand: chain 'H' and resid 174 through 181 removed outlier: 6.959A pdb=" N ASN H 201 " --> pdb=" O SER H 212 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N SER H 214 " --> pdb=" O LEU H 199 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU H 199 " --> pdb=" O SER H 214 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU H 216 " --> pdb=" O ILE H 197 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE H 197 " --> pdb=" O LEU H 216 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLY H 218 " --> pdb=" O GLN H 195 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N GLN H 195 " --> pdb=" O GLY H 218 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 174 through 181 removed outlier: 6.985A pdb=" N THR H 227 " --> pdb=" O ILE H 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 273 through 278 removed outlier: 6.779A pdb=" N ILE I 283 " --> pdb=" O LEU I 275 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N PHE I 277 " --> pdb=" O GLY I 281 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLY I 281 " --> pdb=" O PHE I 277 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 321 through 322 Processing sheet with id=AE3, first strand: chain 'I' and resid 539 through 541 Processing sheet with id=AE4, first strand: chain 'I' and resid 674 through 677 removed outlier: 3.688A pdb=" N ILE I 597 " --> pdb=" O THR I 677 " (cutoff:3.500A) 1366 hydrogen bonds defined for protein. 3897 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 29 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 6.54 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 5032 1.27 - 1.41: 8333 1.41 - 1.55: 17627 1.55 - 1.69: 221 1.69 - 1.82: 186 Bond restraints: 31399 Sorted by residual: bond pdb=" C TYR E 313 " pdb=" O TYR E 313 " ideal model delta sigma weight residual 1.237 1.135 0.102 1.17e-02 7.31e+03 7.53e+01 bond pdb=" C TYR A 313 " pdb=" O TYR A 313 " ideal model delta sigma weight residual 1.237 1.143 0.094 1.19e-02 7.06e+03 6.21e+01 bond pdb=" C TYR C 313 " pdb=" O TYR C 313 " ideal model delta sigma weight residual 1.237 1.147 0.090 1.17e-02 7.31e+03 5.92e+01 bond pdb=" C TYR B 313 " pdb=" O TYR B 313 " ideal model delta sigma weight residual 1.236 1.153 0.084 1.15e-02 7.56e+03 5.31e+01 bond pdb=" C PHE D 115 " pdb=" O PHE D 115 " ideal model delta sigma weight residual 1.234 1.150 0.084 1.20e-02 6.94e+03 4.93e+01 ... (remaining 31394 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 39719 3.67 - 7.35: 2975 7.35 - 11.02: 78 11.02 - 14.70: 7 14.70 - 18.37: 2 Bond angle restraints: 42781 Sorted by residual: angle pdb=" N PHE I 285 " pdb=" CA PHE I 285 " pdb=" C PHE I 285 " ideal model delta sigma weight residual 109.24 90.87 18.37 1.63e+00 3.76e-01 1.27e+02 angle pdb=" N6 DA X 6 " pdb=" C6 DA X 6 " pdb=" N1 DA X 6 " ideal model delta sigma weight residual 118.60 112.19 6.41 6.00e-01 2.78e+00 1.14e+02 angle pdb=" N6 DA X 11 " pdb=" C6 DA X 11 " pdb=" N1 DA X 11 " ideal model delta sigma weight residual 118.60 112.29 6.31 6.00e-01 2.78e+00 1.11e+02 angle pdb=" N6 DA Y 8 " pdb=" C6 DA Y 8 " pdb=" N1 DA Y 8 " ideal model delta sigma weight residual 118.60 112.44 6.16 6.00e-01 2.78e+00 1.05e+02 angle pdb=" O4' DA X 11 " pdb=" C1' DA X 11 " pdb=" N9 DA X 11 " ideal model delta sigma weight residual 108.00 115.15 -7.15 7.00e-01 2.04e+00 1.04e+02 ... (remaining 42776 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.25: 18006 33.25 - 66.50: 624 66.50 - 99.74: 122 99.74 - 132.99: 0 132.99 - 166.24: 1 Dihedral angle restraints: 18753 sinusoidal: 8102 harmonic: 10651 Sorted by residual: dihedral pdb=" C4' U Z 33 " pdb=" C3' U Z 33 " pdb=" C2' U Z 33 " pdb=" C1' U Z 33 " ideal model delta sinusoidal sigma weight residual 36.34 -41.10 77.44 1 3.10e+00 1.04e-01 7.82e+02 dihedral pdb=" C4' U Z 14 " pdb=" C3' U Z 14 " pdb=" C2' U Z 14 " pdb=" C1' U Z 14 " ideal model delta sinusoidal sigma weight residual 36.34 -41.04 77.39 1 3.10e+00 1.04e-01 7.81e+02 dihedral pdb=" C4' U Z 15 " pdb=" C3' U Z 15 " pdb=" C2' U Z 15 " pdb=" C1' U Z 15 " ideal model delta sinusoidal sigma weight residual 36.35 -39.11 75.45 1 3.10e+00 1.04e-01 7.48e+02 ... (remaining 18750 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.272: 4613 0.272 - 0.543: 171 0.543 - 0.815: 2 0.815 - 1.087: 0 1.087 - 1.358: 1 Chirality restraints: 4787 Sorted by residual: chirality pdb=" C3' DT Y 13 " pdb=" C4' DT Y 13 " pdb=" O3' DT Y 13 " pdb=" C2' DT Y 13 " both_signs ideal model delta sigma weight residual False -2.73 -1.37 -1.36 2.00e-01 2.50e+01 4.61e+01 chirality pdb=" CA ARG G 211 " pdb=" N ARG G 211 " pdb=" C ARG G 211 " pdb=" CB ARG G 211 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.88e+00 chirality pdb=" CA LYS J 6 " pdb=" N LYS J 6 " pdb=" C LYS J 6 " pdb=" CB LYS J 6 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.45e+00 ... (remaining 4784 not shown) Planarity restraints: 5308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA X 3 " 0.320 2.00e-02 2.50e+03 1.41e-01 5.48e+02 pdb=" N9 DA X 3 " -0.023 2.00e-02 2.50e+03 pdb=" C8 DA X 3 " -0.091 2.00e-02 2.50e+03 pdb=" N7 DA X 3 " -0.117 2.00e-02 2.50e+03 pdb=" C5 DA X 3 " -0.083 2.00e-02 2.50e+03 pdb=" C6 DA X 3 " 0.039 2.00e-02 2.50e+03 pdb=" N6 DA X 3 " 0.223 2.00e-02 2.50e+03 pdb=" N1 DA X 3 " 0.046 2.00e-02 2.50e+03 pdb=" C2 DA X 3 " -0.077 2.00e-02 2.50e+03 pdb=" N3 DA X 3 " -0.124 2.00e-02 2.50e+03 pdb=" C4 DA X 3 " -0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G Z 13 " 0.299 2.00e-02 2.50e+03 1.23e-01 4.52e+02 pdb=" N9 G Z 13 " -0.047 2.00e-02 2.50e+03 pdb=" C8 G Z 13 " -0.149 2.00e-02 2.50e+03 pdb=" N7 G Z 13 " -0.112 2.00e-02 2.50e+03 pdb=" C5 G Z 13 " -0.029 2.00e-02 2.50e+03 pdb=" C6 G Z 13 " 0.063 2.00e-02 2.50e+03 pdb=" O6 G Z 13 " 0.150 2.00e-02 2.50e+03 pdb=" N1 G Z 13 " 0.082 2.00e-02 2.50e+03 pdb=" C2 G Z 13 " -0.022 2.00e-02 2.50e+03 pdb=" N2 G Z 13 " -0.108 2.00e-02 2.50e+03 pdb=" N3 G Z 13 " -0.065 2.00e-02 2.50e+03 pdb=" C4 G Z 13 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C Z 32 " -0.215 2.00e-02 2.50e+03 1.18e-01 3.15e+02 pdb=" N1 C Z 32 " -0.004 2.00e-02 2.50e+03 pdb=" C2 C Z 32 " 0.019 2.00e-02 2.50e+03 pdb=" O2 C Z 32 " 0.153 2.00e-02 2.50e+03 pdb=" N3 C Z 32 " -0.049 2.00e-02 2.50e+03 pdb=" C4 C Z 32 " -0.030 2.00e-02 2.50e+03 pdb=" N4 C Z 32 " -0.136 2.00e-02 2.50e+03 pdb=" C5 C Z 32 " 0.129 2.00e-02 2.50e+03 pdb=" C6 C Z 32 " 0.133 2.00e-02 2.50e+03 ... (remaining 5305 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 114 2.61 - 3.19: 25668 3.19 - 3.76: 48991 3.76 - 4.33: 69776 4.33 - 4.90: 113682 Nonbonded interactions: 258231 Sorted by model distance: nonbonded pdb=" O PRO I 770 " pdb=" C7 DT Y 13 " model vdw 2.044 3.460 nonbonded pdb=" ND1 HIS E 23 " pdb=" OG SER E 183 " model vdw 2.083 3.120 nonbonded pdb=" NH2 ARG D 28 " pdb=" OE2 GLU D 72 " model vdw 2.216 3.120 nonbonded pdb=" NE2 GLN B 10 " pdb=" OG SER B 18 " model vdw 2.252 3.120 nonbonded pdb=" NH2 ARG A 15 " pdb=" OE1 GLU H 69 " model vdw 2.276 3.120 ... (remaining 258226 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'J' selection = chain 'K' } 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=0.00 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: 9.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 31.940 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 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 : 0.013 0.102 31399 Z= 0.843 Angle : 2.016 18.369 42781 Z= 1.358 Chirality : 0.122 1.358 4787 Planarity : 0.018 0.182 5308 Dihedral : 17.372 166.238 11901 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.20 % Favored : 95.69 % Rotamer: Outliers : 2.75 % Allowed : 6.19 % Favored : 91.07 % Cbeta Deviations : 1.11 % Peptide Plane: Cis-proline : 0.76 % 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: -2.32 (0.12), residues: 3639 helix: -2.07 (0.10), residues: 1540 sheet: -0.23 (0.22), residues: 413 loop : -1.19 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG C 163 TYR 0.179 0.022 TYR G 189 PHE 0.090 0.013 PHE I 722 TRP 0.156 0.025 TRP I 472 HIS 0.023 0.004 HIS I 246 Details of bonding type rmsd/Z covalent geometry : bond 0.01282 / 0.84 (31399) covalent geometry : angle 2.01582 / 1.36 (42781) hydrogen bonds : bond 0.19642 / 12.64 ( 1385) hydrogen bonds : angle 7.88406 / 5.57 ( 3955) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1212 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 1125 time to evaluate : 1.060 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: A 65 LYS cc_start: 0.8033 (mtmm) cc_final: 0.7823 (mtmm) REVERT: A 72 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6782 (mt-10) REVERT: A 101 GLU cc_start: 0.6536 (mt-10) cc_final: 0.6080 (mt-10) REVERT: A 139 GLU cc_start: 0.7751 (mp0) cc_final: 0.7123 (mp0) REVERT: A 157 SER cc_start: 0.8389 (m) cc_final: 0.8131 (p) REVERT: A 247 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8584 (mm) REVERT: A 268 LYS cc_start: 0.8017 (mttp) cc_final: 0.7815 (mttp) REVERT: A 271 VAL cc_start: 0.8702 (m) cc_final: 0.8481 (p) REVERT: B 188 THR cc_start: 0.8364 (p) cc_final: 0.7969 (p) REVERT: B 190 GLU cc_start: 0.7917 (mp0) cc_final: 0.7040 (mp0) REVERT: B 290 ASN cc_start: 0.8058 (m-40) cc_final: 0.7857 (m110) REVERT: C 32 SER cc_start: 0.7967 (m) cc_final: 0.7471 (p) REVERT: C 54 LYS cc_start: 0.8039 (mptt) cc_final: 0.7820 (mmmm) REVERT: C 72 GLU cc_start: 0.6751 (mp0) cc_final: 0.6364 (mp0) REVERT: C 139 GLU cc_start: 0.7338 (mp0) cc_final: 0.6955 (mp0) REVERT: C 151 PHE cc_start: 0.8439 (m-80) cc_final: 0.8236 (m-80) REVERT: C 190 GLU cc_start: 0.7953 (mp0) cc_final: 0.7622 (mp0) REVERT: C 272 ARG cc_start: 0.8108 (mtm180) cc_final: 0.7741 (mtm180) REVERT: C 275 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7303 (mt-10) REVERT: C 298 GLU cc_start: 0.7161 (tp30) cc_final: 0.6944 (tp30) REVERT: D 38 THR cc_start: 0.8092 (p) cc_final: 0.7756 (p) REVERT: D 39 ASP cc_start: 0.7355 (m-30) cc_final: 0.7071 (m-30) REVERT: D 63 MET cc_start: 0.8072 (ttp) cc_final: 0.7777 (ttm) REVERT: D 65 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7458 (pmtt) REVERT: D 66 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.8058 (mtt90) REVERT: D 68 GLN cc_start: 0.7960 (pt0) cc_final: 0.7413 (pt0) REVERT: D 72 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6814 (mt-10) REVERT: D 78 GLU cc_start: 0.7099 (tt0) cc_final: 0.6665 (tt0) REVERT: D 90 LYS cc_start: 0.8313 (mttt) cc_final: 0.8051 (mttt) REVERT: D 147 PHE cc_start: 0.7973 (p90) cc_final: 0.7765 (p90) REVERT: D 156 MET cc_start: 0.7476 (mtp) cc_final: 0.7143 (mtp) REVERT: D 169 LEU cc_start: 0.8640 (tp) cc_final: 0.8431 (tp) REVERT: D 243 MET cc_start: 0.7598 (mmm) cc_final: 0.7278 (mmm) REVERT: D 264 ASP cc_start: 0.7148 (t70) cc_final: 0.6843 (t0) REVERT: D 283 ASP cc_start: 0.7267 (m-30) cc_final: 0.7064 (m-30) REVERT: E 45 THR cc_start: 0.8490 (t) cc_final: 0.8142 (m) REVERT: E 141 SER cc_start: 0.8344 (m) cc_final: 0.7844 (p) REVERT: E 156 MET cc_start: 0.6503 (mmt) cc_final: 0.6255 (mmt) REVERT: E 168 GLU cc_start: 0.6977 (tt0) cc_final: 0.6771 (tt0) REVERT: E 182 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7062 (mm-30) REVERT: E 199 LEU cc_start: 0.8520 (mp) cc_final: 0.8248 (mm) REVERT: E 249 LYS cc_start: 0.7889 (mmpt) cc_final: 0.7563 (mmpt) REVERT: E 273 LYS cc_start: 0.8877 (mtmm) cc_final: 0.8647 (mttm) REVERT: E 286 LEU cc_start: 0.8551 (mp) cc_final: 0.8319 (mm) REVERT: E 288 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7067 (mt-10) REVERT: E 317 PHE cc_start: 0.8443 (m-80) cc_final: 0.8239 (m-10) REVERT: F 2 LEU cc_start: 0.7755 (mp) cc_final: 0.7329 (mt) REVERT: F 45 THR cc_start: 0.8135 (m) cc_final: 0.7924 (m) REVERT: F 72 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6877 (mp0) REVERT: F 141 SER cc_start: 0.8064 (m) cc_final: 0.7421 (p) REVERT: F 182 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6719 (mt-10) REVERT: F 212 THR cc_start: 0.7265 (OUTLIER) cc_final: 0.7029 (p) REVERT: F 226 ASP cc_start: 0.6515 (p0) cc_final: 0.6106 (p0) REVERT: F 267 ASN cc_start: 0.7357 (m-40) cc_final: 0.7103 (m-40) REVERT: F 283 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.7136 (p0) REVERT: F 295 ASN cc_start: 0.8347 (t0) cc_final: 0.7792 (t0) REVERT: F 298 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6588 (mp0) REVERT: F 303 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8315 (mt) REVERT: F 313 TYR cc_start: 0.8528 (t80) cc_final: 0.7859 (t80) REVERT: G 10 GLN cc_start: 0.7563 (mt0) cc_final: 0.7357 (mt0) REVERT: G 68 GLN cc_start: 0.6511 (OUTLIER) cc_final: 0.5815 (pp30) REVERT: G 72 GLU cc_start: 0.6969 (mp0) cc_final: 0.6625 (mp0) REVERT: G 83 LEU cc_start: 0.8026 (tp) cc_final: 0.7752 (tm) REVERT: G 122 SER cc_start: 0.8367 (p) cc_final: 0.8086 (t) REVERT: G 128 TYR cc_start: 0.8173 (m-80) cc_final: 0.7860 (m-80) REVERT: G 130 ASP cc_start: 0.6945 (OUTLIER) cc_final: 0.6583 (m-30) REVERT: G 216 LYS cc_start: 0.7336 (tppt) cc_final: 0.7105 (tppt) REVERT: G 233 LEU cc_start: 0.8556 (tp) cc_final: 0.8168 (tm) REVERT: G 254 LEU cc_start: 0.7671 (mt) cc_final: 0.7340 (mm) REVERT: G 275 GLU cc_start: 0.5962 (OUTLIER) cc_final: 0.5697 (mt-10) REVERT: G 305 SER cc_start: 0.7357 (m) cc_final: 0.7152 (t) REVERT: H 95 ASN cc_start: 0.8268 (m-40) cc_final: 0.8021 (m110) REVERT: H 118 LYS cc_start: 0.8439 (mmtp) cc_final: 0.7969 (mttp) REVERT: H 168 ILE cc_start: 0.8163 (mt) cc_final: 0.7958 (mp) REVERT: H 174 LYS cc_start: 0.7740 (ptpt) cc_final: 0.7528 (ptpt) REVERT: H 181 VAL cc_start: 0.8464 (m) cc_final: 0.8201 (t) REVERT: H 201 ASN cc_start: 0.7351 (m-40) cc_final: 0.7005 (m-40) REVERT: I 22 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8264 (tp) REVERT: I 34 GLU cc_start: 0.7296 (tt0) cc_final: 0.7008 (tt0) REVERT: I 78 LEU cc_start: 0.8218 (mt) cc_final: 0.7937 (tp) REVERT: I 82 ILE cc_start: 0.8677 (mt) cc_final: 0.8433 (mt) REVERT: I 140 ILE cc_start: 0.8904 (pt) cc_final: 0.8639 (pp) REVERT: I 149 ASN cc_start: 0.7968 (m-40) cc_final: 0.7633 (m-40) REVERT: I 161 ILE cc_start: 0.8067 (tt) cc_final: 0.7838 (tp) REVERT: I 213 VAL cc_start: 0.8883 (m) cc_final: 0.8583 (p) REVERT: I 217 SER cc_start: 0.8464 (t) cc_final: 0.8002 (p) REVERT: I 229 ARG cc_start: 0.7474 (ptm160) cc_final: 0.7229 (ptm160) REVERT: I 233 LEU cc_start: 0.8193 (mt) cc_final: 0.7852 (mt) REVERT: I 235 ASN cc_start: 0.8163 (t0) cc_final: 0.7783 (t0) REVERT: I 240 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6425 (pm20) REVERT: I 294 GLU cc_start: 0.7123 (tp30) cc_final: 0.6591 (tm-30) REVERT: I 347 LEU cc_start: 0.8520 (mt) cc_final: 0.8089 (mm) REVERT: I 349 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7344 (tp40) REVERT: I 352 SER cc_start: 0.8257 (t) cc_final: 0.7933 (p) REVERT: I 386 LEU cc_start: 0.7896 (tp) cc_final: 0.7678 (tt) REVERT: I 400 LYS cc_start: 0.7964 (tttm) cc_final: 0.7298 (tppp) REVERT: I 407 GLU cc_start: 0.7188 (pm20) cc_final: 0.6807 (pm20) REVERT: I 460 GLU cc_start: 0.7261 (tm-30) cc_final: 0.6964 (tm-30) REVERT: I 478 TYR cc_start: 0.7704 (m-80) cc_final: 0.7418 (m-80) REVERT: I 510 PHE cc_start: 0.7708 (m-80) cc_final: 0.7420 (m-80) REVERT: I 536 GLU cc_start: 0.6449 (pt0) cc_final: 0.6210 (pt0) REVERT: I 583 PHE cc_start: 0.8439 (m-80) cc_final: 0.8180 (m-10) REVERT: I 590 LYS cc_start: 0.8253 (tmtt) cc_final: 0.7837 (tmtt) REVERT: I 593 ASP cc_start: 0.7117 (t70) cc_final: 0.6509 (t70) REVERT: I 605 TYR cc_start: 0.7072 (m-80) cc_final: 0.6780 (m-80) REVERT: I 632 LYS cc_start: 0.8033 (ttpt) cc_final: 0.7663 (ttpp) REVERT: I 635 VAL cc_start: 0.8531 (m) cc_final: 0.8024 (m) REVERT: I 663 LYS cc_start: 0.7943 (ptpt) cc_final: 0.7731 (ptpt) REVERT: I 721 ASP cc_start: 0.6972 (m-30) cc_final: 0.6717 (m-30) REVERT: I 743 ASP cc_start: 0.7455 (p0) cc_final: 0.7211 (p0) REVERT: I 745 ARG cc_start: 0.7133 (mtp180) cc_final: 0.5891 (mtp180) REVERT: I 746 VAL cc_start: 0.8467 (p) cc_final: 0.8208 (t) REVERT: I 747 GLU cc_start: 0.7149 (mp0) cc_final: 0.6030 (mp0) REVERT: I 777 ASP cc_start: 0.7498 (m-30) cc_final: 0.7269 (m-30) REVERT: I 797 GLU cc_start: 0.6738 (mt-10) cc_final: 0.6510 (mt-10) REVERT: I 804 LYS cc_start: 0.8062 (mttp) cc_final: 0.7858 (mtmm) REVERT: I 807 ARG cc_start: 0.7361 (ptp90) cc_final: 0.6877 (ptp-110) REVERT: I 827 ASN cc_start: 0.7818 (t0) cc_final: 0.7520 (t0) REVERT: I 828 ILE cc_start: 0.8384 (mm) cc_final: 0.8017 (mm) REVERT: I 832 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6908 (mt-10) REVERT: I 835 LYS cc_start: 0.8340 (ttpp) cc_final: 0.8101 (ttmm) REVERT: I 897 ASP cc_start: 0.7329 (m-30) cc_final: 0.6887 (m-30) REVERT: I 922 LEU cc_start: 0.8359 (mt) cc_final: 0.7682 (mm) REVERT: I 927 ILE cc_start: 0.8459 (tt) cc_final: 0.8187 (pt) REVERT: I 969 GLU cc_start: 0.7451 (tm-30) cc_final: 0.7128 (tm-30) REVERT: J 8 THR cc_start: 0.8307 (m) cc_final: 0.7952 (m) REVERT: J 11 LEU cc_start: 0.8286 (tp) cc_final: 0.7939 (tm) REVERT: J 14 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7156 (mm-30) REVERT: J 44 LEU cc_start: 0.8570 (mt) cc_final: 0.8263 (mm) REVERT: J 54 GLU cc_start: 0.7638 (mm-30) cc_final: 0.6832 (tm-30) REVERT: J 57 LEU cc_start: 0.8310 (mp) cc_final: 0.8007 (mt) REVERT: K 100 MET cc_start: 0.7420 (mtm) cc_final: 0.7180 (mtm) outliers start: 87 outliers final: 25 residues processed: 1171 average time/residue: 0.7773 time to fit residues: 1056.7580 Evaluate side-chains 1009 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 971 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain F residue 4 SER Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 142 HIS Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 124 ARG Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain H residue 144 LYS Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 244 VAL Chi-restraints excluded: chain I residue 285 PHE Chi-restraints excluded: chain I residue 324 ASP Chi-restraints excluded: chain I residue 349 GLN Chi-restraints excluded: chain I residue 416 ASP Chi-restraints excluded: chain I residue 479 PHE Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 121 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 197 optimal weight: 0.0980 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.0270 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.5980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 10 GLN A 20 HIS A 290 ASN A 308 GLN B 43 ASN B 68 GLN B 140 GLN B 171 HIS B 217 ASN B 232 ASN B 295 ASN C 10 GLN C 20 HIS C 43 ASN C 68 GLN C 242 GLN C 308 GLN D 31 GLN D 218 HIS D 290 ASN D 295 ASN E 8 GLN E 10 GLN E 48 GLN F 10 GLN F 43 ASN F 217 ASN F 242 GLN G 20 HIS G 217 ASN H 76 ASN H 184 HIS H 187 ASN H 195 GLN I 35 HIS I 399 GLN ** I 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 651 ASN I 825 GLN I 899 GLN J 146 ASN K 62 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.139942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.119633 restraints weight = 47797.414| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.95 r_work: 0.3443 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 31399 Z= 0.205 Angle : 1.027 23.094 42781 Z= 0.479 Chirality : 0.086 1.813 4787 Planarity : 0.005 0.063 5308 Dihedral : 13.630 163.626 4916 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.39 % Allowed : 15.37 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % 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: -1.08 (0.13), residues: 3639 helix: -0.50 (0.12), residues: 1603 sheet: 0.08 (0.24), residues: 401 loop : -1.02 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 774 TYR 0.037 0.002 TYR I 844 PHE 0.027 0.002 PHE G 230 TRP 0.023 0.002 TRP I 628 HIS 0.012 0.001 HIS I 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.20 (31399) covalent geometry : angle 1.02683 / 0.48 (42781) hydrogen bonds : bond 0.05487 / 3.58 ( 1385) hydrogen bonds : angle 5.34916 / 3.74 ( 3955) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1143 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 1004 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8501 (mt) cc_final: 0.8291 (mm) REVERT: A 32 SER cc_start: 0.8244 (t) cc_final: 0.7684 (p) REVERT: A 45 THR cc_start: 0.8721 (p) cc_final: 0.8453 (m) REVERT: A 65 LYS cc_start: 0.8174 (mtmm) cc_final: 0.7778 (mtmm) REVERT: A 101 GLU cc_start: 0.7254 (mt-10) cc_final: 0.6678 (mt-10) REVERT: A 139 GLU cc_start: 0.8105 (mp0) cc_final: 0.7703 (mp0) REVERT: A 148 ASN cc_start: 0.8581 (p0) cc_final: 0.8276 (p0) REVERT: A 156 MET cc_start: 0.8192 (mmm) cc_final: 0.7990 (mmm) REVERT: A 166 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7809 (tt) REVERT: A 209 GLU cc_start: 0.8252 (pt0) cc_final: 0.8002 (pt0) REVERT: A 210 SER cc_start: 0.8779 (m) cc_final: 0.8327 (p) REVERT: A 256 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7561 (mp0) REVERT: A 283 ASP cc_start: 0.8009 (m-30) cc_final: 0.7602 (m-30) REVERT: B 15 ARG cc_start: 0.8251 (ptm-80) cc_final: 0.7913 (ptm-80) REVERT: B 54 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8204 (mptt) REVERT: B 97 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7724 (mm-30) REVERT: B 123 GLU cc_start: 0.8203 (tp30) cc_final: 0.7655 (tp30) REVERT: B 143 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.7729 (ttp80) REVERT: B 190 GLU cc_start: 0.8059 (mp0) cc_final: 0.7784 (mp0) REVERT: B 290 ASN cc_start: 0.8322 (m-40) cc_final: 0.8112 (m-40) REVERT: C 6 LYS cc_start: 0.8870 (mtpt) cc_final: 0.8593 (mtmm) REVERT: C 32 SER cc_start: 0.8496 (m) cc_final: 0.7593 (p) REVERT: C 44 THR cc_start: 0.8835 (OUTLIER) cc_final: 0.8615 (p) REVERT: C 54 LYS cc_start: 0.8344 (mptt) cc_final: 0.7963 (mmmm) REVERT: C 72 GLU cc_start: 0.7456 (mp0) cc_final: 0.7171 (mp0) REVERT: C 97 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7397 (mm-30) REVERT: C 139 GLU cc_start: 0.8175 (mp0) cc_final: 0.7911 (mp0) REVERT: C 140 GLN cc_start: 0.8633 (mp10) cc_final: 0.8427 (mp10) REVERT: C 151 PHE cc_start: 0.8640 (m-80) cc_final: 0.8401 (m-80) REVERT: C 167 ASN cc_start: 0.8088 (t0) cc_final: 0.7863 (t0) REVERT: C 272 ARG cc_start: 0.8541 (mtm180) cc_final: 0.8315 (mtm180) REVERT: C 275 GLU cc_start: 0.8264 (mt-10) cc_final: 0.8047 (mt-10) REVERT: C 283 ASP cc_start: 0.8101 (m-30) cc_final: 0.7864 (m-30) REVERT: C 307 TYR cc_start: 0.8618 (t80) cc_final: 0.8317 (t80) REVERT: C 316 GLU cc_start: 0.8184 (tt0) cc_final: 0.7940 (tt0) REVERT: D 15 ARG cc_start: 0.8621 (ttp80) cc_final: 0.8120 (ttt-90) REVERT: D 38 THR cc_start: 0.8320 (p) cc_final: 0.7949 (p) REVERT: D 65 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7412 (pmtt) REVERT: D 66 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8243 (mtt90) REVERT: D 68 GLN cc_start: 0.8457 (pt0) cc_final: 0.7974 (pt0) REVERT: D 72 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7806 (mt-10) REVERT: D 78 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7696 (tt0) REVERT: D 120 SER cc_start: 0.7845 (OUTLIER) cc_final: 0.7366 (t) REVERT: D 124 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8465 (tmm-80) REVERT: D 130 ASP cc_start: 0.7244 (t0) cc_final: 0.6541 (t0) REVERT: D 156 MET cc_start: 0.7978 (mtp) cc_final: 0.7667 (mtp) REVERT: D 175 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7942 (mm-30) REVERT: D 264 ASP cc_start: 0.7983 (t70) cc_final: 0.7549 (t0) REVERT: D 268 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8589 (mtmm) REVERT: D 283 ASP cc_start: 0.8235 (m-30) cc_final: 0.7928 (m-30) REVERT: D 293 TYR cc_start: 0.8942 (m-80) cc_final: 0.8308 (m-80) REVERT: D 308 GLN cc_start: 0.8321 (mm-40) cc_final: 0.8107 (tp-100) REVERT: E 8 GLN cc_start: 0.8190 (mm-40) cc_final: 0.7861 (mm110) REVERT: E 45 THR cc_start: 0.8589 (t) cc_final: 0.8291 (m) REVERT: E 46 ARG cc_start: 0.8542 (mtp-110) cc_final: 0.8243 (mmm160) REVERT: E 89 ASP cc_start: 0.8593 (p0) cc_final: 0.8365 (p0) REVERT: E 141 SER cc_start: 0.8518 (m) cc_final: 0.8176 (p) REVERT: E 168 GLU cc_start: 0.7597 (tt0) cc_final: 0.7342 (tt0) REVERT: E 182 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7925 (mm-30) REVERT: E 209 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7410 (mt-10) REVERT: E 249 LYS cc_start: 0.8114 (mmpt) cc_final: 0.7685 (mmpt) REVERT: E 256 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7599 (mm-30) REVERT: E 264 ASP cc_start: 0.8128 (t70) cc_final: 0.7843 (t0) REVERT: E 267 ASN cc_start: 0.8396 (m-40) cc_final: 0.8119 (m-40) REVERT: E 273 LYS cc_start: 0.8960 (mtmm) cc_final: 0.8745 (mttm) REVERT: E 288 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7770 (mt-10) REVERT: E 305 SER cc_start: 0.8802 (m) cc_final: 0.8370 (p) REVERT: E 308 GLN cc_start: 0.8065 (tp40) cc_final: 0.7706 (tp40) REVERT: F 2 LEU cc_start: 0.7860 (mp) cc_final: 0.7659 (mp) REVERT: F 15 ARG cc_start: 0.8391 (tpp80) cc_final: 0.8057 (ttp80) REVERT: F 56 ASP cc_start: 0.7753 (t0) cc_final: 0.7461 (t0) REVERT: F 58 LEU cc_start: 0.7759 (tp) cc_final: 0.7511 (tt) REVERT: F 94 ASN cc_start: 0.7632 (t0) cc_final: 0.7300 (t0) REVERT: F 117 ILE cc_start: 0.8174 (mm) cc_final: 0.7954 (mm) REVERT: F 128 TYR cc_start: 0.8690 (m-10) cc_final: 0.8110 (m-80) REVERT: F 139 GLU cc_start: 0.7692 (mp0) cc_final: 0.7311 (mp0) REVERT: F 176 VAL cc_start: 0.8233 (p) cc_final: 0.8010 (m) REVERT: F 190 GLU cc_start: 0.7265 (mp0) cc_final: 0.6610 (mp0) REVERT: F 203 LYS cc_start: 0.8111 (mttm) cc_final: 0.7856 (mttm) REVERT: F 249 LYS cc_start: 0.8596 (mmmt) cc_final: 0.8261 (mmmt) REVERT: F 254 LEU cc_start: 0.8330 (tp) cc_final: 0.7956 (mp) REVERT: F 267 ASN cc_start: 0.8032 (m-40) cc_final: 0.7774 (m-40) REVERT: F 283 ASP cc_start: 0.7943 (p0) cc_final: 0.7578 (p0) REVERT: F 303 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8125 (mt) REVERT: F 309 GLN cc_start: 0.8736 (mt0) cc_final: 0.8189 (mt0) REVERT: F 313 TYR cc_start: 0.8738 (t80) cc_final: 0.8169 (t80) REVERT: G 15 ARG cc_start: 0.7779 (ttt180) cc_final: 0.7568 (ttt180) REVERT: G 68 GLN cc_start: 0.7275 (OUTLIER) cc_final: 0.6820 (pp30) REVERT: G 72 GLU cc_start: 0.7638 (mp0) cc_final: 0.7241 (mp0) REVERT: G 74 LEU cc_start: 0.7312 (mm) cc_final: 0.7091 (mp) REVERT: G 83 LEU cc_start: 0.8472 (tp) cc_final: 0.8231 (tm) REVERT: G 106 GLN cc_start: 0.7597 (pm20) cc_final: 0.7209 (pm20) REVERT: G 122 SER cc_start: 0.8825 (p) cc_final: 0.8524 (t) REVERT: G 233 LEU cc_start: 0.8763 (tp) cc_final: 0.8538 (tm) REVERT: G 237 GLN cc_start: 0.7782 (mt0) cc_final: 0.7457 (mt0) REVERT: G 253 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6974 (mm-30) REVERT: G 254 LEU cc_start: 0.7400 (mt) cc_final: 0.7131 (mm) REVERT: G 275 GLU cc_start: 0.6587 (OUTLIER) cc_final: 0.6356 (mt-10) REVERT: H 19 SER cc_start: 0.8728 (m) cc_final: 0.8227 (p) REVERT: H 27 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7479 (pt0) REVERT: H 65 ASP cc_start: 0.8149 (t0) cc_final: 0.7849 (t0) REVERT: H 95 ASN cc_start: 0.8598 (m-40) cc_final: 0.8255 (m110) REVERT: H 118 LYS cc_start: 0.8752 (mmtp) cc_final: 0.8243 (mttp) REVERT: H 122 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7980 (pt) REVERT: H 153 ARG cc_start: 0.8753 (mtt-85) cc_final: 0.8496 (mtt90) REVERT: H 168 ILE cc_start: 0.8285 (mt) cc_final: 0.8005 (mp) REVERT: H 174 LYS cc_start: 0.8058 (ptpt) cc_final: 0.7839 (ptpt) REVERT: H 201 ASN cc_start: 0.8103 (m-40) cc_final: 0.7715 (m-40) REVERT: I 20 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8570 (mm) REVERT: I 26 GLN cc_start: 0.8567 (mm-40) cc_final: 0.7983 (mt0) REVERT: I 34 GLU cc_start: 0.8062 (tt0) cc_final: 0.7814 (tt0) REVERT: I 78 LEU cc_start: 0.8438 (mt) cc_final: 0.8004 (tp) REVERT: I 82 ILE cc_start: 0.8775 (mt) cc_final: 0.8554 (mt) REVERT: I 148 LEU cc_start: 0.8025 (mp) cc_final: 0.7743 (mp) REVERT: I 149 ASN cc_start: 0.8079 (m-40) cc_final: 0.7710 (m-40) REVERT: I 152 GLU cc_start: 0.7981 (mp0) cc_final: 0.7703 (mp0) REVERT: I 206 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8103 (tp) REVERT: I 208 PHE cc_start: 0.7930 (t80) cc_final: 0.7718 (t80) REVERT: I 226 MET cc_start: 0.7317 (mtt) cc_final: 0.7104 (mtt) REVERT: I 229 ARG cc_start: 0.7527 (ptm160) cc_final: 0.7185 (ptm160) REVERT: I 230 LEU cc_start: 0.8262 (mt) cc_final: 0.7935 (mt) REVERT: I 233 LEU cc_start: 0.8388 (mt) cc_final: 0.7991 (mt) REVERT: I 294 GLU cc_start: 0.7532 (tp30) cc_final: 0.6590 (tm-30) REVERT: I 295 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7885 (ttt90) REVERT: I 296 ASN cc_start: 0.8454 (m-40) cc_final: 0.8096 (m110) REVERT: I 349 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.8037 (tp40) REVERT: I 352 SER cc_start: 0.8684 (t) cc_final: 0.8479 (t) REVERT: I 386 LEU cc_start: 0.7887 (tp) cc_final: 0.7672 (tt) REVERT: I 389 ASP cc_start: 0.7620 (m-30) cc_final: 0.7363 (m-30) REVERT: I 407 GLU cc_start: 0.8152 (pm20) cc_final: 0.7813 (pm20) REVERT: I 416 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7299 (m-30) REVERT: I 427 GLU cc_start: 0.8237 (pt0) cc_final: 0.7795 (pp20) REVERT: I 460 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7509 (tm-30) REVERT: I 478 TYR cc_start: 0.8482 (m-80) cc_final: 0.8267 (m-80) REVERT: I 488 GLN cc_start: 0.8675 (tp40) cc_final: 0.8241 (tm-30) REVERT: I 491 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7547 (mt-10) REVERT: I 495 ASP cc_start: 0.8154 (m-30) cc_final: 0.7834 (m-30) REVERT: I 496 ARG cc_start: 0.8162 (ttm110) cc_final: 0.7899 (ttm110) REVERT: I 504 GLU cc_start: 0.7344 (tp30) cc_final: 0.6755 (tp30) REVERT: I 576 GLU cc_start: 0.8166 (tp30) cc_final: 0.7758 (tp30) REVERT: I 585 SER cc_start: 0.8877 (m) cc_final: 0.8496 (p) REVERT: I 590 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8253 (tmtt) REVERT: I 605 TYR cc_start: 0.7778 (m-80) cc_final: 0.7534 (m-80) REVERT: I 617 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7762 (mm-30) REVERT: I 620 TYR cc_start: 0.8464 (m-80) cc_final: 0.7302 (m-80) REVERT: I 632 LYS cc_start: 0.8313 (ttpt) cc_final: 0.8042 (ttpp) REVERT: I 663 LYS cc_start: 0.8162 (ptpt) cc_final: 0.7911 (ptpt) REVERT: I 666 LYS cc_start: 0.8703 (mmmt) cc_final: 0.8313 (mmmm) REVERT: I 667 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7865 (mm-30) REVERT: I 680 ARG cc_start: 0.7963 (mmp-170) cc_final: 0.7686 (mmp-170) REVERT: I 721 ASP cc_start: 0.7406 (m-30) cc_final: 0.7116 (m-30) REVERT: I 745 ARG cc_start: 0.8022 (mtp180) cc_final: 0.7714 (mtp180) REVERT: I 774 ARG cc_start: 0.8478 (ttm110) cc_final: 0.8153 (ttp-110) REVERT: I 777 ASP cc_start: 0.8067 (m-30) cc_final: 0.7814 (m-30) REVERT: I 780 LYS cc_start: 0.8593 (mptp) cc_final: 0.8298 (mttp) REVERT: I 797 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7640 (mm-30) REVERT: I 827 ASN cc_start: 0.7996 (t0) cc_final: 0.7553 (t0) REVERT: I 828 ILE cc_start: 0.8287 (mm) cc_final: 0.7997 (mm) REVERT: I 829 VAL cc_start: 0.8885 (m) cc_final: 0.8603 (p) REVERT: I 830 MET cc_start: 0.8383 (mmp) cc_final: 0.8051 (mmp) REVERT: I 832 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7902 (mt-10) REVERT: I 870 GLU cc_start: 0.7841 (pp20) cc_final: 0.7528 (pp20) REVERT: I 871 GLN cc_start: 0.8259 (tp-100) cc_final: 0.7906 (tp40) REVERT: I 927 ILE cc_start: 0.8772 (tt) cc_final: 0.8485 (pt) REVERT: I 940 MET cc_start: 0.8033 (mmt) cc_final: 0.7828 (mmt) REVERT: J 8 THR cc_start: 0.8394 (m) cc_final: 0.8015 (m) REVERT: J 14 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7599 (mm-30) REVERT: J 41 GLU cc_start: 0.7646 (tp30) cc_final: 0.6946 (tp30) REVERT: J 53 GLU cc_start: 0.7528 (tp30) cc_final: 0.7241 (mp0) REVERT: J 54 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7485 (tm-30) REVERT: J 57 LEU cc_start: 0.8424 (mp) cc_final: 0.8203 (mt) REVERT: J 94 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7915 (tm-30) REVERT: J 121 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7440 (tm-30) outliers start: 139 outliers final: 49 residues processed: 1064 average time/residue: 0.7828 time to fit residues: 964.3513 Evaluate side-chains 997 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 926 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 268 LYS Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 48 GLN Chi-restraints excluded: chain E residue 151 PHE Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 124 ARG Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 144 LYS Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 206 LEU Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 295 ARG Chi-restraints excluded: chain I residue 309 GLU Chi-restraints excluded: chain I residue 324 ASP Chi-restraints excluded: chain I residue 349 GLN Chi-restraints excluded: chain I residue 416 ASP Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 461 PHE Chi-restraints excluded: chain I residue 479 PHE Chi-restraints excluded: chain I residue 511 ILE Chi-restraints excluded: chain I residue 590 LYS Chi-restraints excluded: chain I residue 650 LEU Chi-restraints excluded: chain I residue 731 VAL Chi-restraints excluded: chain I residue 843 GLU Chi-restraints excluded: chain I residue 916 THR Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 121 GLU Chi-restraints excluded: chain K residue 119 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 225 optimal weight: 0.9990 chunk 278 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 200 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 366 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 364 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 209 optimal weight: 5.9990 chunk 244 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 ASN A 82 ASN A 142 HIS A 198 ASN A 217 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 ASN B 43 ASN B 48 GLN B 68 GLN B 217 ASN B 232 ASN B 267 ASN B 295 ASN C 10 GLN C 29 HIS D 48 GLN D 167 ASN E 48 GLN E 106 GLN E 142 HIS ** E 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 237 GLN E 242 GLN E 295 ASN E 309 GLN F 20 HIS F 43 ASN ** F 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 294 GLN H 14 ASN H 34 ASN H 71 ASN H 76 ASN H 93 GLN H 119 ASN H 195 GLN I 399 GLN I 445 HIS I 450 HIS I 483 GLN I 951 GLN K 70 GLN K 143 GLN K 146 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.137954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.117644 restraints weight = 47871.190| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.93 r_work: 0.3412 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 31399 Z= 0.252 Angle : 0.832 16.972 42781 Z= 0.408 Chirality : 0.066 1.090 4787 Planarity : 0.005 0.104 5308 Dihedral : 13.551 164.656 4882 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.30 % Allowed : 17.20 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % 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: -0.58 (0.14), residues: 3639 helix: 0.16 (0.13), residues: 1603 sheet: 0.02 (0.24), residues: 397 loop : -0.96 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 846 TYR 0.034 0.002 TYR I 497 PHE 0.026 0.002 PHE F 147 TRP 0.019 0.002 TRP I 453 HIS 0.014 0.001 HIS I 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.25 (31399) covalent geometry : angle 0.83187 / 0.41 (42781) hydrogen bonds : bond 0.04742 / 3.07 ( 1385) hydrogen bonds : angle 4.89485 / 3.41 ( 3955) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1143 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 975 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8083 (mtp85) REVERT: A 65 LYS cc_start: 0.8246 (mtmm) cc_final: 0.7811 (mtmm) REVERT: A 87 SER cc_start: 0.8940 (t) cc_final: 0.8613 (t) REVERT: A 101 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6863 (mt-10) REVERT: A 123 GLU cc_start: 0.8248 (tp30) cc_final: 0.7997 (tp30) REVERT: A 126 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8352 (mmtm) REVERT: A 139 GLU cc_start: 0.8192 (mp0) cc_final: 0.7736 (mp0) REVERT: A 148 ASN cc_start: 0.8335 (p0) cc_final: 0.7864 (p0) REVERT: A 166 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7816 (tt) REVERT: A 202 THR cc_start: 0.8607 (t) cc_final: 0.8406 (p) REVERT: A 210 SER cc_start: 0.8806 (m) cc_final: 0.8408 (p) REVERT: A 232 ASN cc_start: 0.8538 (m110) cc_final: 0.8310 (m110) REVERT: A 256 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7667 (mp0) REVERT: A 264 ASP cc_start: 0.8253 (t0) cc_final: 0.7745 (t70) REVERT: A 268 LYS cc_start: 0.8463 (mttp) cc_final: 0.8208 (mttp) REVERT: A 283 ASP cc_start: 0.7992 (m-30) cc_final: 0.7617 (m-30) REVERT: B 6 LYS cc_start: 0.9074 (ttmm) cc_final: 0.8835 (mttp) REVERT: B 15 ARG cc_start: 0.8294 (ptm-80) cc_final: 0.7922 (ptm-80) REVERT: B 48 GLN cc_start: 0.8547 (tt0) cc_final: 0.8319 (tt0) REVERT: B 54 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8111 (mptt) REVERT: B 97 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7729 (mm-30) REVERT: B 109 ASP cc_start: 0.7978 (t0) cc_final: 0.7562 (t0) REVERT: B 123 GLU cc_start: 0.8114 (tp30) cc_final: 0.7667 (tp30) REVERT: B 124 ARG cc_start: 0.8587 (ttm-80) cc_final: 0.8286 (ttm-80) REVERT: B 143 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.7506 (ttp80) REVERT: B 190 GLU cc_start: 0.8157 (mp0) cc_final: 0.7926 (mp0) REVERT: B 268 LYS cc_start: 0.8808 (ttmm) cc_final: 0.8562 (mtpp) REVERT: B 290 ASN cc_start: 0.8327 (m-40) cc_final: 0.8105 (m-40) REVERT: C 32 SER cc_start: 0.8527 (m) cc_final: 0.7601 (p) REVERT: C 54 LYS cc_start: 0.8388 (mptt) cc_final: 0.8038 (mmmm) REVERT: C 139 GLU cc_start: 0.8269 (mp0) cc_final: 0.7969 (mp0) REVERT: C 140 GLN cc_start: 0.8705 (mp10) cc_final: 0.8412 (mp10) REVERT: C 151 PHE cc_start: 0.8555 (m-80) cc_final: 0.8327 (m-80) REVERT: C 283 ASP cc_start: 0.8143 (m-30) cc_final: 0.7900 (m-30) REVERT: C 316 GLU cc_start: 0.8267 (tt0) cc_final: 0.8045 (tt0) REVERT: D 15 ARG cc_start: 0.8681 (ttp80) cc_final: 0.8399 (ttt-90) REVERT: D 65 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7414 (pttt) REVERT: D 66 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8341 (mtt90) REVERT: D 68 GLN cc_start: 0.8432 (pt0) cc_final: 0.7699 (pt0) REVERT: D 72 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7859 (mt-10) REVERT: D 78 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: D 97 GLU cc_start: 0.7760 (tp30) cc_final: 0.7378 (tp30) REVERT: D 120 SER cc_start: 0.7682 (OUTLIER) cc_final: 0.7286 (t) REVERT: D 124 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8579 (tmm-80) REVERT: D 130 ASP cc_start: 0.7286 (t0) cc_final: 0.6595 (t0) REVERT: D 156 MET cc_start: 0.8461 (mtp) cc_final: 0.8125 (mtp) REVERT: D 175 GLU cc_start: 0.8412 (mm-30) cc_final: 0.7947 (mm-30) REVERT: D 209 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7746 (mt-10) REVERT: D 273 LYS cc_start: 0.9006 (mtmm) cc_final: 0.8586 (mttt) REVERT: D 283 ASP cc_start: 0.8204 (m-30) cc_final: 0.7902 (m-30) REVERT: D 308 GLN cc_start: 0.8328 (mm-40) cc_final: 0.8079 (tp-100) REVERT: E 8 GLN cc_start: 0.8239 (mm-40) cc_final: 0.7238 (mp10) REVERT: E 15 ARG cc_start: 0.8739 (ttp80) cc_final: 0.8446 (ttp80) REVERT: E 45 THR cc_start: 0.8597 (t) cc_final: 0.8300 (m) REVERT: E 46 ARG cc_start: 0.8497 (mtp-110) cc_final: 0.8191 (mmm160) REVERT: E 89 ASP cc_start: 0.8547 (p0) cc_final: 0.8328 (p0) REVERT: E 141 SER cc_start: 0.8606 (m) cc_final: 0.8220 (p) REVERT: E 182 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7882 (mm-30) REVERT: E 199 LEU cc_start: 0.8736 (mp) cc_final: 0.8523 (mm) REVERT: E 209 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7412 (mt-10) REVERT: E 212 THR cc_start: 0.8086 (OUTLIER) cc_final: 0.7858 (p) REVERT: E 248 ASN cc_start: 0.7911 (p0) cc_final: 0.7619 (p0) REVERT: E 249 LYS cc_start: 0.8080 (mmpt) cc_final: 0.7663 (mmpt) REVERT: E 256 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7732 (mm-30) REVERT: E 264 ASP cc_start: 0.8191 (t70) cc_final: 0.7928 (t0) REVERT: E 275 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7412 (mt-10) REVERT: E 288 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7538 (mt-10) REVERT: E 291 ASP cc_start: 0.7554 (p0) cc_final: 0.7308 (p0) REVERT: E 308 GLN cc_start: 0.8095 (tp40) cc_final: 0.7748 (tp40) REVERT: E 312 ASP cc_start: 0.8133 (m-30) cc_final: 0.7870 (m-30) REVERT: F 56 ASP cc_start: 0.7716 (t0) cc_final: 0.7407 (t0) REVERT: F 73 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8062 (ttt-90) REVERT: F 89 ASP cc_start: 0.7589 (t0) cc_final: 0.7336 (t0) REVERT: F 94 ASN cc_start: 0.7442 (t0) cc_final: 0.7190 (t0) REVERT: F 117 ILE cc_start: 0.8217 (mm) cc_final: 0.7940 (mm) REVERT: F 128 TYR cc_start: 0.8695 (m-80) cc_final: 0.8138 (m-80) REVERT: F 190 GLU cc_start: 0.7263 (mp0) cc_final: 0.6693 (mp0) REVERT: F 249 LYS cc_start: 0.8636 (mmmt) cc_final: 0.8269 (mmmt) REVERT: F 267 ASN cc_start: 0.8011 (m-40) cc_final: 0.7766 (m-40) REVERT: F 273 LYS cc_start: 0.8740 (mttm) cc_final: 0.8536 (mttt) REVERT: F 288 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7703 (tm-30) REVERT: F 309 GLN cc_start: 0.8793 (mt0) cc_final: 0.8191 (mt0) REVERT: F 313 TYR cc_start: 0.8749 (t80) cc_final: 0.8136 (t80) REVERT: G 2 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7529 (tm) REVERT: G 9 PHE cc_start: 0.8452 (m-80) cc_final: 0.8143 (m-80) REVERT: G 58 LEU cc_start: 0.6302 (tt) cc_final: 0.6057 (tt) REVERT: G 72 GLU cc_start: 0.7649 (mp0) cc_final: 0.7213 (mp0) REVERT: G 83 LEU cc_start: 0.8575 (tp) cc_final: 0.8349 (tm) REVERT: G 106 GLN cc_start: 0.7720 (pm20) cc_final: 0.7378 (pm20) REVERT: G 122 SER cc_start: 0.8902 (p) cc_final: 0.8677 (t) REVERT: G 233 LEU cc_start: 0.8810 (tp) cc_final: 0.8507 (tm) REVERT: G 253 GLU cc_start: 0.7303 (mm-30) cc_final: 0.7082 (mm-30) REVERT: G 275 GLU cc_start: 0.6695 (OUTLIER) cc_final: 0.6330 (mt-10) REVERT: H 27 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7791 (pt0) REVERT: H 65 ASP cc_start: 0.8102 (t0) cc_final: 0.7836 (t0) REVERT: H 118 LYS cc_start: 0.8748 (mmtp) cc_final: 0.8294 (mttp) REVERT: H 122 ILE cc_start: 0.8348 (tp) cc_final: 0.8064 (pt) REVERT: H 168 ILE cc_start: 0.8384 (mt) cc_final: 0.8094 (mp) REVERT: H 173 ILE cc_start: 0.8050 (pt) cc_final: 0.7775 (pp) REVERT: H 201 ASN cc_start: 0.8145 (m-40) cc_final: 0.7734 (m110) REVERT: H 217 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8551 (tp40) REVERT: I 11 ARG cc_start: 0.9019 (mtt180) cc_final: 0.8699 (mtt180) REVERT: I 20 ILE cc_start: 0.8822 (mt) cc_final: 0.8430 (mm) REVERT: I 22 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.7305 (tp) REVERT: I 23 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8145 (mt-10) REVERT: I 26 GLN cc_start: 0.8582 (mm-40) cc_final: 0.7705 (mp10) REVERT: I 78 LEU cc_start: 0.8537 (mt) cc_final: 0.8201 (mt) REVERT: I 82 ILE cc_start: 0.8788 (mt) cc_final: 0.8581 (mt) REVERT: I 106 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.7186 (mtp180) REVERT: I 152 GLU cc_start: 0.8013 (mp0) cc_final: 0.7749 (mp0) REVERT: I 153 PHE cc_start: 0.8780 (t80) cc_final: 0.8303 (t80) REVERT: I 208 PHE cc_start: 0.7966 (t80) cc_final: 0.7710 (t80) REVERT: I 213 VAL cc_start: 0.8954 (m) cc_final: 0.8738 (p) REVERT: I 229 ARG cc_start: 0.7585 (ptm160) cc_final: 0.7108 (ptm160) REVERT: I 230 LEU cc_start: 0.8255 (mt) cc_final: 0.7992 (mp) REVERT: I 233 LEU cc_start: 0.8430 (mt) cc_final: 0.7991 (mt) REVERT: I 291 GLU cc_start: 0.8399 (pm20) cc_final: 0.8176 (pm20) REVERT: I 294 GLU cc_start: 0.7485 (tp30) cc_final: 0.7120 (mm-30) REVERT: I 295 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7910 (ttt180) REVERT: I 329 LYS cc_start: 0.8703 (mtmt) cc_final: 0.8466 (mtmt) REVERT: I 349 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7772 (tp-100) REVERT: I 407 GLU cc_start: 0.8095 (pm20) cc_final: 0.7807 (pm20) REVERT: I 427 GLU cc_start: 0.8214 (pt0) cc_final: 0.7768 (pp20) REVERT: I 460 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7648 (tm-30) REVERT: I 474 GLU cc_start: 0.7481 (pt0) cc_final: 0.7182 (pt0) REVERT: I 476 GLU cc_start: 0.7985 (mp0) cc_final: 0.7414 (mp0) REVERT: I 483 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7436 (pm20) REVERT: I 488 GLN cc_start: 0.8683 (tp40) cc_final: 0.8082 (tm-30) REVERT: I 491 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7628 (mt-10) REVERT: I 495 ASP cc_start: 0.8045 (m-30) cc_final: 0.7751 (m-30) REVERT: I 504 GLU cc_start: 0.7331 (tp30) cc_final: 0.7112 (tp30) REVERT: I 590 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8228 (tmtt) REVERT: I 617 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7746 (mm-30) REVERT: I 632 LYS cc_start: 0.8407 (ttpt) cc_final: 0.8112 (ttpp) REVERT: I 638 LYS cc_start: 0.8702 (mttt) cc_final: 0.8488 (mptt) REVERT: I 663 LYS cc_start: 0.8306 (ptpt) cc_final: 0.8037 (ptpt) REVERT: I 667 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7952 (mm-30) REVERT: I 680 ARG cc_start: 0.8101 (mmp-170) cc_final: 0.7741 (mmp-170) REVERT: I 723 ARG cc_start: 0.7782 (mtp85) cc_final: 0.7218 (mtp85) REVERT: I 745 ARG cc_start: 0.8113 (mtp180) cc_final: 0.7833 (mtp180) REVERT: I 777 ASP cc_start: 0.7986 (m-30) cc_final: 0.7785 (m-30) REVERT: I 780 LYS cc_start: 0.8611 (mttp) cc_final: 0.8329 (mttp) REVERT: I 797 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7842 (mm-30) REVERT: I 827 ASN cc_start: 0.8043 (t0) cc_final: 0.7604 (t0) REVERT: I 828 ILE cc_start: 0.8333 (mm) cc_final: 0.8074 (mm) REVERT: I 829 VAL cc_start: 0.8923 (m) cc_final: 0.8636 (p) REVERT: I 830 MET cc_start: 0.8456 (mmp) cc_final: 0.7936 (mmp) REVERT: I 832 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7903 (mt-10) REVERT: I 835 LYS cc_start: 0.8784 (ttmm) cc_final: 0.8544 (ttpp) REVERT: I 870 GLU cc_start: 0.7816 (pp20) cc_final: 0.7497 (pp20) REVERT: I 882 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7627 (mm-30) REVERT: I 927 ILE cc_start: 0.8783 (tt) cc_final: 0.8485 (pt) REVERT: I 940 MET cc_start: 0.8145 (mmt) cc_final: 0.7907 (mmt) REVERT: I 972 GLN cc_start: 0.8058 (tm-30) cc_final: 0.7749 (pp30) REVERT: J 7 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8386 (tt) REVERT: J 8 THR cc_start: 0.8516 (m) cc_final: 0.8105 (m) REVERT: J 14 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7646 (mm-30) REVERT: J 33 LEU cc_start: 0.7075 (OUTLIER) cc_final: 0.6819 (pp) REVERT: J 41 GLU cc_start: 0.7680 (tp30) cc_final: 0.6903 (tp30) REVERT: J 52 GLU cc_start: 0.7104 (tt0) cc_final: 0.6624 (tm-30) REVERT: J 53 GLU cc_start: 0.7629 (tp30) cc_final: 0.7212 (mp0) REVERT: J 57 LEU cc_start: 0.8496 (mp) cc_final: 0.8257 (mt) REVERT: J 94 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7851 (tm-30) REVERT: J 119 LEU cc_start: 0.8688 (tp) cc_final: 0.8462 (tm) REVERT: J 121 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7629 (tm-30) outliers start: 168 outliers final: 64 residues processed: 1051 average time/residue: 0.7597 time to fit residues: 925.6119 Evaluate side-chains 1009 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 920 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain F residue 73 ARG Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 124 ARG Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 239 LEU Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 144 LYS Chi-restraints excluded: chain H residue 156 LYS Chi-restraints excluded: chain H residue 195 GLN Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 217 GLN Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 106 ARG Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 288 GLN Chi-restraints excluded: chain I residue 295 ARG Chi-restraints excluded: chain I residue 349 GLN Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 461 PHE Chi-restraints excluded: chain I residue 479 PHE Chi-restraints excluded: chain I residue 483 GLN Chi-restraints excluded: chain I residue 590 LYS Chi-restraints excluded: chain I residue 650 LEU Chi-restraints excluded: chain I residue 712 MET Chi-restraints excluded: chain I residue 724 GLU Chi-restraints excluded: chain I residue 725 SER Chi-restraints excluded: chain I residue 731 VAL Chi-restraints excluded: chain I residue 786 MET Chi-restraints excluded: chain I residue 843 GLU Chi-restraints excluded: chain I residue 916 THR Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 121 GLU Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 63 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 192 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 132 optimal weight: 0.0370 chunk 207 optimal weight: 0.8980 chunk 135 optimal weight: 0.5980 chunk 41 optimal weight: 0.0980 chunk 273 optimal weight: 1.9990 chunk 257 optimal weight: 0.2980 chunk 139 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 ASN A 82 ASN A 198 ASN A 217 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 ASN B 217 ASN B 232 ASN ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 ASN B 295 ASN C 68 GLN C 99 ASN C 232 ASN C 290 ASN C 295 ASN D 290 ASN D 295 ASN F 10 GLN F 43 ASN F 68 GLN ** F 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 217 ASN H 34 ASN ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 222 GLN ** I 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 399 GLN ** I 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 893 GLN I 951 GLN ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 143 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.139594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.119257 restraints weight = 47553.184| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.95 r_work: 0.3441 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31399 Z= 0.151 Angle : 0.746 13.089 42781 Z= 0.362 Chirality : 0.058 0.826 4787 Planarity : 0.005 0.060 5308 Dihedral : 13.115 164.538 4871 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 5.59 % Allowed : 19.29 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % 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: -0.29 (0.14), residues: 3639 helix: 0.51 (0.13), residues: 1595 sheet: 0.01 (0.23), residues: 433 loop : -0.90 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 774 TYR 0.028 0.002 TYR I 446 PHE 0.029 0.001 PHE G 230 TRP 0.020 0.001 TRP I 453 HIS 0.012 0.001 HIS I 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (31399) covalent geometry : angle 0.74640 / 0.36 (42781) hydrogen bonds : bond 0.03990 / 2.59 ( 1385) hydrogen bonds : angle 4.69590 / 3.28 ( 3955) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1134 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 957 time to evaluate : 1.192 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: A 60 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8066 (mtp85) REVERT: A 87 SER cc_start: 0.8861 (t) cc_final: 0.8457 (p) REVERT: A 101 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6997 (mt-10) REVERT: A 139 GLU cc_start: 0.8193 (mp0) cc_final: 0.7748 (mp0) REVERT: A 210 SER cc_start: 0.8774 (m) cc_final: 0.8373 (p) REVERT: A 232 ASN cc_start: 0.8562 (m-40) cc_final: 0.8349 (m110) REVERT: A 256 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7657 (mp0) REVERT: A 264 ASP cc_start: 0.8255 (t0) cc_final: 0.7697 (t70) REVERT: A 268 LYS cc_start: 0.8393 (mttp) cc_final: 0.8061 (mttp) REVERT: A 283 ASP cc_start: 0.7996 (m-30) cc_final: 0.7630 (m-30) REVERT: A 298 GLU cc_start: 0.8456 (tp30) cc_final: 0.8142 (tp30) REVERT: B 48 GLN cc_start: 0.8405 (tt0) cc_final: 0.8199 (tt0) REVERT: B 54 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.8101 (mtpp) REVERT: B 109 ASP cc_start: 0.7974 (t0) cc_final: 0.7627 (t0) REVERT: B 123 GLU cc_start: 0.8062 (tp30) cc_final: 0.7630 (tp30) REVERT: B 124 ARG cc_start: 0.8562 (ttm-80) cc_final: 0.8265 (ttm-80) REVERT: B 143 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.7486 (ttp80) REVERT: B 190 GLU cc_start: 0.8121 (mp0) cc_final: 0.7907 (mp0) REVERT: B 268 LYS cc_start: 0.8793 (ttmm) cc_final: 0.8542 (mtpp) REVERT: B 283 ASP cc_start: 0.7784 (p0) cc_final: 0.7557 (p0) REVERT: B 290 ASN cc_start: 0.8313 (m-40) cc_final: 0.8097 (m-40) REVERT: B 309 GLN cc_start: 0.8840 (mt0) cc_final: 0.8481 (mt0) REVERT: C 32 SER cc_start: 0.8422 (m) cc_final: 0.7366 (p) REVERT: C 54 LYS cc_start: 0.8415 (mptt) cc_final: 0.8124 (mmmm) REVERT: C 139 GLU cc_start: 0.8230 (mp0) cc_final: 0.7928 (mp0) REVERT: C 140 GLN cc_start: 0.8712 (mp10) cc_final: 0.8402 (mp10) REVERT: C 151 PHE cc_start: 0.8550 (m-80) cc_final: 0.8338 (m-80) REVERT: C 283 ASP cc_start: 0.8109 (m-30) cc_final: 0.7853 (m-30) REVERT: C 316 GLU cc_start: 0.8245 (tt0) cc_final: 0.8033 (tt0) REVERT: D 15 ARG cc_start: 0.8587 (ttp80) cc_final: 0.8296 (ttt180) REVERT: D 66 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8166 (mtt90) REVERT: D 68 GLN cc_start: 0.8369 (pt0) cc_final: 0.7539 (pt0) REVERT: D 78 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7729 (tt0) REVERT: D 97 GLU cc_start: 0.7776 (tp30) cc_final: 0.7419 (tp30) REVERT: D 120 SER cc_start: 0.7455 (OUTLIER) cc_final: 0.7074 (t) REVERT: D 124 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8568 (tmm-80) REVERT: D 127 VAL cc_start: 0.8936 (OUTLIER) cc_final: 0.8647 (t) REVERT: D 130 ASP cc_start: 0.7262 (t0) cc_final: 0.6446 (t0) REVERT: D 156 MET cc_start: 0.8385 (mtp) cc_final: 0.8011 (mtp) REVERT: D 242 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8137 (tm-30) REVERT: D 283 ASP cc_start: 0.8147 (m-30) cc_final: 0.7842 (m-30) REVERT: E 8 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7870 (mm110) REVERT: E 15 ARG cc_start: 0.8709 (ttp80) cc_final: 0.8425 (ttp80) REVERT: E 26 MET cc_start: 0.8492 (mtp) cc_final: 0.8147 (ttm) REVERT: E 45 THR cc_start: 0.8600 (t) cc_final: 0.8312 (m) REVERT: E 46 ARG cc_start: 0.8431 (mtp-110) cc_final: 0.8111 (mmm160) REVERT: E 89 ASP cc_start: 0.8523 (p0) cc_final: 0.8318 (p0) REVERT: E 141 SER cc_start: 0.8573 (m) cc_final: 0.8170 (p) REVERT: E 182 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7847 (mm-30) REVERT: E 190 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7545 (pm20) REVERT: E 199 LEU cc_start: 0.8682 (mp) cc_final: 0.8477 (mm) REVERT: E 209 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7410 (mt-10) REVERT: E 212 THR cc_start: 0.8045 (OUTLIER) cc_final: 0.7793 (p) REVERT: E 241 ASP cc_start: 0.7903 (t0) cc_final: 0.7630 (t70) REVERT: E 249 LYS cc_start: 0.8037 (mmpt) cc_final: 0.7615 (mmpt) REVERT: E 256 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7695 (mm-30) REVERT: E 264 ASP cc_start: 0.8181 (t70) cc_final: 0.7926 (t0) REVERT: E 288 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7476 (mt-10) REVERT: E 291 ASP cc_start: 0.7492 (p0) cc_final: 0.7177 (p0) REVERT: E 305 SER cc_start: 0.8842 (m) cc_final: 0.8291 (p) REVERT: E 308 GLN cc_start: 0.8059 (tp40) cc_final: 0.7685 (tp40) REVERT: E 309 GLN cc_start: 0.8449 (mt0) cc_final: 0.8160 (mt0) REVERT: E 312 ASP cc_start: 0.8100 (m-30) cc_final: 0.7810 (m-30) REVERT: F 15 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8192 (ttp80) REVERT: F 56 ASP cc_start: 0.7825 (t0) cc_final: 0.7489 (t0) REVERT: F 68 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7486 (tp40) REVERT: F 89 ASP cc_start: 0.7561 (t0) cc_final: 0.7264 (t0) REVERT: F 94 ASN cc_start: 0.7397 (t0) cc_final: 0.7120 (t0) REVERT: F 117 ILE cc_start: 0.8214 (mm) cc_final: 0.7919 (mm) REVERT: F 123 GLU cc_start: 0.8054 (tp30) cc_final: 0.7598 (tm-30) REVERT: F 128 TYR cc_start: 0.8707 (m-80) cc_final: 0.8181 (m-80) REVERT: F 180 THR cc_start: 0.8628 (p) cc_final: 0.8321 (t) REVERT: F 205 TYR cc_start: 0.7381 (m-80) cc_final: 0.7015 (m-80) REVERT: F 249 LYS cc_start: 0.8670 (mmmt) cc_final: 0.8289 (mmmt) REVERT: F 267 ASN cc_start: 0.7941 (m-40) cc_final: 0.7714 (m-40) REVERT: F 288 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7778 (tm-30) REVERT: F 313 TYR cc_start: 0.8732 (t80) cc_final: 0.8066 (t80) REVERT: G 58 LEU cc_start: 0.6313 (tt) cc_final: 0.6052 (tt) REVERT: G 72 GLU cc_start: 0.7621 (mp0) cc_final: 0.7240 (mp0) REVERT: G 83 LEU cc_start: 0.8536 (tp) cc_final: 0.8319 (tm) REVERT: G 106 GLN cc_start: 0.7628 (pm20) cc_final: 0.7301 (pm20) REVERT: G 122 SER cc_start: 0.8864 (p) cc_final: 0.8595 (t) REVERT: G 223 VAL cc_start: 0.8418 (OUTLIER) cc_final: 0.8097 (m) REVERT: G 233 LEU cc_start: 0.8798 (tp) cc_final: 0.8518 (tm) REVERT: G 253 GLU cc_start: 0.7447 (mm-30) cc_final: 0.6988 (mm-30) REVERT: G 288 GLU cc_start: 0.8134 (tp30) cc_final: 0.7507 (tp30) REVERT: G 302 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7119 (tm) REVERT: H 27 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7762 (pt0) REVERT: H 65 ASP cc_start: 0.8130 (t0) cc_final: 0.7903 (t0) REVERT: H 122 ILE cc_start: 0.8285 (tp) cc_final: 0.8008 (pt) REVERT: H 153 ARG cc_start: 0.8911 (mtt90) cc_final: 0.8627 (mtt90) REVERT: H 168 ILE cc_start: 0.8411 (mt) cc_final: 0.8209 (mp) REVERT: H 173 ILE cc_start: 0.7990 (pt) cc_final: 0.7695 (pp) REVERT: H 201 ASN cc_start: 0.8213 (m-40) cc_final: 0.7626 (m110) REVERT: H 205 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.8023 (ttm) REVERT: H 217 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8516 (tp40) REVERT: H 227 THR cc_start: 0.8341 (OUTLIER) cc_final: 0.7971 (p) REVERT: I 11 ARG cc_start: 0.8990 (mtt180) cc_final: 0.8371 (mtt180) REVERT: I 20 ILE cc_start: 0.8785 (mt) cc_final: 0.8436 (mm) REVERT: I 22 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8149 (tp) REVERT: I 23 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8097 (mt-10) REVERT: I 26 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8084 (mt0) REVERT: I 78 LEU cc_start: 0.8510 (mt) cc_final: 0.8162 (mt) REVERT: I 82 ILE cc_start: 0.8776 (mt) cc_final: 0.8575 (mt) REVERT: I 106 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.7091 (mtp180) REVERT: I 110 LEU cc_start: 0.8696 (mp) cc_final: 0.8474 (mt) REVERT: I 149 ASN cc_start: 0.8147 (m-40) cc_final: 0.7712 (m-40) REVERT: I 152 GLU cc_start: 0.8080 (mp0) cc_final: 0.7598 (mp0) REVERT: I 206 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8197 (mm) REVERT: I 213 VAL cc_start: 0.8935 (m) cc_final: 0.8724 (p) REVERT: I 229 ARG cc_start: 0.7525 (ptm160) cc_final: 0.7124 (ptm160) REVERT: I 230 LEU cc_start: 0.8210 (mt) cc_final: 0.7987 (mp) REVERT: I 233 LEU cc_start: 0.8319 (mt) cc_final: 0.7968 (mt) REVERT: I 256 SER cc_start: 0.8676 (t) cc_final: 0.8414 (p) REVERT: I 291 GLU cc_start: 0.8476 (pm20) cc_final: 0.8000 (pm20) REVERT: I 294 GLU cc_start: 0.7473 (tp30) cc_final: 0.7147 (mm-30) REVERT: I 295 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7841 (ttt180) REVERT: I 324 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.7233 (p0) REVERT: I 329 LYS cc_start: 0.8582 (mtmt) cc_final: 0.7967 (mtmp) REVERT: I 346 ILE cc_start: 0.8663 (mp) cc_final: 0.8269 (pp) REVERT: I 349 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7800 (tp-100) REVERT: I 351 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8669 (mp) REVERT: I 400 LYS cc_start: 0.8667 (ttmm) cc_final: 0.8422 (mtpp) REVERT: I 427 GLU cc_start: 0.8207 (pt0) cc_final: 0.7756 (pp20) REVERT: I 445 HIS cc_start: 0.7928 (OUTLIER) cc_final: 0.7645 (m-70) REVERT: I 460 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7618 (tm-30) REVERT: I 472 TRP cc_start: 0.8692 (t60) cc_final: 0.8437 (t60) REVERT: I 474 GLU cc_start: 0.7485 (pt0) cc_final: 0.7234 (pt0) REVERT: I 488 GLN cc_start: 0.8436 (tp40) cc_final: 0.7611 (tm-30) REVERT: I 491 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7457 (mt-10) REVERT: I 495 ASP cc_start: 0.8000 (m-30) cc_final: 0.7675 (m-30) REVERT: I 544 ASP cc_start: 0.8123 (t70) cc_final: 0.7856 (t0) REVERT: I 576 GLU cc_start: 0.8306 (tp30) cc_final: 0.7961 (mm-30) REVERT: I 590 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8201 (tmtt) REVERT: I 595 GLN cc_start: 0.8350 (mm-40) cc_final: 0.8046 (mm-40) REVERT: I 606 VAL cc_start: 0.8392 (OUTLIER) cc_final: 0.8080 (p) REVERT: I 613 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7839 (mt-10) REVERT: I 617 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7571 (mm-30) REVERT: I 632 LYS cc_start: 0.8362 (ttpt) cc_final: 0.8071 (ttpp) REVERT: I 642 THR cc_start: 0.8613 (m) cc_final: 0.8364 (p) REVERT: I 663 LYS cc_start: 0.8193 (ptpt) cc_final: 0.7933 (ptpt) REVERT: I 667 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7970 (mm-30) REVERT: I 680 ARG cc_start: 0.8077 (mmp-170) cc_final: 0.7514 (mtp180) REVERT: I 721 ASP cc_start: 0.7457 (m-30) cc_final: 0.7227 (m-30) REVERT: I 723 ARG cc_start: 0.7778 (mtp85) cc_final: 0.7214 (mtp85) REVERT: I 745 ARG cc_start: 0.8048 (mtp180) cc_final: 0.7767 (mtp180) REVERT: I 774 ARG cc_start: 0.8510 (ttm110) cc_final: 0.8123 (mtp85) REVERT: I 780 LYS cc_start: 0.8570 (mttp) cc_final: 0.8286 (mttp) REVERT: I 797 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7825 (mm-30) REVERT: I 815 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7859 (tt0) REVERT: I 827 ASN cc_start: 0.7965 (t0) cc_final: 0.7463 (t0) REVERT: I 828 ILE cc_start: 0.8264 (mm) cc_final: 0.8021 (mm) REVERT: I 829 VAL cc_start: 0.8801 (m) cc_final: 0.8518 (p) REVERT: I 832 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7886 (mt-10) REVERT: I 867 LYS cc_start: 0.8802 (mttp) cc_final: 0.8584 (mtpp) REVERT: I 870 GLU cc_start: 0.7719 (pp20) cc_final: 0.7404 (pp20) REVERT: I 882 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7589 (mm-30) REVERT: I 921 GLU cc_start: 0.8071 (tt0) cc_final: 0.7858 (tt0) REVERT: I 927 ILE cc_start: 0.8803 (tt) cc_final: 0.8501 (pt) REVERT: I 940 MET cc_start: 0.8183 (mmt) cc_final: 0.7942 (mmt) REVERT: J 5 LEU cc_start: 0.5540 (OUTLIER) cc_final: 0.4584 (pt) REVERT: J 14 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7623 (mm-30) REVERT: J 33 LEU cc_start: 0.7075 (OUTLIER) cc_final: 0.6832 (pp) REVERT: J 41 GLU cc_start: 0.7675 (tp30) cc_final: 0.6838 (tp30) REVERT: J 52 GLU cc_start: 0.7090 (tt0) cc_final: 0.6609 (tm-30) REVERT: J 53 GLU cc_start: 0.7555 (tp30) cc_final: 0.7109 (mp0) REVERT: J 54 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7311 (tm-30) REVERT: J 57 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8265 (mp) REVERT: J 94 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7827 (tm-30) REVERT: J 121 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7599 (tm-30) outliers start: 177 outliers final: 71 residues processed: 1034 average time/residue: 0.7761 time to fit residues: 928.3934 Evaluate side-chains 1019 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 914 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain F residue 4 SER Chi-restraints excluded: chain F residue 15 ARG Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 142 HIS Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 124 ARG Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 239 LEU Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 144 LYS Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 196 GLN Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 217 GLN Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 106 ARG Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 206 LEU Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 295 ARG Chi-restraints excluded: chain I residue 309 GLU Chi-restraints excluded: chain I residue 324 ASP Chi-restraints excluded: chain I residue 326 LYS Chi-restraints excluded: chain I residue 349 GLN Chi-restraints excluded: chain I residue 351 ILE Chi-restraints excluded: chain I residue 368 GLU Chi-restraints excluded: chain I residue 415 LYS Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 445 HIS Chi-restraints excluded: chain I residue 461 PHE Chi-restraints excluded: chain I residue 476 GLU Chi-restraints excluded: chain I residue 479 PHE Chi-restraints excluded: chain I residue 590 LYS Chi-restraints excluded: chain I residue 606 VAL Chi-restraints excluded: chain I residue 689 VAL Chi-restraints excluded: chain I residue 712 MET Chi-restraints excluded: chain I residue 724 GLU Chi-restraints excluded: chain I residue 725 SER Chi-restraints excluded: chain I residue 731 VAL Chi-restraints excluded: chain I residue 742 THR Chi-restraints excluded: chain I residue 815 GLU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 121 GLU Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 92 GLU Chi-restraints excluded: chain K residue 119 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 158 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 187 optimal weight: 0.0980 chunk 88 optimal weight: 0.0270 chunk 2 optimal weight: 1.9990 chunk 334 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 29 optimal weight: 0.7980 chunk 363 optimal weight: 0.5980 chunk 249 optimal weight: 2.9990 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 ASN A 82 ASN A 198 ASN A 217 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 ASN B 68 GLN B 217 ASN ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 ASN B 295 ASN C 10 GLN C 232 ASN C 267 ASN C 290 ASN C 295 ASN D 290 ASN E 68 GLN E 106 GLN E 198 ASN E 242 GLN E 295 ASN F 20 HIS F 43 ASN F 68 GLN G 311 GLN H 14 ASN H 34 ASN H 95 ASN H 119 ASN H 222 GLN I 6 GLN ** I 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 399 GLN ** I 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 893 GLN ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.139756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.119499 restraints weight = 47922.937| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.95 r_work: 0.3441 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31399 Z= 0.150 Angle : 0.714 10.458 42781 Z= 0.348 Chirality : 0.055 0.757 4787 Planarity : 0.005 0.078 5308 Dihedral : 12.997 164.328 4867 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 5.24 % Allowed : 21.12 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % 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: -0.14 (0.14), residues: 3639 helix: 0.72 (0.13), residues: 1591 sheet: 0.00 (0.23), residues: 433 loop : -0.88 (0.15), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 28 TYR 0.031 0.002 TYR I 902 PHE 0.026 0.001 PHE B 151 TRP 0.016 0.001 TRP I 453 HIS 0.011 0.001 HIS I 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (31399) covalent geometry : angle 0.71425 / 0.35 (42781) hydrogen bonds : bond 0.03816 / 2.48 ( 1385) hydrogen bonds : angle 4.58624 / 3.19 ( 3955) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1122 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 956 time to evaluate : 0.920 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: A 60 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8051 (mtp85) REVERT: A 87 SER cc_start: 0.8813 (t) cc_final: 0.8441 (p) REVERT: A 101 GLU cc_start: 0.7161 (mt-10) cc_final: 0.6927 (mt-10) REVERT: A 210 SER cc_start: 0.8776 (m) cc_final: 0.8390 (p) REVERT: A 232 ASN cc_start: 0.8574 (m-40) cc_final: 0.8347 (m110) REVERT: A 264 ASP cc_start: 0.8304 (t0) cc_final: 0.7748 (t70) REVERT: A 268 LYS cc_start: 0.8396 (mttp) cc_final: 0.8057 (mttp) REVERT: A 283 ASP cc_start: 0.7998 (m-30) cc_final: 0.7649 (m-30) REVERT: A 298 GLU cc_start: 0.8432 (tp30) cc_final: 0.8114 (tp30) REVERT: B 48 GLN cc_start: 0.8441 (tt0) cc_final: 0.8189 (tt0) REVERT: B 54 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8163 (mtpp) REVERT: B 109 ASP cc_start: 0.7995 (t0) cc_final: 0.7612 (t0) REVERT: B 119 ASP cc_start: 0.7816 (t0) cc_final: 0.7611 (t0) REVERT: B 123 GLU cc_start: 0.8072 (tp30) cc_final: 0.7701 (tp30) REVERT: B 124 ARG cc_start: 0.8574 (ttm-80) cc_final: 0.8294 (ttm-80) REVERT: B 143 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.7529 (ttp80) REVERT: B 190 GLU cc_start: 0.8140 (mp0) cc_final: 0.7899 (mp0) REVERT: B 226 ASP cc_start: 0.7526 (t0) cc_final: 0.7297 (t0) REVERT: B 268 LYS cc_start: 0.8795 (ttmm) cc_final: 0.8524 (mtpp) REVERT: B 283 ASP cc_start: 0.7768 (p0) cc_final: 0.7510 (p0) REVERT: B 290 ASN cc_start: 0.8286 (m-40) cc_final: 0.8079 (m-40) REVERT: B 309 GLN cc_start: 0.8842 (mt0) cc_final: 0.8464 (mt0) REVERT: C 32 SER cc_start: 0.8347 (m) cc_final: 0.7312 (p) REVERT: C 54 LYS cc_start: 0.8387 (mptt) cc_final: 0.8148 (mmmm) REVERT: C 89 ASP cc_start: 0.8085 (m-30) cc_final: 0.7859 (m-30) REVERT: C 139 GLU cc_start: 0.8210 (mp0) cc_final: 0.7925 (mp0) REVERT: C 151 PHE cc_start: 0.8596 (m-80) cc_final: 0.8383 (m-80) REVERT: C 190 GLU cc_start: 0.8260 (mp0) cc_final: 0.7495 (mp0) REVERT: C 283 ASP cc_start: 0.8110 (m-30) cc_final: 0.7834 (m-30) REVERT: C 316 GLU cc_start: 0.8250 (tt0) cc_final: 0.8043 (tt0) REVERT: D 15 ARG cc_start: 0.8597 (ttp80) cc_final: 0.8306 (ttt180) REVERT: D 47 THR cc_start: 0.8707 (m) cc_final: 0.8466 (p) REVERT: D 65 LYS cc_start: 0.7572 (OUTLIER) cc_final: 0.7144 (pttt) REVERT: D 66 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8190 (mtt90) REVERT: D 68 GLN cc_start: 0.8379 (pt0) cc_final: 0.7771 (pt0) REVERT: D 78 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7680 (tt0) REVERT: D 109 ASP cc_start: 0.8099 (t0) cc_final: 0.7865 (t0) REVERT: D 120 SER cc_start: 0.7388 (OUTLIER) cc_final: 0.6997 (t) REVERT: D 124 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8511 (tmm-80) REVERT: D 127 VAL cc_start: 0.8949 (OUTLIER) cc_final: 0.8721 (t) REVERT: D 130 ASP cc_start: 0.7192 (t0) cc_final: 0.6444 (t0) REVERT: D 156 MET cc_start: 0.8436 (mtp) cc_final: 0.8075 (mtp) REVERT: D 242 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8224 (tm-30) REVERT: D 273 LYS cc_start: 0.8962 (mtmm) cc_final: 0.8629 (mtmt) REVERT: D 283 ASP cc_start: 0.8111 (m-30) cc_final: 0.7801 (m-30) REVERT: E 8 GLN cc_start: 0.8195 (mm-40) cc_final: 0.7983 (mm110) REVERT: E 15 ARG cc_start: 0.8684 (ttp80) cc_final: 0.8448 (ttp80) REVERT: E 45 THR cc_start: 0.8598 (t) cc_final: 0.8333 (m) REVERT: E 46 ARG cc_start: 0.8436 (mtp-110) cc_final: 0.8167 (mmm160) REVERT: E 89 ASP cc_start: 0.8526 (p0) cc_final: 0.8311 (p0) REVERT: E 141 SER cc_start: 0.8525 (m) cc_final: 0.8135 (p) REVERT: E 182 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7880 (mm-30) REVERT: E 190 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7517 (pm20) REVERT: E 209 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7363 (mt-10) REVERT: E 212 THR cc_start: 0.8066 (OUTLIER) cc_final: 0.7834 (p) REVERT: E 233 LEU cc_start: 0.8552 (tp) cc_final: 0.8317 (tp) REVERT: E 241 ASP cc_start: 0.7894 (t0) cc_final: 0.7603 (t70) REVERT: E 249 LYS cc_start: 0.8070 (mmpt) cc_final: 0.7705 (mmpt) REVERT: E 256 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7685 (mm-30) REVERT: E 264 ASP cc_start: 0.8169 (t70) cc_final: 0.7910 (t0) REVERT: E 286 LEU cc_start: 0.8738 (mm) cc_final: 0.8524 (mp) REVERT: E 288 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7739 (mt-10) REVERT: E 305 SER cc_start: 0.8844 (m) cc_final: 0.8248 (p) REVERT: E 308 GLN cc_start: 0.8095 (tp40) cc_final: 0.7692 (tp40) REVERT: E 309 GLN cc_start: 0.8427 (mt0) cc_final: 0.7962 (mt0) REVERT: E 311 GLN cc_start: 0.8555 (mt0) cc_final: 0.8344 (mt0) REVERT: E 312 ASP cc_start: 0.8143 (m-30) cc_final: 0.7826 (m-30) REVERT: F 15 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8157 (ttp80) REVERT: F 56 ASP cc_start: 0.7828 (t0) cc_final: 0.7472 (t0) REVERT: F 73 ARG cc_start: 0.8363 (ttm-80) cc_final: 0.7987 (ttt-90) REVERT: F 89 ASP cc_start: 0.7593 (t0) cc_final: 0.7311 (t0) REVERT: F 109 ASP cc_start: 0.7730 (t70) cc_final: 0.7180 (t70) REVERT: F 117 ILE cc_start: 0.8213 (mm) cc_final: 0.7925 (mm) REVERT: F 123 GLU cc_start: 0.8077 (tp30) cc_final: 0.7617 (tm-30) REVERT: F 128 TYR cc_start: 0.8670 (m-80) cc_final: 0.8125 (m-80) REVERT: F 180 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8381 (t) REVERT: F 190 GLU cc_start: 0.7641 (mp0) cc_final: 0.7424 (mp0) REVERT: F 205 TYR cc_start: 0.7344 (m-80) cc_final: 0.7107 (m-80) REVERT: F 267 ASN cc_start: 0.7963 (m-40) cc_final: 0.7717 (m-40) REVERT: F 288 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7730 (tm-30) REVERT: F 313 TYR cc_start: 0.8753 (t80) cc_final: 0.8012 (t80) REVERT: G 9 PHE cc_start: 0.8547 (m-80) cc_final: 0.8126 (m-80) REVERT: G 58 LEU cc_start: 0.6343 (tt) cc_final: 0.6040 (tt) REVERT: G 72 GLU cc_start: 0.7593 (mp0) cc_final: 0.7196 (mp0) REVERT: G 83 LEU cc_start: 0.8532 (tp) cc_final: 0.8304 (tm) REVERT: G 106 GLN cc_start: 0.7640 (pm20) cc_final: 0.7401 (pm20) REVERT: G 122 SER cc_start: 0.8896 (p) cc_final: 0.8656 (t) REVERT: G 223 VAL cc_start: 0.8427 (OUTLIER) cc_final: 0.8101 (m) REVERT: G 233 LEU cc_start: 0.8782 (tp) cc_final: 0.8411 (tm) REVERT: G 253 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7084 (mm-30) REVERT: G 275 GLU cc_start: 0.6631 (OUTLIER) cc_final: 0.6308 (mt-10) REVERT: G 288 GLU cc_start: 0.8129 (tp30) cc_final: 0.7522 (tp30) REVERT: H 37 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8351 (mm) REVERT: H 65 ASP cc_start: 0.8082 (t0) cc_final: 0.7823 (t0) REVERT: H 86 GLN cc_start: 0.8406 (tt0) cc_final: 0.8137 (tt0) REVERT: H 95 ASN cc_start: 0.8656 (m-40) cc_final: 0.8408 (m-40) REVERT: H 122 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7919 (pt) REVERT: H 137 LEU cc_start: 0.8614 (tp) cc_final: 0.8355 (tt) REVERT: H 201 ASN cc_start: 0.8196 (m-40) cc_final: 0.7635 (m110) REVERT: H 205 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.8021 (ttm) REVERT: H 217 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8531 (tp40) REVERT: H 231 GLN cc_start: 0.8671 (tt0) cc_final: 0.8350 (tt0) REVERT: I 11 ARG cc_start: 0.9006 (mtt180) cc_final: 0.8378 (mtt180) REVERT: I 20 ILE cc_start: 0.8772 (mt) cc_final: 0.8501 (mm) REVERT: I 22 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.7923 (tp) REVERT: I 23 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8200 (tt0) REVERT: I 26 GLN cc_start: 0.8587 (mm-40) cc_final: 0.8101 (mt0) REVERT: I 78 LEU cc_start: 0.8491 (mt) cc_final: 0.8155 (mt) REVERT: I 82 ILE cc_start: 0.8769 (mt) cc_final: 0.8557 (mt) REVERT: I 105 ARG cc_start: 0.8073 (mtm-85) cc_final: 0.7856 (mtt180) REVERT: I 106 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.6991 (mtp180) REVERT: I 149 ASN cc_start: 0.8123 (m-40) cc_final: 0.7809 (m-40) REVERT: I 152 GLU cc_start: 0.8111 (mp0) cc_final: 0.7723 (mp0) REVERT: I 206 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8250 (mm) REVERT: I 216 SER cc_start: 0.8440 (m) cc_final: 0.8172 (t) REVERT: I 229 ARG cc_start: 0.7503 (ptm160) cc_final: 0.7186 (ptm160) REVERT: I 230 LEU cc_start: 0.8203 (mt) cc_final: 0.7996 (mp) REVERT: I 233 LEU cc_start: 0.8295 (mt) cc_final: 0.7995 (mt) REVERT: I 236 ARG cc_start: 0.8176 (ttm-80) cc_final: 0.7951 (ttp-110) REVERT: I 291 GLU cc_start: 0.8512 (pm20) cc_final: 0.8130 (pm20) REVERT: I 294 GLU cc_start: 0.7428 (tp30) cc_final: 0.7096 (mm-30) REVERT: I 295 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7843 (ttt180) REVERT: I 298 ILE cc_start: 0.8840 (pp) cc_final: 0.8558 (mt) REVERT: I 329 LYS cc_start: 0.8632 (mtmt) cc_final: 0.8305 (mtpt) REVERT: I 346 ILE cc_start: 0.8657 (mp) cc_final: 0.8257 (pp) REVERT: I 349 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7811 (tp-100) REVERT: I 351 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8631 (mp) REVERT: I 389 ASP cc_start: 0.7699 (m-30) cc_final: 0.7362 (m-30) REVERT: I 400 LYS cc_start: 0.8663 (ttmm) cc_final: 0.8128 (mtpp) REVERT: I 401 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7343 (mm-30) REVERT: I 423 ILE cc_start: 0.8636 (mm) cc_final: 0.8307 (mm) REVERT: I 427 GLU cc_start: 0.8240 (pt0) cc_final: 0.7771 (pp20) REVERT: I 460 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7639 (tm-30) REVERT: I 472 TRP cc_start: 0.8657 (t60) cc_final: 0.8395 (t60) REVERT: I 474 GLU cc_start: 0.7445 (pt0) cc_final: 0.7181 (pt0) REVERT: I 488 GLN cc_start: 0.8483 (tp40) cc_final: 0.7847 (tp-100) REVERT: I 491 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8095 (mt-10) REVERT: I 504 GLU cc_start: 0.7629 (tp30) cc_final: 0.7189 (tp30) REVERT: I 544 ASP cc_start: 0.8175 (t70) cc_final: 0.7901 (t0) REVERT: I 576 GLU cc_start: 0.8322 (tp30) cc_final: 0.7981 (mm-30) REVERT: I 590 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8198 (tmtt) REVERT: I 595 GLN cc_start: 0.8341 (mm-40) cc_final: 0.8032 (mm-40) REVERT: I 606 VAL cc_start: 0.8328 (OUTLIER) cc_final: 0.7998 (p) REVERT: I 613 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7801 (mt-10) REVERT: I 617 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7581 (mm-30) REVERT: I 632 LYS cc_start: 0.8349 (ttpt) cc_final: 0.8030 (ttpp) REVERT: I 642 THR cc_start: 0.8610 (m) cc_final: 0.8364 (p) REVERT: I 663 LYS cc_start: 0.8199 (ptpt) cc_final: 0.7930 (ptpt) REVERT: I 667 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7969 (mm-30) REVERT: I 680 ARG cc_start: 0.8126 (mmp-170) cc_final: 0.7493 (mtp180) REVERT: I 721 ASP cc_start: 0.7587 (m-30) cc_final: 0.7236 (m-30) REVERT: I 723 ARG cc_start: 0.7721 (mtp85) cc_final: 0.7196 (mtp85) REVERT: I 745 ARG cc_start: 0.8058 (mtp180) cc_final: 0.7772 (mtp180) REVERT: I 774 ARG cc_start: 0.8539 (ttm110) cc_final: 0.7972 (mtm110) REVERT: I 780 LYS cc_start: 0.8538 (mttp) cc_final: 0.8253 (mttp) REVERT: I 797 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7862 (mm-30) REVERT: I 827 ASN cc_start: 0.8019 (t0) cc_final: 0.7533 (t0) REVERT: I 828 ILE cc_start: 0.8265 (mm) cc_final: 0.8022 (mm) REVERT: I 829 VAL cc_start: 0.8813 (m) cc_final: 0.8533 (p) REVERT: I 830 MET cc_start: 0.8523 (mmp) cc_final: 0.8033 (mmp) REVERT: I 832 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7926 (mt-10) REVERT: I 870 GLU cc_start: 0.7701 (pp20) cc_final: 0.7418 (pp20) REVERT: I 882 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7682 (mm-30) REVERT: I 907 ILE cc_start: 0.8749 (mp) cc_final: 0.8191 (mp) REVERT: I 940 MET cc_start: 0.8250 (mmt) cc_final: 0.8000 (mmt) REVERT: I 972 GLN cc_start: 0.7889 (tm-30) cc_final: 0.7444 (pp30) REVERT: J 7 LEU cc_start: 0.8786 (tm) cc_final: 0.8558 (tt) REVERT: J 14 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7601 (mm-30) REVERT: J 41 GLU cc_start: 0.7616 (tp30) cc_final: 0.6785 (tp30) REVERT: J 52 GLU cc_start: 0.7111 (tt0) cc_final: 0.6645 (tm-30) REVERT: J 53 GLU cc_start: 0.7562 (tp30) cc_final: 0.7211 (mp0) REVERT: J 54 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7300 (tm-30) REVERT: J 94 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7769 (tm-30) REVERT: J 119 LEU cc_start: 0.8634 (tp) cc_final: 0.8428 (tm) REVERT: J 121 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7627 (tm-30) outliers start: 166 outliers final: 77 residues processed: 1033 average time/residue: 0.7571 time to fit residues: 908.2252 Evaluate side-chains 1020 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 914 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain F residue 15 ARG Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 180 THR Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 124 ARG Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 243 MET Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 144 LYS Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 217 GLN Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 106 ARG Chi-restraints excluded: chain I residue 206 LEU Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 226 MET Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 295 ARG Chi-restraints excluded: chain I residue 309 GLU Chi-restraints excluded: chain I residue 326 LYS Chi-restraints excluded: chain I residue 349 GLN Chi-restraints excluded: chain I residue 351 ILE Chi-restraints excluded: chain I residue 368 GLU Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 461 PHE Chi-restraints excluded: chain I residue 476 GLU Chi-restraints excluded: chain I residue 479 PHE Chi-restraints excluded: chain I residue 515 GLU Chi-restraints excluded: chain I residue 590 LYS Chi-restraints excluded: chain I residue 606 VAL Chi-restraints excluded: chain I residue 689 VAL Chi-restraints excluded: chain I residue 712 MET Chi-restraints excluded: chain I residue 724 GLU Chi-restraints excluded: chain I residue 725 SER Chi-restraints excluded: chain I residue 731 VAL Chi-restraints excluded: chain I residue 843 GLU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 121 GLU Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 92 GLU Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain K residue 119 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 215 optimal weight: 1.9990 chunk 324 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 363 optimal weight: 6.9990 chunk 251 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 236 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 ASN A 82 ASN A 171 HIS A 198 ASN A 217 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 ASN B 68 GLN B 217 ASN B 232 ASN ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 ASN B 295 ASN C 10 GLN C 232 ASN C 267 ASN C 290 ASN C 295 ASN D 171 HIS D 267 ASN D 290 ASN E 106 GLN E 171 HIS E 198 ASN ** E 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 237 GLN E 242 GLN E 295 ASN F 20 HIS F 43 ASN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN H 34 ASN H 93 GLN H 119 ASN H 195 GLN ** I 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 399 GLN ** I 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 727 HIS ** I 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 893 GLN K 122 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.138154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.117831 restraints weight = 47880.213| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.94 r_work: 0.3414 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 31399 Z= 0.225 Angle : 0.737 10.165 42781 Z= 0.360 Chirality : 0.056 0.715 4787 Planarity : 0.005 0.093 5308 Dihedral : 12.909 162.850 4864 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 5.30 % Allowed : 21.94 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % 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: -0.07 (0.14), residues: 3639 helix: 0.80 (0.13), residues: 1591 sheet: -0.06 (0.22), residues: 461 loop : -0.86 (0.16), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 126 TYR 0.031 0.002 TYR I 844 PHE 0.026 0.002 PHE B 151 TRP 0.016 0.002 TRP I 453 HIS 0.011 0.001 HIS I 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.23 (31399) covalent geometry : angle 0.73655 / 0.36 (42781) hydrogen bonds : bond 0.04003 / 2.61 ( 1385) hydrogen bonds : angle 4.58968 / 3.19 ( 3955) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1136 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 968 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8042 (mtp85) REVERT: A 87 SER cc_start: 0.8822 (t) cc_final: 0.8446 (p) REVERT: A 101 GLU cc_start: 0.7318 (mt-10) cc_final: 0.7053 (mt-10) REVERT: A 139 GLU cc_start: 0.8145 (mp0) cc_final: 0.7781 (mp0) REVERT: A 210 SER cc_start: 0.8803 (m) cc_final: 0.8421 (p) REVERT: A 232 ASN cc_start: 0.8560 (m-40) cc_final: 0.8252 (m110) REVERT: A 264 ASP cc_start: 0.8343 (t0) cc_final: 0.7793 (t70) REVERT: A 268 LYS cc_start: 0.8489 (mttp) cc_final: 0.8154 (mttp) REVERT: A 283 ASP cc_start: 0.7963 (m-30) cc_final: 0.7614 (m-30) REVERT: B 48 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8160 (tt0) REVERT: B 54 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8093 (mmmm) REVERT: B 90 LYS cc_start: 0.8715 (mmtp) cc_final: 0.8482 (mmtp) REVERT: B 109 ASP cc_start: 0.8067 (t0) cc_final: 0.7673 (t0) REVERT: B 119 ASP cc_start: 0.7810 (t0) cc_final: 0.7598 (t0) REVERT: B 123 GLU cc_start: 0.8046 (tp30) cc_final: 0.7664 (tp30) REVERT: B 124 ARG cc_start: 0.8580 (ttm-80) cc_final: 0.8311 (ttm-80) REVERT: B 143 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.7531 (ttp80) REVERT: B 226 ASP cc_start: 0.7713 (t0) cc_final: 0.7397 (t0) REVERT: B 268 LYS cc_start: 0.8817 (ttmm) cc_final: 0.8539 (mtpp) REVERT: B 283 ASP cc_start: 0.7755 (p0) cc_final: 0.7425 (p0) REVERT: B 290 ASN cc_start: 0.8288 (m-40) cc_final: 0.8068 (m-40) REVERT: B 316 GLU cc_start: 0.8329 (tt0) cc_final: 0.7996 (tt0) REVERT: C 32 SER cc_start: 0.8390 (m) cc_final: 0.7349 (p) REVERT: C 54 LYS cc_start: 0.8369 (mptt) cc_final: 0.8137 (mmtp) REVERT: C 89 ASP cc_start: 0.8076 (m-30) cc_final: 0.7850 (m-30) REVERT: C 139 GLU cc_start: 0.8251 (mp0) cc_final: 0.7930 (mp0) REVERT: C 151 PHE cc_start: 0.8639 (m-80) cc_final: 0.8395 (m-80) REVERT: C 156 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7511 (mmm) REVERT: C 169 LEU cc_start: 0.8990 (tp) cc_final: 0.8689 (tt) REVERT: C 215 MET cc_start: 0.8897 (mtp) cc_final: 0.8686 (mtm) REVERT: C 283 ASP cc_start: 0.8142 (m-30) cc_final: 0.7870 (m-30) REVERT: C 316 GLU cc_start: 0.8240 (tt0) cc_final: 0.7981 (tt0) REVERT: D 15 ARG cc_start: 0.8607 (ttp80) cc_final: 0.8337 (ttt180) REVERT: D 47 THR cc_start: 0.8693 (m) cc_final: 0.8478 (p) REVERT: D 66 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8268 (mtt90) REVERT: D 68 GLN cc_start: 0.8323 (pt0) cc_final: 0.7852 (pt0) REVERT: D 72 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7562 (mt-10) REVERT: D 78 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7681 (tt0) REVERT: D 97 GLU cc_start: 0.7863 (tp30) cc_final: 0.7541 (tp30) REVERT: D 109 ASP cc_start: 0.8092 (t0) cc_final: 0.7884 (t0) REVERT: D 120 SER cc_start: 0.7573 (OUTLIER) cc_final: 0.7225 (t) REVERT: D 124 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8572 (tmm-80) REVERT: D 127 VAL cc_start: 0.8969 (OUTLIER) cc_final: 0.8708 (t) REVERT: D 130 ASP cc_start: 0.7297 (t0) cc_final: 0.6549 (t0) REVERT: D 156 MET cc_start: 0.8555 (mtp) cc_final: 0.8131 (mtp) REVERT: D 242 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8251 (tm-30) REVERT: D 273 LYS cc_start: 0.8945 (mtmm) cc_final: 0.8567 (mttt) REVERT: D 283 ASP cc_start: 0.8099 (m-30) cc_final: 0.7805 (m-30) REVERT: E 15 ARG cc_start: 0.8683 (ttp80) cc_final: 0.8403 (ttp80) REVERT: E 45 THR cc_start: 0.8605 (t) cc_final: 0.8337 (m) REVERT: E 46 ARG cc_start: 0.8458 (mtp-110) cc_final: 0.8164 (mmm160) REVERT: E 89 ASP cc_start: 0.8534 (p0) cc_final: 0.8284 (p0) REVERT: E 141 SER cc_start: 0.8552 (m) cc_final: 0.8164 (p) REVERT: E 182 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7795 (mm-30) REVERT: E 190 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7601 (pm20) REVERT: E 209 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7414 (mt-10) REVERT: E 231 SER cc_start: 0.8645 (OUTLIER) cc_final: 0.8343 (t) REVERT: E 241 ASP cc_start: 0.7953 (t0) cc_final: 0.7672 (t70) REVERT: E 249 LYS cc_start: 0.8172 (mmpt) cc_final: 0.7790 (mmpt) REVERT: E 256 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7712 (mm-30) REVERT: E 264 ASP cc_start: 0.8219 (t70) cc_final: 0.7958 (t0) REVERT: E 288 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7490 (mt-10) REVERT: E 291 ASP cc_start: 0.7418 (p0) cc_final: 0.7017 (p0) REVERT: E 305 SER cc_start: 0.8853 (m) cc_final: 0.8315 (p) REVERT: E 308 GLN cc_start: 0.8124 (tp40) cc_final: 0.7720 (tp40) REVERT: E 309 GLN cc_start: 0.8379 (mt0) cc_final: 0.8105 (mt0) REVERT: E 311 GLN cc_start: 0.8543 (mt0) cc_final: 0.8324 (mt0) REVERT: E 312 ASP cc_start: 0.8110 (m-30) cc_final: 0.7775 (m-30) REVERT: F 56 ASP cc_start: 0.7823 (t0) cc_final: 0.7472 (t0) REVERT: F 89 ASP cc_start: 0.7639 (t0) cc_final: 0.7348 (t0) REVERT: F 94 ASN cc_start: 0.7480 (t160) cc_final: 0.7195 (t0) REVERT: F 117 ILE cc_start: 0.8214 (mm) cc_final: 0.7940 (mm) REVERT: F 128 TYR cc_start: 0.8692 (m-80) cc_final: 0.8159 (m-80) REVERT: F 190 GLU cc_start: 0.7617 (mp0) cc_final: 0.7381 (mp0) REVERT: F 205 TYR cc_start: 0.7452 (m-80) cc_final: 0.7207 (m-80) REVERT: F 247 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.8000 (mt) REVERT: F 267 ASN cc_start: 0.7998 (m-40) cc_final: 0.7792 (m-40) REVERT: F 288 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7753 (tm-30) REVERT: G 47 THR cc_start: 0.7938 (OUTLIER) cc_final: 0.7358 (p) REVERT: G 72 GLU cc_start: 0.7703 (mp0) cc_final: 0.7276 (mp0) REVERT: G 83 LEU cc_start: 0.8565 (tp) cc_final: 0.8330 (tm) REVERT: G 106 GLN cc_start: 0.7723 (pm20) cc_final: 0.7444 (pm20) REVERT: G 122 SER cc_start: 0.8925 (p) cc_final: 0.8706 (t) REVERT: G 185 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7812 (ttm110) REVERT: G 216 LYS cc_start: 0.7503 (tppt) cc_final: 0.7221 (tppt) REVERT: G 223 VAL cc_start: 0.8419 (OUTLIER) cc_final: 0.8078 (m) REVERT: G 233 LEU cc_start: 0.8842 (tp) cc_final: 0.8565 (tm) REVERT: G 253 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7176 (mm-30) REVERT: G 288 GLU cc_start: 0.8173 (tp30) cc_final: 0.7525 (tp30) REVERT: G 295 ASN cc_start: 0.7639 (t0) cc_final: 0.7114 (t0) REVERT: H 28 THR cc_start: 0.8691 (m) cc_final: 0.8449 (p) REVERT: H 37 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8382 (mm) REVERT: H 65 ASP cc_start: 0.8132 (t0) cc_final: 0.7837 (t0) REVERT: H 95 ASN cc_start: 0.8639 (m-40) cc_final: 0.8389 (m-40) REVERT: H 122 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8088 (pt) REVERT: H 137 LEU cc_start: 0.8613 (tp) cc_final: 0.8353 (tt) REVERT: H 153 ARG cc_start: 0.8933 (mtt90) cc_final: 0.8578 (mtt90) REVERT: H 181 VAL cc_start: 0.8811 (OUTLIER) cc_final: 0.8516 (t) REVERT: H 201 ASN cc_start: 0.8200 (m-40) cc_final: 0.7632 (m110) REVERT: H 217 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8573 (tp40) REVERT: I 22 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8154 (tp) REVERT: I 26 GLN cc_start: 0.8554 (mm-40) cc_final: 0.8132 (mt0) REVERT: I 78 LEU cc_start: 0.8521 (mt) cc_final: 0.8200 (mt) REVERT: I 82 ILE cc_start: 0.8803 (mt) cc_final: 0.8600 (mt) REVERT: I 105 ARG cc_start: 0.8111 (mtm-85) cc_final: 0.7863 (mtt180) REVERT: I 106 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.7178 (mtp180) REVERT: I 152 GLU cc_start: 0.8155 (mp0) cc_final: 0.7760 (mp0) REVERT: I 216 SER cc_start: 0.8476 (m) cc_final: 0.8217 (t) REVERT: I 229 ARG cc_start: 0.7563 (ptm160) cc_final: 0.7239 (ptm160) REVERT: I 230 LEU cc_start: 0.8245 (mt) cc_final: 0.8030 (mp) REVERT: I 233 LEU cc_start: 0.8380 (mt) cc_final: 0.8040 (mt) REVERT: I 295 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7791 (ttt180) REVERT: I 298 ILE cc_start: 0.8872 (pp) cc_final: 0.8606 (mt) REVERT: I 346 ILE cc_start: 0.8726 (mp) cc_final: 0.8331 (pp) REVERT: I 349 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7800 (tp-100) REVERT: I 351 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8691 (mp) REVERT: I 378 GLU cc_start: 0.7781 (pm20) cc_final: 0.7572 (pm20) REVERT: I 389 ASP cc_start: 0.7738 (m-30) cc_final: 0.7386 (m-30) REVERT: I 401 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7469 (mp0) REVERT: I 460 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7775 (tp30) REVERT: I 472 TRP cc_start: 0.8657 (t60) cc_final: 0.8351 (t60) REVERT: I 474 GLU cc_start: 0.7471 (pt0) cc_final: 0.7161 (pp20) REVERT: I 476 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7548 (mp0) REVERT: I 488 GLN cc_start: 0.8604 (tp40) cc_final: 0.8338 (tm-30) REVERT: I 491 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8137 (mm-30) REVERT: I 515 GLU cc_start: 0.8468 (tt0) cc_final: 0.8130 (tp30) REVERT: I 540 GLU cc_start: 0.8039 (pt0) cc_final: 0.7748 (pm20) REVERT: I 544 ASP cc_start: 0.8226 (t70) cc_final: 0.7948 (t0) REVERT: I 590 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8205 (tmtt) REVERT: I 595 GLN cc_start: 0.8352 (mm-40) cc_final: 0.8025 (mm-40) REVERT: I 606 VAL cc_start: 0.8408 (OUTLIER) cc_final: 0.8078 (p) REVERT: I 613 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7830 (mt-10) REVERT: I 632 LYS cc_start: 0.8383 (ttpt) cc_final: 0.8102 (ttpp) REVERT: I 642 THR cc_start: 0.8648 (m) cc_final: 0.8377 (p) REVERT: I 663 LYS cc_start: 0.8296 (ptpt) cc_final: 0.8049 (ptpt) REVERT: I 667 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7964 (mp0) REVERT: I 668 ASP cc_start: 0.7873 (m-30) cc_final: 0.7662 (m-30) REVERT: I 680 ARG cc_start: 0.8166 (mmp-170) cc_final: 0.7567 (mtp180) REVERT: I 681 GLU cc_start: 0.7919 (mp0) cc_final: 0.7629 (mp0) REVERT: I 721 ASP cc_start: 0.7695 (m-30) cc_final: 0.7399 (m-30) REVERT: I 723 ARG cc_start: 0.7787 (mtp85) cc_final: 0.7289 (mtp85) REVERT: I 780 LYS cc_start: 0.8544 (mttp) cc_final: 0.8258 (mttp) REVERT: I 827 ASN cc_start: 0.8054 (t0) cc_final: 0.7564 (t0) REVERT: I 829 VAL cc_start: 0.8921 (m) cc_final: 0.8643 (p) REVERT: I 830 MET cc_start: 0.8508 (mmp) cc_final: 0.8043 (mmp) REVERT: I 870 GLU cc_start: 0.7749 (pp20) cc_final: 0.7316 (tm-30) REVERT: I 882 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7286 (mm-30) REVERT: I 927 ILE cc_start: 0.8806 (tt) cc_final: 0.8524 (pt) REVERT: I 940 MET cc_start: 0.8278 (mmt) cc_final: 0.8025 (mmt) REVERT: I 969 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7661 (tm-30) REVERT: I 972 GLN cc_start: 0.7942 (tm-30) cc_final: 0.7534 (pp30) REVERT: J 5 LEU cc_start: 0.5729 (OUTLIER) cc_final: 0.4832 (pt) REVERT: J 14 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7599 (mm-30) REVERT: J 41 GLU cc_start: 0.7731 (tp30) cc_final: 0.6853 (tp30) REVERT: J 52 GLU cc_start: 0.7143 (tt0) cc_final: 0.6705 (tm-30) REVERT: J 53 GLU cc_start: 0.7573 (tp30) cc_final: 0.7305 (mp0) REVERT: J 54 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7407 (tm-30) REVERT: J 121 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7597 (tm-30) outliers start: 168 outliers final: 83 residues processed: 1047 average time/residue: 0.7438 time to fit residues: 905.9878 Evaluate side-chains 1036 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 922 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain F residue 4 SER Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 142 HIS Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 232 ASN Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 124 ARG Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 185 ARG Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 231 SER Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 239 LEU Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 281 HIS Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 144 LYS Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 196 GLN Chi-restraints excluded: chain H residue 217 GLN Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 106 ARG Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 295 ARG Chi-restraints excluded: chain I residue 326 LYS Chi-restraints excluded: chain I residue 349 GLN Chi-restraints excluded: chain I residue 351 ILE Chi-restraints excluded: chain I residue 368 GLU Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 461 PHE Chi-restraints excluded: chain I residue 476 GLU Chi-restraints excluded: chain I residue 479 PHE Chi-restraints excluded: chain I residue 495 ASP Chi-restraints excluded: chain I residue 590 LYS Chi-restraints excluded: chain I residue 606 VAL Chi-restraints excluded: chain I residue 689 VAL Chi-restraints excluded: chain I residue 731 VAL Chi-restraints excluded: chain I residue 750 THR Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 121 GLU Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain K residue 119 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 157 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 229 optimal weight: 0.5980 chunk 145 optimal weight: 0.8980 chunk 243 optimal weight: 0.7980 chunk 230 optimal weight: 0.5980 chunk 163 optimal weight: 0.9990 chunk 312 optimal weight: 1.9990 chunk 335 optimal weight: 0.0980 chunk 329 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 ASN A 82 ASN A 198 ASN A 217 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 ASN B 68 GLN B 217 ASN B 232 ASN B 234 HIS B 267 ASN B 295 ASN C 10 GLN C 267 ASN C 290 ASN C 295 ASN D 267 ASN D 290 ASN E 8 GLN E 68 GLN E 106 GLN E 198 ASN ** E 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 GLN E 295 ASN F 20 HIS F 43 ASN F 94 ASN ** G 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN H 34 ASN H 119 ASN I 81 HIS ** I 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 399 GLN ** I 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 519 ASN I 791 ASN ** I 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 893 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.138822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.118544 restraints weight = 47912.841| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.95 r_work: 0.3429 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31399 Z= 0.178 Angle : 0.719 9.756 42781 Z= 0.350 Chirality : 0.053 0.667 4787 Planarity : 0.005 0.074 5308 Dihedral : 12.851 161.708 4864 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.99 % Allowed : 23.77 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % 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: -0.00 (0.14), residues: 3639 helix: 0.91 (0.13), residues: 1601 sheet: -0.07 (0.22), residues: 459 loop : -0.88 (0.16), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 846 TYR 0.028 0.002 TYR I 446 PHE 0.022 0.001 PHE B 151 TRP 0.019 0.001 TRP I 453 HIS 0.010 0.001 HIS I 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (31399) covalent geometry : angle 0.71858 / 0.35 (42781) hydrogen bonds : bond 0.03769 / 2.46 ( 1385) hydrogen bonds : angle 4.53052 / 3.16 ( 3955) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1093 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 935 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.8815 (t) cc_final: 0.8487 (p) REVERT: A 101 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6990 (mt-10) REVERT: A 209 GLU cc_start: 0.8278 (pt0) cc_final: 0.7978 (pt0) REVERT: A 210 SER cc_start: 0.8797 (m) cc_final: 0.8415 (p) REVERT: A 215 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8391 (mtm) REVERT: A 232 ASN cc_start: 0.8538 (m-40) cc_final: 0.8262 (m110) REVERT: A 264 ASP cc_start: 0.8377 (t0) cc_final: 0.7846 (t70) REVERT: A 268 LYS cc_start: 0.8460 (mttp) cc_final: 0.8130 (mttp) REVERT: A 269 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7024 (mm-30) REVERT: A 283 ASP cc_start: 0.7929 (m-30) cc_final: 0.7603 (m-30) REVERT: A 308 GLN cc_start: 0.8166 (tp40) cc_final: 0.7963 (tp40) REVERT: B 48 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8207 (tt0) REVERT: B 54 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8136 (mtpp) REVERT: B 72 GLU cc_start: 0.7673 (mp0) cc_final: 0.7387 (mp0) REVERT: B 90 LYS cc_start: 0.8692 (mmtp) cc_final: 0.8462 (mmtp) REVERT: B 123 GLU cc_start: 0.8041 (tp30) cc_final: 0.7693 (tp30) REVERT: B 124 ARG cc_start: 0.8581 (ttm-80) cc_final: 0.8314 (ttm-80) REVERT: B 143 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.7490 (ttp80) REVERT: B 226 ASP cc_start: 0.7724 (t0) cc_final: 0.7418 (t0) REVERT: B 253 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7736 (mm-30) REVERT: B 268 LYS cc_start: 0.8833 (ttmm) cc_final: 0.8558 (mtpp) REVERT: B 283 ASP cc_start: 0.7748 (p0) cc_final: 0.7392 (p0) REVERT: B 290 ASN cc_start: 0.8253 (m-40) cc_final: 0.8047 (m-40) REVERT: C 32 SER cc_start: 0.8307 (m) cc_final: 0.7287 (p) REVERT: C 54 LYS cc_start: 0.8341 (mptt) cc_final: 0.8129 (mmtp) REVERT: C 72 GLU cc_start: 0.7856 (mp0) cc_final: 0.7636 (mp0) REVERT: C 89 ASP cc_start: 0.8078 (m-30) cc_final: 0.7830 (m-30) REVERT: C 139 GLU cc_start: 0.8216 (mp0) cc_final: 0.7887 (mp0) REVERT: C 151 PHE cc_start: 0.8622 (m-80) cc_final: 0.8390 (m-80) REVERT: C 156 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7465 (mmm) REVERT: C 215 MET cc_start: 0.8879 (mtp) cc_final: 0.8666 (mtm) REVERT: C 283 ASP cc_start: 0.8100 (m-30) cc_final: 0.7826 (m-30) REVERT: C 316 GLU cc_start: 0.8217 (tt0) cc_final: 0.7974 (tt0) REVERT: D 66 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8338 (mtt90) REVERT: D 68 GLN cc_start: 0.8378 (pt0) cc_final: 0.7846 (pt0) REVERT: D 72 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7491 (mt-10) REVERT: D 78 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: D 97 GLU cc_start: 0.7852 (tp30) cc_final: 0.7557 (tp30) REVERT: D 109 ASP cc_start: 0.8057 (t0) cc_final: 0.7846 (t0) REVERT: D 120 SER cc_start: 0.7566 (OUTLIER) cc_final: 0.7263 (t) REVERT: D 124 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8574 (tmm-80) REVERT: D 127 VAL cc_start: 0.8966 (OUTLIER) cc_final: 0.8666 (t) REVERT: D 130 ASP cc_start: 0.7318 (t0) cc_final: 0.6592 (t0) REVERT: D 156 MET cc_start: 0.8535 (mtp) cc_final: 0.8161 (mtp) REVERT: D 182 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7829 (mt-10) REVERT: D 242 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8280 (tm-30) REVERT: D 273 LYS cc_start: 0.8956 (mtmm) cc_final: 0.8600 (mttt) REVERT: D 283 ASP cc_start: 0.8071 (m-30) cc_final: 0.7763 (m-30) REVERT: E 15 ARG cc_start: 0.8624 (ttp80) cc_final: 0.8376 (ttp80) REVERT: E 45 THR cc_start: 0.8599 (t) cc_final: 0.8342 (m) REVERT: E 46 ARG cc_start: 0.8418 (mtp-110) cc_final: 0.8129 (mmm160) REVERT: E 89 ASP cc_start: 0.8505 (p0) cc_final: 0.8255 (p0) REVERT: E 141 SER cc_start: 0.8530 (m) cc_final: 0.8159 (p) REVERT: E 182 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7773 (mm-30) REVERT: E 190 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7537 (pm20) REVERT: E 209 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7328 (mt-10) REVERT: E 231 SER cc_start: 0.8638 (OUTLIER) cc_final: 0.8340 (t) REVERT: E 241 ASP cc_start: 0.7978 (t0) cc_final: 0.7678 (t0) REVERT: E 249 LYS cc_start: 0.8122 (mmpt) cc_final: 0.7744 (mmpt) REVERT: E 256 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7712 (mm-30) REVERT: E 264 ASP cc_start: 0.8206 (t70) cc_final: 0.7952 (t0) REVERT: E 288 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7531 (mt-10) REVERT: E 291 ASP cc_start: 0.7371 (p0) cc_final: 0.6973 (p0) REVERT: E 305 SER cc_start: 0.8810 (m) cc_final: 0.8263 (p) REVERT: E 308 GLN cc_start: 0.8138 (tp40) cc_final: 0.7712 (tp40) REVERT: E 309 GLN cc_start: 0.8351 (mt0) cc_final: 0.8066 (mt0) REVERT: E 311 GLN cc_start: 0.8537 (mt0) cc_final: 0.8313 (mt0) REVERT: E 312 ASP cc_start: 0.8097 (m-30) cc_final: 0.7744 (m-30) REVERT: F 56 ASP cc_start: 0.7851 (t0) cc_final: 0.7505 (t0) REVERT: F 89 ASP cc_start: 0.7637 (t0) cc_final: 0.7339 (t0) REVERT: F 94 ASN cc_start: 0.7381 (t0) cc_final: 0.7016 (t0) REVERT: F 128 TYR cc_start: 0.8676 (m-80) cc_final: 0.8140 (m-80) REVERT: F 190 GLU cc_start: 0.7576 (mp0) cc_final: 0.7336 (mp0) REVERT: F 205 TYR cc_start: 0.7418 (m-80) cc_final: 0.7202 (m-80) REVERT: F 247 LEU cc_start: 0.8219 (mp) cc_final: 0.8013 (mt) REVERT: F 267 ASN cc_start: 0.7981 (m-40) cc_final: 0.7766 (m-40) REVERT: F 288 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7690 (tm-30) REVERT: F 289 VAL cc_start: 0.8645 (t) cc_final: 0.8404 (p) REVERT: F 298 GLU cc_start: 0.7698 (mp0) cc_final: 0.7435 (mp0) REVERT: G 8 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.7184 (mp10) REVERT: G 47 THR cc_start: 0.7919 (OUTLIER) cc_final: 0.7318 (p) REVERT: G 68 GLN cc_start: 0.7450 (pp30) cc_final: 0.7187 (pp30) REVERT: G 72 GLU cc_start: 0.7703 (mp0) cc_final: 0.7254 (mp0) REVERT: G 83 LEU cc_start: 0.8532 (tp) cc_final: 0.8296 (tm) REVERT: G 106 GLN cc_start: 0.7722 (pm20) cc_final: 0.7440 (pm20) REVERT: G 122 SER cc_start: 0.8951 (p) cc_final: 0.8736 (t) REVERT: G 216 LYS cc_start: 0.7536 (tppt) cc_final: 0.7243 (tppt) REVERT: G 223 VAL cc_start: 0.8428 (OUTLIER) cc_final: 0.8101 (m) REVERT: G 233 LEU cc_start: 0.8836 (tp) cc_final: 0.8575 (tm) REVERT: G 253 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7156 (mm-30) REVERT: G 288 GLU cc_start: 0.8161 (tp30) cc_final: 0.7499 (tp30) REVERT: G 295 ASN cc_start: 0.7534 (t0) cc_final: 0.6988 (t0) REVERT: H 8 LYS cc_start: 0.8823 (ptmt) cc_final: 0.8403 (ptmt) REVERT: H 37 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8378 (mm) REVERT: H 65 ASP cc_start: 0.8190 (t0) cc_final: 0.7869 (t0) REVERT: H 95 ASN cc_start: 0.8630 (m-40) cc_final: 0.8367 (m-40) REVERT: H 122 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8098 (pt) REVERT: H 137 LEU cc_start: 0.8608 (tp) cc_final: 0.8346 (tt) REVERT: H 174 LYS cc_start: 0.8064 (ptpt) cc_final: 0.7730 (ptpt) REVERT: H 181 VAL cc_start: 0.8808 (OUTLIER) cc_final: 0.8512 (t) REVERT: H 201 ASN cc_start: 0.8236 (m-40) cc_final: 0.7636 (m110) REVERT: H 205 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8193 (ttm) REVERT: H 227 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.8000 (p) REVERT: I 22 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8006 (tp) REVERT: I 26 GLN cc_start: 0.8518 (mm-40) cc_final: 0.8093 (mt0) REVERT: I 78 LEU cc_start: 0.8510 (mt) cc_final: 0.8177 (mt) REVERT: I 93 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8180 (tmm) REVERT: I 105 ARG cc_start: 0.8080 (mtm-85) cc_final: 0.7536 (mtt180) REVERT: I 106 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.7115 (mtp180) REVERT: I 109 CYS cc_start: 0.8659 (m) cc_final: 0.8219 (m) REVERT: I 150 PHE cc_start: 0.8744 (m-80) cc_final: 0.8370 (m-80) REVERT: I 152 GLU cc_start: 0.8047 (mp0) cc_final: 0.7520 (mp0) REVERT: I 206 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8306 (mm) REVERT: I 216 SER cc_start: 0.8455 (m) cc_final: 0.8210 (t) REVERT: I 229 ARG cc_start: 0.7534 (ptm160) cc_final: 0.7228 (ptm160) REVERT: I 230 LEU cc_start: 0.8254 (mt) cc_final: 0.8027 (mp) REVERT: I 233 LEU cc_start: 0.8378 (mt) cc_final: 0.8042 (mt) REVERT: I 295 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7829 (ttt180) REVERT: I 298 ILE cc_start: 0.8865 (pp) cc_final: 0.8620 (mt) REVERT: I 346 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8299 (pp) REVERT: I 349 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7796 (tp-100) REVERT: I 351 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8687 (mp) REVERT: I 389 ASP cc_start: 0.7750 (m-30) cc_final: 0.7380 (m-30) REVERT: I 400 LYS cc_start: 0.8714 (ttmm) cc_final: 0.8463 (mtpp) REVERT: I 426 GLU cc_start: 0.8423 (tm-30) cc_final: 0.8172 (tp30) REVERT: I 460 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7771 (tp30) REVERT: I 472 TRP cc_start: 0.8664 (t60) cc_final: 0.8320 (t60) REVERT: I 474 GLU cc_start: 0.7379 (pt0) cc_final: 0.7103 (pp20) REVERT: I 476 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7532 (mp0) REVERT: I 488 GLN cc_start: 0.8612 (tp40) cc_final: 0.8038 (tm-30) REVERT: I 491 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8118 (mm-30) REVERT: I 504 GLU cc_start: 0.7635 (tp30) cc_final: 0.7253 (tp30) REVERT: I 540 GLU cc_start: 0.8086 (pt0) cc_final: 0.7754 (pm20) REVERT: I 544 ASP cc_start: 0.8242 (t70) cc_final: 0.7933 (t0) REVERT: I 590 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8181 (tmtt) REVERT: I 595 GLN cc_start: 0.8345 (mm-40) cc_final: 0.8008 (mm-40) REVERT: I 606 VAL cc_start: 0.8286 (OUTLIER) cc_final: 0.8047 (t) REVERT: I 613 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7766 (mt-10) REVERT: I 632 LYS cc_start: 0.8367 (ttpt) cc_final: 0.8083 (ttpp) REVERT: I 642 THR cc_start: 0.8636 (m) cc_final: 0.8376 (p) REVERT: I 667 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7963 (mp0) REVERT: I 668 ASP cc_start: 0.7840 (m-30) cc_final: 0.7628 (m-30) REVERT: I 680 ARG cc_start: 0.8176 (mmp-170) cc_final: 0.7579 (mtp180) REVERT: I 681 GLU cc_start: 0.7916 (mp0) cc_final: 0.7627 (mp0) REVERT: I 721 ASP cc_start: 0.7718 (m-30) cc_final: 0.7404 (m-30) REVERT: I 723 ARG cc_start: 0.7789 (mtp85) cc_final: 0.7302 (mtp85) REVERT: I 774 ARG cc_start: 0.8575 (ttp-110) cc_final: 0.7866 (mtm110) REVERT: I 777 ASP cc_start: 0.7904 (m-30) cc_final: 0.7428 (m-30) REVERT: I 780 LYS cc_start: 0.8505 (mttp) cc_final: 0.8230 (mttp) REVERT: I 797 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7767 (mm-30) REVERT: I 827 ASN cc_start: 0.8043 (t0) cc_final: 0.7546 (t0) REVERT: I 829 VAL cc_start: 0.8935 (m) cc_final: 0.8644 (p) REVERT: I 830 MET cc_start: 0.8497 (mmp) cc_final: 0.8111 (mmp) REVERT: I 842 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7733 (tp30) REVERT: I 870 GLU cc_start: 0.7738 (pp20) cc_final: 0.7264 (tm-30) REVERT: I 882 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7736 (mm-30) REVERT: I 927 ILE cc_start: 0.8778 (tt) cc_final: 0.8479 (pt) REVERT: I 935 ASP cc_start: 0.8329 (m-30) cc_final: 0.8118 (m-30) REVERT: I 940 MET cc_start: 0.8278 (mmt) cc_final: 0.8015 (mmt) REVERT: I 969 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7623 (tm-30) REVERT: I 972 GLN cc_start: 0.7949 (tm-30) cc_final: 0.7453 (pp30) REVERT: J 7 LEU cc_start: 0.8828 (tm) cc_final: 0.8585 (tt) REVERT: J 14 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7561 (mm-30) REVERT: J 41 GLU cc_start: 0.7711 (tp30) cc_final: 0.6812 (tp30) REVERT: J 52 GLU cc_start: 0.7162 (tt0) cc_final: 0.6749 (tm-30) REVERT: J 53 GLU cc_start: 0.7614 (tp30) cc_final: 0.7357 (mp0) REVERT: J 54 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7399 (tm-30) REVERT: J 111 MET cc_start: 0.8388 (mtp) cc_final: 0.8165 (ttp) REVERT: J 121 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7611 (tm-30) outliers start: 158 outliers final: 76 residues processed: 1007 average time/residue: 0.7871 time to fit residues: 919.7939 Evaluate side-chains 1022 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 913 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 267 ASN Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 8 GLN Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 124 ARG Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 239 LEU Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 281 HIS Chi-restraints excluded: chain G residue 284 THR Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 144 LYS Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain H residue 228 PHE Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 106 ARG Chi-restraints excluded: chain I residue 206 LEU Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 295 ARG Chi-restraints excluded: chain I residue 346 ILE Chi-restraints excluded: chain I residue 349 GLN Chi-restraints excluded: chain I residue 351 ILE Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 461 PHE Chi-restraints excluded: chain I residue 476 GLU Chi-restraints excluded: chain I residue 479 PHE Chi-restraints excluded: chain I residue 495 ASP Chi-restraints excluded: chain I residue 515 GLU Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 590 LYS Chi-restraints excluded: chain I residue 606 VAL Chi-restraints excluded: chain I residue 689 VAL Chi-restraints excluded: chain I residue 750 THR Chi-restraints excluded: chain I residue 854 LYS Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 121 GLU Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain K residue 119 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 225 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 224 optimal weight: 0.9990 chunk 364 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 332 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 147 optimal weight: 0.5980 chunk 191 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 ASN A 82 ASN A 198 ASN A 217 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 ASN B 68 GLN B 217 ASN B 232 ASN B 267 ASN B 295 ASN C 10 GLN C 267 ASN C 290 ASN C 295 ASN D 10 GLN D 267 ASN D 290 ASN E 8 GLN E 68 GLN E 198 ASN ** E 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 GLN E 295 ASN F 20 HIS F 43 ASN ** G 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN H 34 ASN H 119 ASN H 172 GLN H 195 GLN I 35 HIS I 399 GLN ** I 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 893 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.137944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.117698 restraints weight = 47756.312| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.93 r_work: 0.3417 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 31399 Z= 0.225 Angle : 0.735 11.866 42781 Z= 0.360 Chirality : 0.055 0.688 4787 Planarity : 0.005 0.092 5308 Dihedral : 12.877 160.650 4864 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 5.02 % Allowed : 24.15 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % 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: 0.00 (0.14), residues: 3639 helix: 0.94 (0.13), residues: 1602 sheet: -0.09 (0.22), residues: 459 loop : -0.89 (0.16), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG I 846 TYR 0.029 0.002 TYR I 446 PHE 0.029 0.002 PHE B 151 TRP 0.014 0.002 TRP I 453 HIS 0.010 0.001 HIS I 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.23 (31399) covalent geometry : angle 0.73532 / 0.36 (42781) hydrogen bonds : bond 0.03897 / 2.54 ( 1385) hydrogen bonds : angle 4.54737 / 3.17 ( 3955) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1086 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 927 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.8852 (t) cc_final: 0.8424 (p) REVERT: A 101 GLU cc_start: 0.7334 (mt-10) cc_final: 0.7060 (mt-10) REVERT: A 139 GLU cc_start: 0.8183 (mp0) cc_final: 0.7791 (mp0) REVERT: A 209 GLU cc_start: 0.8248 (pt0) cc_final: 0.7963 (pt0) REVERT: A 210 SER cc_start: 0.8817 (m) cc_final: 0.8443 (p) REVERT: A 215 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8414 (mtm) REVERT: A 232 ASN cc_start: 0.8532 (m-40) cc_final: 0.8255 (m110) REVERT: A 264 ASP cc_start: 0.8355 (t0) cc_final: 0.7824 (t70) REVERT: A 268 LYS cc_start: 0.8472 (mttp) cc_final: 0.8125 (mttp) REVERT: A 269 GLU cc_start: 0.7425 (mm-30) cc_final: 0.6985 (mm-30) REVERT: A 283 ASP cc_start: 0.7951 (m-30) cc_final: 0.7635 (m-30) REVERT: A 298 GLU cc_start: 0.8420 (tp30) cc_final: 0.8090 (tp30) REVERT: B 6 LYS cc_start: 0.9052 (ttmm) cc_final: 0.8840 (mttp) REVERT: B 48 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8219 (tt0) REVERT: B 51 LEU cc_start: 0.8947 (mt) cc_final: 0.8723 (mp) REVERT: B 54 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8136 (mtpp) REVERT: B 90 LYS cc_start: 0.8718 (mmtp) cc_final: 0.8495 (mmtp) REVERT: B 109 ASP cc_start: 0.8090 (t0) cc_final: 0.7680 (t0) REVERT: B 123 GLU cc_start: 0.8056 (tp30) cc_final: 0.7643 (tp30) REVERT: B 124 ARG cc_start: 0.8579 (ttm-80) cc_final: 0.8308 (ttm-80) REVERT: B 143 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.7488 (ttp80) REVERT: B 226 ASP cc_start: 0.7804 (t0) cc_final: 0.7455 (t0) REVERT: B 253 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7752 (mm-30) REVERT: B 268 LYS cc_start: 0.8837 (ttmm) cc_final: 0.8570 (mtpp) REVERT: B 283 ASP cc_start: 0.7773 (p0) cc_final: 0.7382 (p0) REVERT: B 290 ASN cc_start: 0.8233 (m-40) cc_final: 0.8018 (m-40) REVERT: C 32 SER cc_start: 0.8335 (m) cc_final: 0.7273 (p) REVERT: C 54 LYS cc_start: 0.8289 (mptt) cc_final: 0.8051 (mmmm) REVERT: C 72 GLU cc_start: 0.7902 (mp0) cc_final: 0.7669 (mp0) REVERT: C 89 ASP cc_start: 0.8095 (m-30) cc_final: 0.7839 (m-30) REVERT: C 139 GLU cc_start: 0.8261 (mp0) cc_final: 0.7929 (mp0) REVERT: C 151 PHE cc_start: 0.8606 (m-80) cc_final: 0.8370 (m-80) REVERT: C 156 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7371 (mmm) REVERT: C 215 MET cc_start: 0.8868 (mtp) cc_final: 0.8668 (mtm) REVERT: C 269 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7763 (mm-30) REVERT: C 283 ASP cc_start: 0.8111 (m-30) cc_final: 0.7837 (m-30) REVERT: C 316 GLU cc_start: 0.8237 (tt0) cc_final: 0.7993 (tt0) REVERT: D 66 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8303 (mtt90) REVERT: D 68 GLN cc_start: 0.8366 (pt0) cc_final: 0.7825 (pt0) REVERT: D 72 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7591 (mt-10) REVERT: D 78 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7793 (tt0) REVERT: D 97 GLU cc_start: 0.7838 (tp30) cc_final: 0.7538 (tp30) REVERT: D 124 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8569 (tmm-80) REVERT: D 127 VAL cc_start: 0.8967 (OUTLIER) cc_final: 0.8645 (t) REVERT: D 130 ASP cc_start: 0.7364 (t0) cc_final: 0.6566 (t0) REVERT: D 156 MET cc_start: 0.8574 (mtp) cc_final: 0.8194 (mtp) REVERT: D 242 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8314 (tm-30) REVERT: D 273 LYS cc_start: 0.8936 (mtmm) cc_final: 0.8586 (mttt) REVERT: D 283 ASP cc_start: 0.8067 (m-30) cc_final: 0.7762 (m-30) REVERT: E 8 GLN cc_start: 0.8045 (mm-40) cc_final: 0.6982 (mp10) REVERT: E 15 ARG cc_start: 0.8677 (ttp80) cc_final: 0.8414 (ttp80) REVERT: E 45 THR cc_start: 0.8579 (t) cc_final: 0.8317 (m) REVERT: E 46 ARG cc_start: 0.8411 (mtp-110) cc_final: 0.7937 (mmm160) REVERT: E 89 ASP cc_start: 0.8499 (p0) cc_final: 0.8246 (p0) REVERT: E 141 SER cc_start: 0.8579 (m) cc_final: 0.8205 (p) REVERT: E 182 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7801 (mm-30) REVERT: E 190 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7467 (pm20) REVERT: E 209 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7345 (mt-10) REVERT: E 231 SER cc_start: 0.8653 (OUTLIER) cc_final: 0.8372 (t) REVERT: E 241 ASP cc_start: 0.7996 (t0) cc_final: 0.7685 (t0) REVERT: E 249 LYS cc_start: 0.8167 (mmpt) cc_final: 0.7782 (mmpt) REVERT: E 256 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7733 (mm-30) REVERT: E 264 ASP cc_start: 0.8205 (t70) cc_final: 0.7950 (t0) REVERT: E 275 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7317 (mt-10) REVERT: E 286 LEU cc_start: 0.8806 (mm) cc_final: 0.8532 (mp) REVERT: E 287 GLN cc_start: 0.8434 (tp40) cc_final: 0.7844 (tp40) REVERT: E 288 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7547 (mt-10) REVERT: E 291 ASP cc_start: 0.7431 (p0) cc_final: 0.6994 (p0) REVERT: E 305 SER cc_start: 0.8819 (m) cc_final: 0.8228 (p) REVERT: E 308 GLN cc_start: 0.8152 (tp40) cc_final: 0.7730 (tp40) REVERT: E 309 GLN cc_start: 0.8367 (mt0) cc_final: 0.8041 (mt0) REVERT: E 312 ASP cc_start: 0.8107 (m-30) cc_final: 0.7737 (m-30) REVERT: F 56 ASP cc_start: 0.7848 (t0) cc_final: 0.7508 (t0) REVERT: F 89 ASP cc_start: 0.7717 (t0) cc_final: 0.7399 (t0) REVERT: F 94 ASN cc_start: 0.7452 (t0) cc_final: 0.7210 (t0) REVERT: F 128 TYR cc_start: 0.8700 (m-80) cc_final: 0.8168 (m-80) REVERT: F 190 GLU cc_start: 0.7619 (mp0) cc_final: 0.7370 (mp0) REVERT: F 215 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7772 (mtp) REVERT: F 247 LEU cc_start: 0.8203 (mp) cc_final: 0.7982 (mt) REVERT: F 267 ASN cc_start: 0.7997 (m-40) cc_final: 0.7781 (m-40) REVERT: F 275 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8101 (mt-10) REVERT: F 288 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7712 (tm-30) REVERT: F 289 VAL cc_start: 0.8654 (t) cc_final: 0.8449 (p) REVERT: G 8 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7108 (mp10) REVERT: G 47 THR cc_start: 0.7818 (OUTLIER) cc_final: 0.7320 (p) REVERT: G 68 GLN cc_start: 0.7502 (pp30) cc_final: 0.7239 (pp30) REVERT: G 72 GLU cc_start: 0.7743 (mp0) cc_final: 0.7302 (mp0) REVERT: G 83 LEU cc_start: 0.8543 (tp) cc_final: 0.8302 (tm) REVERT: G 106 GLN cc_start: 0.7744 (pm20) cc_final: 0.7465 (pm20) REVERT: G 216 LYS cc_start: 0.7564 (tppt) cc_final: 0.7266 (tppt) REVERT: G 223 VAL cc_start: 0.8420 (OUTLIER) cc_final: 0.8091 (m) REVERT: G 233 LEU cc_start: 0.8846 (tp) cc_final: 0.8527 (tm) REVERT: G 253 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7144 (mm-30) REVERT: G 288 GLU cc_start: 0.8167 (tp30) cc_final: 0.7502 (tp30) REVERT: G 295 ASN cc_start: 0.7594 (t0) cc_final: 0.7057 (t0) REVERT: H 8 LYS cc_start: 0.8813 (ptmt) cc_final: 0.8386 (ptmt) REVERT: H 37 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8389 (mm) REVERT: H 65 ASP cc_start: 0.8195 (t0) cc_final: 0.7857 (t0) REVERT: H 86 GLN cc_start: 0.8483 (tt0) cc_final: 0.8225 (tt0) REVERT: H 95 ASN cc_start: 0.8654 (m-40) cc_final: 0.8382 (m-40) REVERT: H 122 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8157 (pt) REVERT: H 137 LEU cc_start: 0.8620 (tp) cc_final: 0.8365 (tt) REVERT: H 174 LYS cc_start: 0.8060 (ptpt) cc_final: 0.7720 (ptpt) REVERT: H 181 VAL cc_start: 0.8811 (OUTLIER) cc_final: 0.8509 (t) REVERT: H 201 ASN cc_start: 0.8196 (m-40) cc_final: 0.7633 (m110) REVERT: H 205 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8220 (ttm) REVERT: H 227 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.8029 (p) REVERT: I 11 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.8664 (mtm-85) REVERT: I 22 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8066 (tp) REVERT: I 26 GLN cc_start: 0.8516 (mm-40) cc_final: 0.8081 (mt0) REVERT: I 93 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8061 (tmm) REVERT: I 94 GLN cc_start: 0.8697 (mm110) cc_final: 0.8458 (mm-40) REVERT: I 106 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.7212 (mtp180) REVERT: I 150 PHE cc_start: 0.8762 (m-80) cc_final: 0.8318 (m-80) REVERT: I 152 GLU cc_start: 0.8054 (mp0) cc_final: 0.7739 (mp0) REVERT: I 216 SER cc_start: 0.8468 (m) cc_final: 0.8230 (t) REVERT: I 229 ARG cc_start: 0.7579 (ptm160) cc_final: 0.7259 (ptm160) REVERT: I 230 LEU cc_start: 0.8285 (mt) cc_final: 0.8064 (mp) REVERT: I 233 LEU cc_start: 0.8437 (mt) cc_final: 0.8089 (mt) REVERT: I 295 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7856 (ttt180) REVERT: I 298 ILE cc_start: 0.8866 (pp) cc_final: 0.8636 (mt) REVERT: I 308 GLN cc_start: 0.8384 (mm-40) cc_final: 0.8179 (mm-40) REVERT: I 346 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8343 (pp) REVERT: I 349 GLN cc_start: 0.8419 (tm-30) cc_final: 0.7816 (tp-100) REVERT: I 351 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8745 (mm) REVERT: I 389 ASP cc_start: 0.7770 (m-30) cc_final: 0.7382 (m-30) REVERT: I 401 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7507 (mp0) REVERT: I 460 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7781 (tp30) REVERT: I 474 GLU cc_start: 0.7403 (pt0) cc_final: 0.7185 (pt0) REVERT: I 488 GLN cc_start: 0.8630 (tp40) cc_final: 0.8054 (tm-30) REVERT: I 491 GLU cc_start: 0.8316 (mt-10) cc_final: 0.8116 (mm-30) REVERT: I 495 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.8048 (t0) REVERT: I 504 GLU cc_start: 0.7654 (tp30) cc_final: 0.7305 (tp30) REVERT: I 540 GLU cc_start: 0.8128 (pt0) cc_final: 0.7799 (pm20) REVERT: I 544 ASP cc_start: 0.8253 (t70) cc_final: 0.7946 (t0) REVERT: I 590 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8185 (tmtt) REVERT: I 595 GLN cc_start: 0.8336 (mm-40) cc_final: 0.8005 (mm-40) REVERT: I 606 VAL cc_start: 0.8341 (OUTLIER) cc_final: 0.8101 (t) REVERT: I 613 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7752 (mt-10) REVERT: I 632 LYS cc_start: 0.8359 (ttpt) cc_final: 0.8119 (ttpp) REVERT: I 642 THR cc_start: 0.8648 (m) cc_final: 0.8388 (p) REVERT: I 667 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7961 (mp0) REVERT: I 680 ARG cc_start: 0.8195 (mmp-170) cc_final: 0.7593 (mtp180) REVERT: I 681 GLU cc_start: 0.7916 (mp0) cc_final: 0.7601 (mp0) REVERT: I 721 ASP cc_start: 0.7745 (m-30) cc_final: 0.7399 (m-30) REVERT: I 723 ARG cc_start: 0.7765 (mtp85) cc_final: 0.7302 (mtp85) REVERT: I 780 LYS cc_start: 0.8537 (mttp) cc_final: 0.8272 (mttp) REVERT: I 797 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7777 (mm-30) REVERT: I 827 ASN cc_start: 0.8020 (t0) cc_final: 0.7569 (t0) REVERT: I 829 VAL cc_start: 0.8930 (m) cc_final: 0.8646 (p) REVERT: I 830 MET cc_start: 0.8526 (mmp) cc_final: 0.8214 (mmp) REVERT: I 832 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7974 (mt-10) REVERT: I 842 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7781 (tp30) REVERT: I 851 GLU cc_start: 0.7555 (pm20) cc_final: 0.6825 (pp20) REVERT: I 854 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8155 (tppp) REVERT: I 870 GLU cc_start: 0.7777 (pp20) cc_final: 0.7494 (pp20) REVERT: I 882 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7778 (mm-30) REVERT: I 898 ARG cc_start: 0.8175 (mtp-110) cc_final: 0.7899 (ttm-80) REVERT: I 927 ILE cc_start: 0.8781 (tt) cc_final: 0.8492 (pt) REVERT: I 940 MET cc_start: 0.8314 (mmt) cc_final: 0.8046 (mmt) REVERT: I 969 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7681 (tm-30) REVERT: I 972 GLN cc_start: 0.7943 (tm-30) cc_final: 0.7492 (pp30) REVERT: J 5 LEU cc_start: 0.5765 (OUTLIER) cc_final: 0.4576 (pt) REVERT: J 14 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7559 (mm-30) REVERT: J 41 GLU cc_start: 0.7681 (tp30) cc_final: 0.6794 (tp30) REVERT: J 52 GLU cc_start: 0.7178 (tt0) cc_final: 0.6762 (tm-30) REVERT: J 53 GLU cc_start: 0.7662 (tp30) cc_final: 0.7401 (mp0) REVERT: J 54 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7477 (tm-30) REVERT: J 121 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7622 (tm-30) outliers start: 159 outliers final: 89 residues processed: 1000 average time/residue: 0.7582 time to fit residues: 880.3465 Evaluate side-chains 1035 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 911 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 26 MET Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 215 MET Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 232 ASN Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 8 GLN Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 124 ARG Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 239 LEU Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 281 HIS Chi-restraints excluded: chain G residue 284 THR Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 144 LYS Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 195 GLN Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain I residue 11 ARG Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 106 ARG Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 295 ARG Chi-restraints excluded: chain I residue 326 LYS Chi-restraints excluded: chain I residue 346 ILE Chi-restraints excluded: chain I residue 351 ILE Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain I residue 368 GLU Chi-restraints excluded: chain I residue 411 GLU Chi-restraints excluded: chain I residue 415 LYS Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 461 PHE Chi-restraints excluded: chain I residue 479 PHE Chi-restraints excluded: chain I residue 495 ASP Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 590 LYS Chi-restraints excluded: chain I residue 606 VAL Chi-restraints excluded: chain I residue 650 LEU Chi-restraints excluded: chain I residue 689 VAL Chi-restraints excluded: chain I residue 705 LYS Chi-restraints excluded: chain I residue 750 THR Chi-restraints excluded: chain I residue 854 LYS Chi-restraints excluded: chain I residue 907 ILE Chi-restraints excluded: chain I residue 916 THR Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 121 GLU Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain K residue 119 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 61 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 chunk 238 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 269 optimal weight: 0.9990 chunk 334 optimal weight: 0.1980 chunk 335 optimal weight: 0.5980 chunk 320 optimal weight: 0.0370 chunk 232 optimal weight: 0.3980 chunk 164 optimal weight: 0.4980 overall best weight: 0.3458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 ASN A 82 ASN A 198 ASN A 217 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 ASN B 68 GLN B 217 ASN B 232 ASN B 295 ASN C 10 GLN C 48 GLN C 267 ASN C 290 ASN C 295 ASN D 267 ASN D 290 ASN E 10 GLN E 198 ASN E 232 ASN E 295 ASN F 20 HIS F 43 ASN ** G 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN H 34 ASN H 119 ASN H 195 GLN I 35 HIS I 399 GLN ** I 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 893 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.139554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.119318 restraints weight = 47842.477| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.95 r_work: 0.3445 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 31399 Z= 0.146 Angle : 0.715 16.641 42781 Z= 0.348 Chirality : 0.051 0.624 4787 Planarity : 0.005 0.066 5308 Dihedral : 12.765 159.737 4860 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.55 % Allowed : 24.94 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % 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: 0.08 (0.14), residues: 3639 helix: 1.05 (0.13), residues: 1601 sheet: -0.27 (0.22), residues: 478 loop : -0.84 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 846 TYR 0.033 0.002 TYR I 844 PHE 0.020 0.001 PHE B 151 TRP 0.016 0.001 TRP H 221 HIS 0.009 0.001 HIS I 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (31399) covalent geometry : angle 0.71482 / 0.35 (42781) hydrogen bonds : bond 0.03650 / 2.37 ( 1385) hydrogen bonds : angle 4.48996 / 3.13 ( 3955) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1056 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 912 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.8776 (t) cc_final: 0.8433 (p) REVERT: A 101 GLU cc_start: 0.7250 (mt-10) cc_final: 0.6988 (mt-10) REVERT: A 156 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.7980 (tpp) REVERT: A 209 GLU cc_start: 0.8230 (pt0) cc_final: 0.7953 (pt0) REVERT: A 210 SER cc_start: 0.8796 (m) cc_final: 0.8434 (p) REVERT: A 264 ASP cc_start: 0.8354 (t0) cc_final: 0.7828 (t70) REVERT: A 268 LYS cc_start: 0.8452 (mttp) cc_final: 0.8095 (mttp) REVERT: A 269 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7006 (mm-30) REVERT: A 283 ASP cc_start: 0.7962 (m-30) cc_final: 0.7644 (m-30) REVERT: A 287 GLN cc_start: 0.7983 (tm-30) cc_final: 0.7752 (tm-30) REVERT: A 298 GLU cc_start: 0.8415 (tp30) cc_final: 0.8078 (tp30) REVERT: B 6 LYS cc_start: 0.9040 (ttmm) cc_final: 0.8837 (mttp) REVERT: B 48 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8197 (tt0) REVERT: B 51 LEU cc_start: 0.8947 (mt) cc_final: 0.8726 (mp) REVERT: B 90 LYS cc_start: 0.8710 (mmtp) cc_final: 0.8477 (mmtp) REVERT: B 109 ASP cc_start: 0.8058 (t0) cc_final: 0.7659 (t0) REVERT: B 123 GLU cc_start: 0.8004 (tp30) cc_final: 0.7624 (tp30) REVERT: B 151 PHE cc_start: 0.8589 (m-10) cc_final: 0.8370 (m-80) REVERT: B 162 MET cc_start: 0.8557 (mmm) cc_final: 0.8345 (tpp) REVERT: B 226 ASP cc_start: 0.7778 (t0) cc_final: 0.7457 (t0) REVERT: B 253 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7701 (mm-30) REVERT: B 268 LYS cc_start: 0.8823 (ttmm) cc_final: 0.8561 (mtpp) REVERT: B 283 ASP cc_start: 0.7760 (p0) cc_final: 0.7342 (p0) REVERT: C 32 SER cc_start: 0.8247 (m) cc_final: 0.7209 (p) REVERT: C 139 GLU cc_start: 0.8196 (mp0) cc_final: 0.7884 (mp0) REVERT: C 151 PHE cc_start: 0.8609 (m-80) cc_final: 0.8369 (m-80) REVERT: C 156 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7374 (mmm) REVERT: C 283 ASP cc_start: 0.8081 (m-30) cc_final: 0.7805 (m-30) REVERT: C 316 GLU cc_start: 0.8239 (tt0) cc_final: 0.7993 (tt0) REVERT: D 15 ARG cc_start: 0.8595 (ttp80) cc_final: 0.8320 (ttt180) REVERT: D 66 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8262 (mtt90) REVERT: D 78 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7708 (tt0) REVERT: D 97 GLU cc_start: 0.7817 (tp30) cc_final: 0.7525 (tp30) REVERT: D 124 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8570 (tmm-80) REVERT: D 127 VAL cc_start: 0.8936 (OUTLIER) cc_final: 0.8625 (t) REVERT: D 130 ASP cc_start: 0.7295 (t0) cc_final: 0.6540 (t0) REVERT: D 156 MET cc_start: 0.8517 (mtp) cc_final: 0.8142 (mtp) REVERT: D 242 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8314 (tm-30) REVERT: D 273 LYS cc_start: 0.8904 (mtmm) cc_final: 0.8558 (mttt) REVERT: D 283 ASP cc_start: 0.8055 (m-30) cc_final: 0.7740 (m-30) REVERT: E 15 ARG cc_start: 0.8640 (ttp80) cc_final: 0.8374 (ttp80) REVERT: E 45 THR cc_start: 0.8547 (t) cc_final: 0.8298 (m) REVERT: E 46 ARG cc_start: 0.8370 (mtp-110) cc_final: 0.7911 (mmm160) REVERT: E 89 ASP cc_start: 0.8498 (p0) cc_final: 0.8250 (p0) REVERT: E 141 SER cc_start: 0.8560 (m) cc_final: 0.8175 (p) REVERT: E 148 ASN cc_start: 0.7429 (p0) cc_final: 0.7177 (p0) REVERT: E 182 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7717 (mm-30) REVERT: E 190 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7511 (pm20) REVERT: E 209 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7271 (mt-10) REVERT: E 231 SER cc_start: 0.8608 (OUTLIER) cc_final: 0.8331 (t) REVERT: E 241 ASP cc_start: 0.7966 (t0) cc_final: 0.7659 (t0) REVERT: E 249 LYS cc_start: 0.8116 (mmpt) cc_final: 0.7751 (mmpt) REVERT: E 256 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7669 (mm-30) REVERT: E 264 ASP cc_start: 0.8216 (t70) cc_final: 0.7974 (t0) REVERT: E 286 LEU cc_start: 0.8797 (mm) cc_final: 0.8502 (mp) REVERT: E 288 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7475 (mt-10) REVERT: E 291 ASP cc_start: 0.7370 (p0) cc_final: 0.6973 (p0) REVERT: E 305 SER cc_start: 0.8808 (m) cc_final: 0.8258 (p) REVERT: E 308 GLN cc_start: 0.8122 (tp40) cc_final: 0.7698 (tp40) REVERT: E 309 GLN cc_start: 0.8375 (mt0) cc_final: 0.8090 (mt0) REVERT: E 311 GLN cc_start: 0.8532 (mt0) cc_final: 0.8295 (mt0) REVERT: E 312 ASP cc_start: 0.8097 (m-30) cc_final: 0.7703 (m-30) REVERT: F 56 ASP cc_start: 0.7789 (t0) cc_final: 0.7456 (t0) REVERT: F 89 ASP cc_start: 0.7704 (t0) cc_final: 0.7383 (t0) REVERT: F 94 ASN cc_start: 0.7457 (t0) cc_final: 0.7189 (t0) REVERT: F 128 TYR cc_start: 0.8678 (m-80) cc_final: 0.8100 (m-80) REVERT: F 190 GLU cc_start: 0.7667 (mp0) cc_final: 0.7409 (mp0) REVERT: F 205 TYR cc_start: 0.7030 (m-80) cc_final: 0.6546 (m-80) REVERT: F 247 LEU cc_start: 0.8190 (mp) cc_final: 0.7978 (mt) REVERT: F 267 ASN cc_start: 0.7987 (m-40) cc_final: 0.7774 (m-40) REVERT: F 275 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8119 (mt-10) REVERT: F 288 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7686 (tm-30) REVERT: G 8 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.7102 (mp10) REVERT: G 68 GLN cc_start: 0.7482 (pp30) cc_final: 0.7211 (pp30) REVERT: G 70 THR cc_start: 0.7600 (OUTLIER) cc_final: 0.7396 (p) REVERT: G 72 GLU cc_start: 0.7634 (mp0) cc_final: 0.7227 (mp0) REVERT: G 83 LEU cc_start: 0.8465 (tp) cc_final: 0.8220 (tm) REVERT: G 106 GLN cc_start: 0.7722 (pm20) cc_final: 0.7447 (pm20) REVERT: G 216 LYS cc_start: 0.7541 (tppt) cc_final: 0.7250 (tppt) REVERT: G 223 VAL cc_start: 0.8429 (OUTLIER) cc_final: 0.8092 (m) REVERT: G 233 LEU cc_start: 0.8843 (tp) cc_final: 0.8573 (tm) REVERT: G 239 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8341 (tm) REVERT: G 288 GLU cc_start: 0.8164 (tp30) cc_final: 0.7497 (tp30) REVERT: G 295 ASN cc_start: 0.7465 (t0) cc_final: 0.6919 (t0) REVERT: H 8 LYS cc_start: 0.8816 (ptmt) cc_final: 0.8379 (ptmt) REVERT: H 37 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8370 (mm) REVERT: H 65 ASP cc_start: 0.8185 (t0) cc_final: 0.7839 (t0) REVERT: H 86 GLN cc_start: 0.8466 (tt0) cc_final: 0.8214 (tt0) REVERT: H 95 ASN cc_start: 0.8638 (m-40) cc_final: 0.8360 (m-40) REVERT: H 122 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8123 (pt) REVERT: H 137 LEU cc_start: 0.8608 (tp) cc_final: 0.8331 (tt) REVERT: H 174 LYS cc_start: 0.8037 (ptpt) cc_final: 0.7713 (ptpt) REVERT: H 181 VAL cc_start: 0.8794 (OUTLIER) cc_final: 0.8502 (t) REVERT: H 201 ASN cc_start: 0.8191 (m-40) cc_final: 0.7628 (m110) REVERT: H 205 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8140 (ttm) REVERT: H 227 THR cc_start: 0.8361 (OUTLIER) cc_final: 0.7984 (p) REVERT: I 22 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.7981 (tp) REVERT: I 26 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8081 (mt0) REVERT: I 93 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8006 (tmm) REVERT: I 94 GLN cc_start: 0.8669 (mm110) cc_final: 0.8406 (mm-40) REVERT: I 150 PHE cc_start: 0.8759 (m-80) cc_final: 0.8478 (m-80) REVERT: I 152 GLU cc_start: 0.8098 (mp0) cc_final: 0.7661 (mp0) REVERT: I 206 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8297 (mm) REVERT: I 216 SER cc_start: 0.8433 (m) cc_final: 0.8208 (t) REVERT: I 229 ARG cc_start: 0.7536 (ptm160) cc_final: 0.7247 (ptm160) REVERT: I 230 LEU cc_start: 0.8273 (mt) cc_final: 0.8056 (mp) REVERT: I 233 LEU cc_start: 0.8427 (mt) cc_final: 0.8055 (mt) REVERT: I 250 ASP cc_start: 0.7201 (t70) cc_final: 0.6926 (t70) REVERT: I 295 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7855 (ttt180) REVERT: I 298 ILE cc_start: 0.8841 (pp) cc_final: 0.8635 (mt) REVERT: I 308 GLN cc_start: 0.8385 (mm-40) cc_final: 0.8185 (mm-40) REVERT: I 346 ILE cc_start: 0.8690 (mp) cc_final: 0.8294 (pp) REVERT: I 349 GLN cc_start: 0.8418 (tm-30) cc_final: 0.7818 (tp-100) REVERT: I 351 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8691 (mm) REVERT: I 389 ASP cc_start: 0.7695 (m-30) cc_final: 0.7296 (m-30) REVERT: I 400 LYS cc_start: 0.8710 (ttmm) cc_final: 0.8477 (mtpp) REVERT: I 460 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7746 (tp30) REVERT: I 488 GLN cc_start: 0.8569 (tp40) cc_final: 0.7973 (tm-30) REVERT: I 495 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.7999 (t0) REVERT: I 504 GLU cc_start: 0.7626 (tp30) cc_final: 0.7261 (tp30) REVERT: I 540 GLU cc_start: 0.8073 (pt0) cc_final: 0.7740 (pm20) REVERT: I 544 ASP cc_start: 0.8236 (t70) cc_final: 0.7916 (t0) REVERT: I 590 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8149 (tmtt) REVERT: I 595 GLN cc_start: 0.8322 (mm-40) cc_final: 0.8074 (mm-40) REVERT: I 606 VAL cc_start: 0.8225 (OUTLIER) cc_final: 0.7980 (t) REVERT: I 613 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7722 (mt-10) REVERT: I 632 LYS cc_start: 0.8319 (ttpt) cc_final: 0.8049 (ttpp) REVERT: I 642 THR cc_start: 0.8658 (m) cc_final: 0.8405 (p) REVERT: I 667 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7964 (mp0) REVERT: I 680 ARG cc_start: 0.8162 (mmp-170) cc_final: 0.7587 (mtp180) REVERT: I 681 GLU cc_start: 0.7885 (mp0) cc_final: 0.7584 (mp0) REVERT: I 721 ASP cc_start: 0.7725 (m-30) cc_final: 0.7365 (m-30) REVERT: I 723 ARG cc_start: 0.7801 (mtp85) cc_final: 0.7323 (mtp85) REVERT: I 767 ARG cc_start: 0.8455 (ttm-80) cc_final: 0.8229 (ttm-80) REVERT: I 774 ARG cc_start: 0.8670 (ttp-110) cc_final: 0.8229 (mtm110) REVERT: I 780 LYS cc_start: 0.8498 (mttp) cc_final: 0.8202 (mttp) REVERT: I 797 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7760 (mm-30) REVERT: I 829 VAL cc_start: 0.8913 (m) cc_final: 0.8640 (p) REVERT: I 832 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7971 (mt-10) REVERT: I 842 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7760 (tp30) REVERT: I 851 GLU cc_start: 0.7523 (pm20) cc_final: 0.6960 (pm20) REVERT: I 854 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8217 (tppp) REVERT: I 870 GLU cc_start: 0.7710 (pp20) cc_final: 0.7413 (pp20) REVERT: I 871 GLN cc_start: 0.8214 (tp40) cc_final: 0.7709 (tm-30) REVERT: I 882 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7744 (mm-30) REVERT: I 906 ILE cc_start: 0.8497 (mm) cc_final: 0.8127 (mt) REVERT: I 921 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7733 (mt-10) REVERT: I 927 ILE cc_start: 0.8761 (tt) cc_final: 0.8461 (pt) REVERT: I 940 MET cc_start: 0.8313 (mmt) cc_final: 0.8047 (mmt) REVERT: I 969 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7640 (tm-30) REVERT: I 972 GLN cc_start: 0.7946 (tm-30) cc_final: 0.7474 (pp30) REVERT: J 14 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7560 (mm-30) REVERT: J 41 GLU cc_start: 0.7674 (tp30) cc_final: 0.6742 (tp30) REVERT: J 54 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7401 (tm-30) REVERT: J 121 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7614 (tm-30) outliers start: 144 outliers final: 82 residues processed: 981 average time/residue: 0.7786 time to fit residues: 884.6071 Evaluate side-chains 1012 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 902 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 287 GLN Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 26 MET Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 267 ASN Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain F residue 4 SER Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 8 GLN Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 124 ARG Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 239 LEU Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 281 HIS Chi-restraints excluded: chain G residue 284 THR Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 144 LYS Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain H residue 228 PHE Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 206 LEU Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 295 ARG Chi-restraints excluded: chain I residue 326 LYS Chi-restraints excluded: chain I residue 351 ILE Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain I residue 368 GLU Chi-restraints excluded: chain I residue 411 GLU Chi-restraints excluded: chain I residue 415 LYS Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 461 PHE Chi-restraints excluded: chain I residue 479 PHE Chi-restraints excluded: chain I residue 495 ASP Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 590 LYS Chi-restraints excluded: chain I residue 606 VAL Chi-restraints excluded: chain I residue 650 LEU Chi-restraints excluded: chain I residue 689 VAL Chi-restraints excluded: chain I residue 750 THR Chi-restraints excluded: chain I residue 843 GLU Chi-restraints excluded: chain I residue 854 LYS Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain K residue 119 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 120 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 286 optimal weight: 1.9990 chunk 364 optimal weight: 9.9990 chunk 142 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 219 optimal weight: 0.0980 chunk 334 optimal weight: 1.9990 chunk 256 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 ASN A 82 ASN A 198 ASN A 267 ASN B 68 GLN B 217 ASN B 232 ASN B 295 ASN C 10 GLN C 48 GLN C 267 ASN C 290 ASN C 295 ASN D 267 ASN D 290 ASN E 8 GLN E 68 GLN E 198 ASN E 232 ASN E 242 GLN E 295 ASN F 20 HIS F 43 ASN ** G 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN I 35 HIS ** I 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 399 GLN ** I 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 893 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.137716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.117537 restraints weight = 47680.728| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.93 r_work: 0.3415 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 31399 Z= 0.255 Angle : 0.761 12.421 42781 Z= 0.373 Chirality : 0.055 0.681 4787 Planarity : 0.005 0.105 5308 Dihedral : 12.826 158.782 4857 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.91 % Allowed : 26.01 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.14), residues: 3639 helix: 1.00 (0.13), residues: 1600 sheet: -0.25 (0.22), residues: 477 loop : -0.87 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG I 846 TYR 0.042 0.002 TYR I 844 PHE 0.032 0.002 PHE B 151 TRP 0.013 0.002 TRP I 453 HIS 0.010 0.001 HIS I 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.26 (31399) covalent geometry : angle 0.76120 / 0.37 (42781) hydrogen bonds : bond 0.03947 / 2.57 ( 1385) hydrogen bonds : angle 4.55527 / 3.17 ( 3955) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1037 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 913 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8522 (ptm160) REVERT: A 87 SER cc_start: 0.8818 (t) cc_final: 0.8488 (p) REVERT: A 101 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7119 (mt-10) REVERT: A 148 ASN cc_start: 0.8345 (p0) cc_final: 0.8085 (p0) REVERT: A 209 GLU cc_start: 0.8254 (pt0) cc_final: 0.7970 (pt0) REVERT: A 210 SER cc_start: 0.8808 (m) cc_final: 0.8471 (p) REVERT: A 264 ASP cc_start: 0.8357 (t0) cc_final: 0.7838 (t70) REVERT: A 268 LYS cc_start: 0.8468 (mttp) cc_final: 0.8104 (mttp) REVERT: A 269 GLU cc_start: 0.7436 (mm-30) cc_final: 0.6980 (mm-30) REVERT: A 283 ASP cc_start: 0.7951 (m-30) cc_final: 0.7635 (m-30) REVERT: A 287 GLN cc_start: 0.8008 (tm-30) cc_final: 0.7762 (tm-30) REVERT: A 298 GLU cc_start: 0.8429 (tp30) cc_final: 0.8100 (tp30) REVERT: B 6 LYS cc_start: 0.9042 (ttmm) cc_final: 0.8831 (mttp) REVERT: B 48 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8328 (tt0) REVERT: B 51 LEU cc_start: 0.8960 (mt) cc_final: 0.8747 (mp) REVERT: B 54 LYS cc_start: 0.8503 (mtpp) cc_final: 0.8199 (mmmm) REVERT: B 72 GLU cc_start: 0.7776 (mp0) cc_final: 0.7478 (mp0) REVERT: B 90 LYS cc_start: 0.8715 (mmtp) cc_final: 0.8513 (mmtp) REVERT: B 109 ASP cc_start: 0.8101 (t0) cc_final: 0.7696 (t0) REVERT: B 123 GLU cc_start: 0.8076 (tp30) cc_final: 0.7619 (tp30) REVERT: B 226 ASP cc_start: 0.7829 (t0) cc_final: 0.7546 (t0) REVERT: B 268 LYS cc_start: 0.8820 (ttmm) cc_final: 0.8603 (mtpp) REVERT: B 283 ASP cc_start: 0.7783 (p0) cc_final: 0.7361 (p0) REVERT: C 32 SER cc_start: 0.8320 (m) cc_final: 0.7476 (p) REVERT: C 72 GLU cc_start: 0.7897 (mp0) cc_final: 0.7672 (mp0) REVERT: C 101 GLU cc_start: 0.7322 (tp30) cc_final: 0.7058 (tp30) REVERT: C 139 GLU cc_start: 0.8246 (mp0) cc_final: 0.7943 (mp0) REVERT: C 151 PHE cc_start: 0.8609 (m-80) cc_final: 0.8373 (m-80) REVERT: C 156 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7417 (mmm) REVERT: C 269 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7766 (mm-30) REVERT: C 283 ASP cc_start: 0.8124 (m-30) cc_final: 0.7852 (m-30) REVERT: C 316 GLU cc_start: 0.8243 (tt0) cc_final: 0.8007 (tt0) REVERT: D 66 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8333 (mtt90) REVERT: D 78 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7772 (tt0) REVERT: D 97 GLU cc_start: 0.7811 (tp30) cc_final: 0.7592 (tp30) REVERT: D 124 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8582 (tmm-80) REVERT: D 130 ASP cc_start: 0.7312 (t0) cc_final: 0.6630 (t0) REVERT: D 156 MET cc_start: 0.8567 (mtp) cc_final: 0.8187 (mtp) REVERT: D 242 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8306 (tm-30) REVERT: D 273 LYS cc_start: 0.8928 (mtmm) cc_final: 0.8585 (mttt) REVERT: D 283 ASP cc_start: 0.8070 (m-30) cc_final: 0.7774 (m-30) REVERT: E 8 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7134 (mp10) REVERT: E 45 THR cc_start: 0.8568 (t) cc_final: 0.8311 (m) REVERT: E 46 ARG cc_start: 0.8409 (mtp-110) cc_final: 0.7995 (mmm160) REVERT: E 72 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7625 (mt-10) REVERT: E 89 ASP cc_start: 0.8483 (p0) cc_final: 0.8234 (p0) REVERT: E 141 SER cc_start: 0.8596 (m) cc_final: 0.8215 (p) REVERT: E 182 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7805 (mm-30) REVERT: E 190 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7546 (pm20) REVERT: E 209 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7325 (mt-10) REVERT: E 231 SER cc_start: 0.8624 (OUTLIER) cc_final: 0.8365 (t) REVERT: E 241 ASP cc_start: 0.8003 (t0) cc_final: 0.7674 (t0) REVERT: E 249 LYS cc_start: 0.8196 (mmpt) cc_final: 0.7840 (mmpt) REVERT: E 256 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7685 (mm-30) REVERT: E 264 ASP cc_start: 0.8219 (t70) cc_final: 0.7970 (t0) REVERT: E 275 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7341 (mt-10) REVERT: E 286 LEU cc_start: 0.8807 (mm) cc_final: 0.8518 (mp) REVERT: E 288 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7509 (mt-10) REVERT: E 291 ASP cc_start: 0.7415 (p0) cc_final: 0.6997 (p0) REVERT: E 305 SER cc_start: 0.8820 (m) cc_final: 0.8262 (p) REVERT: E 308 GLN cc_start: 0.8105 (tp40) cc_final: 0.7667 (tp40) REVERT: E 312 ASP cc_start: 0.8134 (m-30) cc_final: 0.7741 (m-30) REVERT: F 56 ASP cc_start: 0.7830 (t0) cc_final: 0.7501 (t0) REVERT: F 89 ASP cc_start: 0.7738 (t0) cc_final: 0.7418 (t0) REVERT: F 94 ASN cc_start: 0.7453 (t0) cc_final: 0.7220 (t0) REVERT: F 128 TYR cc_start: 0.8705 (m-80) cc_final: 0.8167 (m-80) REVERT: F 205 TYR cc_start: 0.7267 (m-80) cc_final: 0.6732 (m-80) REVERT: F 247 LEU cc_start: 0.8159 (mp) cc_final: 0.7955 (mt) REVERT: F 267 ASN cc_start: 0.8032 (m-40) cc_final: 0.7814 (m-40) REVERT: F 287 GLN cc_start: 0.8299 (tt0) cc_final: 0.8077 (mm-40) REVERT: F 288 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7591 (tm-30) REVERT: F 298 GLU cc_start: 0.7763 (mp0) cc_final: 0.7471 (mp0) REVERT: F 313 TYR cc_start: 0.8753 (t80) cc_final: 0.8423 (t80) REVERT: G 8 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.7398 (mp-120) REVERT: G 58 LEU cc_start: 0.6317 (tt) cc_final: 0.6009 (tt) REVERT: G 68 GLN cc_start: 0.7474 (pp30) cc_final: 0.7208 (pp30) REVERT: G 70 THR cc_start: 0.7572 (OUTLIER) cc_final: 0.7361 (p) REVERT: G 72 GLU cc_start: 0.7692 (mp0) cc_final: 0.7303 (mp0) REVERT: G 83 LEU cc_start: 0.8546 (tp) cc_final: 0.8302 (tm) REVERT: G 106 GLN cc_start: 0.7752 (pm20) cc_final: 0.7473 (pm20) REVERT: G 140 GLN cc_start: 0.8548 (mm110) cc_final: 0.7604 (tm130) REVERT: G 216 LYS cc_start: 0.7576 (tppt) cc_final: 0.7265 (tppt) REVERT: G 223 VAL cc_start: 0.8420 (OUTLIER) cc_final: 0.8083 (m) REVERT: G 233 LEU cc_start: 0.8887 (tp) cc_final: 0.8579 (tm) REVERT: G 243 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8151 (mtm) REVERT: G 288 GLU cc_start: 0.8175 (tp30) cc_final: 0.7506 (tp30) REVERT: G 295 ASN cc_start: 0.7611 (t0) cc_final: 0.7073 (t0) REVERT: H 37 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8381 (mm) REVERT: H 65 ASP cc_start: 0.8190 (t0) cc_final: 0.7846 (t0) REVERT: H 86 GLN cc_start: 0.8471 (tt0) cc_final: 0.8186 (tt0) REVERT: H 95 ASN cc_start: 0.8664 (m-40) cc_final: 0.8382 (m-40) REVERT: H 122 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8228 (pt) REVERT: H 137 LEU cc_start: 0.8625 (tp) cc_final: 0.8362 (tt) REVERT: H 174 LYS cc_start: 0.8058 (ptpt) cc_final: 0.7732 (ptpt) REVERT: H 201 ASN cc_start: 0.8195 (m-40) cc_final: 0.7644 (m110) REVERT: H 205 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8226 (ttm) REVERT: H 227 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.8026 (p) REVERT: I 18 ASP cc_start: 0.7339 (p0) cc_final: 0.7090 (p0) REVERT: I 22 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.7888 (tp) REVERT: I 26 GLN cc_start: 0.8501 (mm-40) cc_final: 0.8012 (mt0) REVERT: I 35 HIS cc_start: 0.8689 (OUTLIER) cc_final: 0.7423 (m-70) REVERT: I 93 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8086 (tmm) REVERT: I 94 GLN cc_start: 0.8694 (mm110) cc_final: 0.8453 (mm-40) REVERT: I 112 ILE cc_start: 0.8776 (tp) cc_final: 0.8553 (tp) REVERT: I 147 ARG cc_start: 0.7862 (mtp85) cc_final: 0.7362 (mtp180) REVERT: I 150 PHE cc_start: 0.8826 (m-80) cc_final: 0.8367 (m-80) REVERT: I 152 GLU cc_start: 0.8079 (mp0) cc_final: 0.7779 (mp0) REVERT: I 216 SER cc_start: 0.8483 (m) cc_final: 0.8245 (t) REVERT: I 229 ARG cc_start: 0.7612 (ptm160) cc_final: 0.7294 (ptm160) REVERT: I 230 LEU cc_start: 0.8303 (mt) cc_final: 0.8080 (mp) REVERT: I 233 LEU cc_start: 0.8477 (mt) cc_final: 0.8125 (mt) REVERT: I 236 ARG cc_start: 0.8371 (ttm110) cc_final: 0.8127 (ttp-110) REVERT: I 295 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7862 (ttt180) REVERT: I 298 ILE cc_start: 0.8865 (pp) cc_final: 0.8631 (mt) REVERT: I 308 GLN cc_start: 0.8370 (mm-40) cc_final: 0.8048 (mm-40) REVERT: I 346 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8372 (pp) REVERT: I 349 GLN cc_start: 0.8426 (tm-30) cc_final: 0.7842 (tp-100) REVERT: I 351 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8732 (mm) REVERT: I 389 ASP cc_start: 0.7752 (m-30) cc_final: 0.7356 (m-30) REVERT: I 401 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7501 (mp0) REVERT: I 426 GLU cc_start: 0.8378 (tp30) cc_final: 0.8163 (tm-30) REVERT: I 460 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7812 (tp30) REVERT: I 488 GLN cc_start: 0.8615 (tp40) cc_final: 0.8070 (tm-30) REVERT: I 495 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.8016 (t0) REVERT: I 540 GLU cc_start: 0.8133 (pt0) cc_final: 0.7819 (pm20) REVERT: I 544 ASP cc_start: 0.8254 (t70) cc_final: 0.7957 (t0) REVERT: I 590 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8178 (tmtt) REVERT: I 595 GLN cc_start: 0.8336 (mm-40) cc_final: 0.8092 (mm-40) REVERT: I 606 VAL cc_start: 0.8325 (OUTLIER) cc_final: 0.8078 (t) REVERT: I 613 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7742 (mt-10) REVERT: I 632 LYS cc_start: 0.8355 (ttpt) cc_final: 0.8108 (ttpp) REVERT: I 642 THR cc_start: 0.8653 (m) cc_final: 0.8384 (p) REVERT: I 667 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7971 (mp0) REVERT: I 680 ARG cc_start: 0.8180 (mmp-170) cc_final: 0.7570 (mtp180) REVERT: I 681 GLU cc_start: 0.7903 (mp0) cc_final: 0.7602 (mp0) REVERT: I 721 ASP cc_start: 0.7764 (m-30) cc_final: 0.7377 (m-30) REVERT: I 723 ARG cc_start: 0.7805 (mtp85) cc_final: 0.7346 (mtp85) REVERT: I 774 ARG cc_start: 0.8671 (ttp-110) cc_final: 0.8261 (mtm110) REVERT: I 780 LYS cc_start: 0.8522 (mttp) cc_final: 0.8226 (mttp) REVERT: I 797 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7721 (mm-30) REVERT: I 827 ASN cc_start: 0.8044 (t0) cc_final: 0.7638 (t0) REVERT: I 829 VAL cc_start: 0.8921 (m) cc_final: 0.8616 (p) REVERT: I 832 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7977 (mt-10) REVERT: I 842 GLU cc_start: 0.8270 (tm-30) cc_final: 0.8029 (tp30) REVERT: I 870 GLU cc_start: 0.7813 (pp20) cc_final: 0.7516 (pp20) REVERT: I 871 GLN cc_start: 0.8333 (tp40) cc_final: 0.7814 (tm-30) REVERT: I 882 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7798 (mm-30) REVERT: I 907 ILE cc_start: 0.8478 (mp) cc_final: 0.8044 (mp) REVERT: I 921 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7710 (mt-10) REVERT: I 927 ILE cc_start: 0.8760 (tt) cc_final: 0.8463 (pt) REVERT: I 940 MET cc_start: 0.8371 (mmt) cc_final: 0.8092 (mmt) REVERT: I 969 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7686 (tm-30) REVERT: I 972 GLN cc_start: 0.7960 (tm-30) cc_final: 0.7475 (pp30) REVERT: J 5 LEU cc_start: 0.5920 (OUTLIER) cc_final: 0.4845 (pt) REVERT: J 14 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7558 (mm-30) REVERT: J 41 GLU cc_start: 0.7700 (tp30) cc_final: 0.6816 (tp30) REVERT: J 52 GLU cc_start: 0.7064 (tt0) cc_final: 0.6850 (tm-30) REVERT: J 53 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: J 54 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7477 (tm-30) outliers start: 124 outliers final: 77 residues processed: 970 average time/residue: 0.7579 time to fit residues: 853.3490 Evaluate side-chains 1001 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 895 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 8 GLN Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 124 ARG Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 243 MET Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 281 HIS Chi-restraints excluded: chain G residue 284 THR Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 144 LYS Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 196 GLN Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 295 ARG Chi-restraints excluded: chain I residue 346 ILE Chi-restraints excluded: chain I residue 351 ILE Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain I residue 368 GLU Chi-restraints excluded: chain I residue 411 GLU Chi-restraints excluded: chain I residue 415 LYS Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 461 PHE Chi-restraints excluded: chain I residue 479 PHE Chi-restraints excluded: chain I residue 495 ASP Chi-restraints excluded: chain I residue 536 GLU Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 590 LYS Chi-restraints excluded: chain I residue 606 VAL Chi-restraints excluded: chain I residue 689 VAL Chi-restraints excluded: chain I residue 750 THR Chi-restraints excluded: chain I residue 854 LYS Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain K residue 119 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 264 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 272 optimal weight: 0.3980 chunk 282 optimal weight: 0.1980 chunk 0 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 279 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 273 optimal weight: 0.6980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 ASN A 82 ASN A 198 ASN A 217 ASN A 267 ASN B 43 ASN B 68 GLN B 217 ASN B 232 ASN B 295 ASN C 10 GLN C 267 ASN C 290 ASN C 295 ASN D 10 GLN D 267 ASN D 290 ASN E 198 ASN E 217 ASN E 232 ASN E 267 ASN E 295 ASN F 8 GLN F 20 HIS F 43 ASN ** G 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN H 34 ASN H 119 ASN I 35 HIS ** I 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.138577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.118372 restraints weight = 47872.317| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.94 r_work: 0.3428 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 31399 Z= 0.192 Angle : 0.744 11.065 42781 Z= 0.364 Chirality : 0.053 0.645 4787 Planarity : 0.005 0.144 5308 Dihedral : 12.827 158.216 4857 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.82 % Allowed : 26.42 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.14), residues: 3639 helix: 1.01 (0.13), residues: 1600 sheet: -0.35 (0.22), residues: 489 loop : -0.86 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 236 TYR 0.038 0.002 TYR I 844 PHE 0.029 0.002 PHE I 36 TRP 0.014 0.002 TRP I 453 HIS 0.010 0.001 HIS I 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (31399) covalent geometry : angle 0.74398 / 0.36 (42781) hydrogen bonds : bond 0.03810 / 2.49 ( 1385) hydrogen bonds : angle 4.51829 / 3.15 ( 3955) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17584.91 seconds wall clock time: 298 minutes 56.55 seconds (17936.55 seconds total)