Starting phenix.real_space_refine on Sun Jul 5 20:00:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e85_47707/07_2026/9e85_47707.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e85_47707/07_2026/9e85_47707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e85_47707/07_2026/9e85_47707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e85_47707/07_2026/9e85_47707.map" model { file = "/net/cci-nas-00/data/ceres_data/9e85_47707/07_2026/9e85_47707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e85_47707/07_2026/9e85_47707.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.103 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 103 5.49 5 Mg 1 5.21 5 S 98 5.16 5 C 18042 2.51 5 N 5224 2.21 5 O 5828 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29298 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1716 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 210} Chain: "B" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1756 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 220} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 8604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1110, 8604 Classifications: {'peptide': 1110} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1047} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 9884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1265, 9884 Classifications: {'peptide': 1265} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 3, 'PTRANS': 57, 'TRANS': 1204} Chain breaks: 2 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 645 Classifications: {'peptide': 82} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 75} Chain: "F" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2494 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 8, 'TRANS': 307} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "J" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 870 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 99} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "M" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1241 Classifications: {'peptide': 159} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 153} Chain: "N" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 987 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain breaks: 1 Chain: "R" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 133 Classifications: {'RNA': 6} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 1} Link IDs: {'rna3p': 5} Chain: "T" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 955 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Chain breaks: 1 Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'POP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12562 SG CYS D 60 78.803 58.723 57.470 1.00106.98 S ATOM 12580 SG CYS D 62 77.311 58.620 54.414 1.00105.74 S ATOM 12689 SG CYS D 75 81.026 58.393 54.632 1.00108.48 S ATOM 12715 SG CYS D 78 79.091 61.654 55.465 1.00 96.18 S ATOM 19131 SG CYS D 891 109.674 95.831 103.726 1.00 82.25 S ATOM 19698 SG CYS D 968 106.345 96.634 102.872 1.00 87.44 S ATOM 19740 SG CYS D 975 107.272 94.069 105.333 1.00 67.60 S ATOM 19758 SG CYS D 978 107.893 97.526 106.170 1.00 81.52 S Time building chain proxies: 5.27, per 1000 atoms: 0.18 Number of scatterers: 29298 At special positions: 0 Unit cell: (133.424, 163.552, 185.072, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 98 16.00 P 103 15.00 Mg 1 11.99 O 5828 8.00 N 5224 7.00 C 18042 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: 2.30 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 75 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 975 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 968 " Number of angles added : 12 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6452 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 46 sheets defined 43.7% alpha, 14.7% beta 41 base pairs and 70 stacking pairs defined. Time for finding SS restraints: 3.44 Creating SS restraints... Processing helix chain 'A' and resid 29 through 46 removed outlier: 4.293A pdb=" N THR A 33 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER A 44 " --> pdb=" O ARG A 40 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 82 removed outlier: 3.622A pdb=" N SER A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 203 through 225 removed outlier: 3.740A pdb=" N LEU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 44 removed outlier: 4.311A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 203 through 226 removed outlier: 3.526A pdb=" N LEU B 218 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASN B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.042A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 77 removed outlier: 3.693A pdb=" N ARG C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 225 through 229 removed outlier: 3.819A pdb=" N ARG C 228 " --> pdb=" O ARG C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 244 through 252 Processing helix chain 'C' and resid 255 through 266 removed outlier: 3.610A pdb=" N ARG C 259 " --> pdb=" O SER C 255 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASN C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 289 through 301 removed outlier: 3.903A pdb=" N LEU C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 380 through 406 removed outlier: 3.837A pdb=" N THR C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 444 through 452 Processing helix chain 'C' and resid 476 through 480 Processing helix chain 'C' and resid 532 through 538 Processing helix chain 'C' and resid 590 through 594 removed outlier: 3.533A pdb=" N ILE C 594 " --> pdb=" O THR C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 613 removed outlier: 3.965A pdb=" N ARG C 613 " --> pdb=" O ALA C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 639 removed outlier: 4.323A pdb=" N ARG C 633 " --> pdb=" O GLY C 629 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY C 639 " --> pdb=" O ALA C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 815 through 826 Processing helix chain 'C' and resid 918 through 920 No H-bonds generated for 'chain 'C' and resid 918 through 920' Processing helix chain 'C' and resid 921 through 926 removed outlier: 3.749A pdb=" N ARG C 925 " --> pdb=" O GLY C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 953 through 957 removed outlier: 3.531A pdb=" N ALA C 957 " --> pdb=" O ASP C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 991 Processing helix chain 'C' and resid 1036 through 1041 Processing helix chain 'C' and resid 1069 through 1080 Processing helix chain 'C' and resid 1081 through 1091 removed outlier: 3.583A pdb=" N LEU C1085 " --> pdb=" O ALA C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1097 through 1109 Processing helix chain 'C' and resid 1118 through 1131 removed outlier: 3.787A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 84 through 90 removed outlier: 3.536A pdb=" N VAL D 87 " --> pdb=" O ARG D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 107 Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 140 through 147 Processing helix chain 'D' and resid 149 through 187 Processing helix chain 'D' and resid 190 through 228 removed outlier: 3.640A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG D 195 " --> pdb=" O ALA D 191 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE D 222 " --> pdb=" O ARG D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 removed outlier: 3.650A pdb=" N TYR D 241 " --> pdb=" O ASP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 269 through 284 Processing helix chain 'D' and resid 286 through 300 removed outlier: 3.978A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 305 Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.953A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 340 through 361 Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 484 through 491 Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 560 through 564 Processing helix chain 'D' and resid 579 through 590 Processing helix chain 'D' and resid 614 through 624 Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 667 through 675 Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 728 removed outlier: 4.176A pdb=" N GLY D 728 " --> pdb=" O ALA D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 762 removed outlier: 3.724A pdb=" N ARG D 752 " --> pdb=" O HIS D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 793 Processing helix chain 'D' and resid 797 through 805 Processing helix chain 'D' and resid 810 through 818 removed outlier: 3.660A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 881 removed outlier: 3.789A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA D 856 " --> pdb=" O ASN D 852 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA D 864 " --> pdb=" O LEU D 860 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER D 881 " --> pdb=" O LEU D 877 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 964 through 968 Processing helix chain 'D' and resid 976 through 980 Processing helix chain 'D' and resid 994 through 1005 Processing helix chain 'D' and resid 1027 through 1036 Processing helix chain 'D' and resid 1117 through 1146 removed outlier: 3.605A pdb=" N VAL D1121 " --> pdb=" O ASP D1117 " (cutoff:3.500A) Proline residue: D1127 - end of helix removed outlier: 3.760A pdb=" N VAL D1130 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY D1146 " --> pdb=" O TYR D1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1162 removed outlier: 4.222A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1195 removed outlier: 4.291A pdb=" N ALA D1195 " --> pdb=" O ARG D1191 " (cutoff:3.500A) Processing helix chain 'D' and resid 1209 through 1216 Processing helix chain 'D' and resid 1219 through 1227 Processing helix chain 'D' and resid 1228 through 1240 Processing helix chain 'D' and resid 1247 through 1254 removed outlier: 3.692A pdb=" N ASN D1251 " --> pdb=" O GLY D1247 " (cutoff:3.500A) Processing helix chain 'D' and resid 1260 through 1263 Processing helix chain 'D' and resid 1264 through 1269 removed outlier: 4.149A pdb=" N ASN D1269 " --> pdb=" O ASN D1265 " (cutoff:3.500A) Processing helix chain 'D' and resid 1275 through 1282 Processing helix chain 'E' and resid 33 through 37 removed outlier: 3.919A pdb=" N THR E 36 " --> pdb=" O LEU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 49 through 70 Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'F' and resid 211 through 221 Processing helix chain 'F' and resid 226 through 236 removed outlier: 3.805A pdb=" N GLY F 236 " --> pdb=" O LEU F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 267 Processing helix chain 'F' and resid 274 through 308 removed outlier: 4.754A pdb=" N ARG F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LEU F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 316 through 334 removed outlier: 3.546A pdb=" N LEU F 320 " --> pdb=" O ALA F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 362 removed outlier: 3.662A pdb=" N TYR F 346 " --> pdb=" O LYS F 342 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TRP F 349 " --> pdb=" O THR F 345 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TRP F 350 " --> pdb=" O TYR F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 391 Processing helix chain 'F' and resid 395 through 404 removed outlier: 3.635A pdb=" N LEU F 399 " --> pdb=" O THR F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 417 removed outlier: 3.721A pdb=" N ALA F 417 " --> pdb=" O ILE F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 439 Processing helix chain 'F' and resid 448 through 467 removed outlier: 3.719A pdb=" N LEU F 467 " --> pdb=" O VAL F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 468 through 480 Processing helix chain 'F' and resid 488 through 496 removed outlier: 3.641A pdb=" N ILE F 492 " --> pdb=" O THR F 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 516 removed outlier: 3.909A pdb=" N ILE F 503 " --> pdb=" O THR F 499 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS F 516 " --> pdb=" O SER F 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 517 through 520 removed outlier: 3.518A pdb=" N SER F 520 " --> pdb=" O PRO F 517 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 517 through 520' Processing helix chain 'J' and resid 80 through 87 Processing helix chain 'J' and resid 90 through 110 removed outlier: 3.537A pdb=" N LEU J 94 " --> pdb=" O SER J 90 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 57 Processing helix chain 'M' and resid 63 through 75 removed outlier: 3.534A pdb=" N LEU M 67 " --> pdb=" O GLY M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 99 removed outlier: 3.874A pdb=" N GLY M 99 " --> pdb=" O LYS M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 119 Processing helix chain 'M' and resid 121 through 143 Processing helix chain 'M' and resid 146 through 158 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 5.520A pdb=" N GLN A 20 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL A 196 " --> pdb=" O GLN A 20 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL A 22 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU A 194 " --> pdb=" O VAL A 22 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU A 24 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU A 192 " --> pdb=" O GLU A 24 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP A 190 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.416A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 54 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 removed outlier: 6.630A pdb=" N GLY A 103 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N THR A 127 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL A 105 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 15 removed outlier: 6.796A pdb=" N ARG B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 100 removed outlier: 7.590A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 removed outlier: 4.156A pdb=" N GLY B 103 " --> pdb=" O LEU B 128 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB2, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.407A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 96 through 97 removed outlier: 5.426A pdb=" N LEU C 105 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE C 140 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N PHE C 107 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLU C 138 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ASP C 109 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR C 136 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY C 155 " --> pdb=" O LEU C 133 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 96 through 97 removed outlier: 5.426A pdb=" N LEU C 105 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE C 140 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N PHE C 107 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLU C 138 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ASP C 109 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR C 136 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN C 150 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE C 147 " --> pdb=" O ARG M 47 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU M 44 " --> pdb=" O VAL M 39 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N TYR M 34 " --> pdb=" O ILE M 22 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ILE M 22 " --> pdb=" O TYR M 34 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL M 36 " --> pdb=" O GLU M 20 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 160 through 161 removed outlier: 3.667A pdb=" N THR C 165 " --> pdb=" O THR C 161 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 376 through 379 removed outlier: 6.628A pdb=" N SER C 177 " --> pdb=" O SER C 456 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 184 through 191 Processing sheet with id=AB8, first strand: chain 'C' and resid 215 through 216 Processing sheet with id=AB9, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AC1, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AC2, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AC3, first strand: chain 'C' and resid 541 through 542 removed outlier: 5.024A pdb=" N VAL C 561 " --> pdb=" O GLU C 569 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLU C 569 " --> pdb=" O VAL C 561 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.795A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 667 through 671 removed outlier: 3.509A pdb=" N TYR C 657 " --> pdb=" O SER C 654 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N MET C 661 " --> pdb=" O ILE C 650 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ILE C 650 " --> pdb=" O MET C 661 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC7, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 7.733A pdb=" N LEU C 737 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE C 898 " --> pdb=" O LEU C 737 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N ILE C 915 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU C 720 " --> pdb=" O ILE C 915 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 765 through 766 removed outlier: 6.454A pdb=" N ASP C 761 " --> pdb=" O VAL C 865 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL C 865 " --> pdb=" O ASP C 761 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AD1, first strand: chain 'C' and resid 784 through 785 removed outlier: 5.268A pdb=" N ILE C 789 " --> pdb=" O ASP C 785 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 801 through 803 removed outlier: 6.775A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 944 through 945 Processing sheet with id=AD4, first strand: chain 'C' and resid 1066 through 1068 removed outlier: 3.652A pdb=" N GLN C1066 " --> pdb=" O VAL D 422 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL D 422 " --> pdb=" O GLN C1066 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1133 through 1136 Processing sheet with id=AD6, first strand: chain 'D' and resid 73 through 74 removed outlier: 4.262A pdb=" N ILE D 73 " --> pdb=" O VAL D 82 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 93 through 102 removed outlier: 10.185A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.456A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 234 through 235 removed outlier: 6.711A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 328 through 329 Processing sheet with id=AE1, first strand: chain 'D' and resid 440 through 444 Processing sheet with id=AE2, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AE3, first strand: chain 'D' and resid 822 through 825 removed outlier: 10.028A pdb=" N GLY D 822 " --> pdb=" O ARG D 834 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ARG D 834 " --> pdb=" O GLY D 822 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL D 824 " --> pdb=" O ILE D 832 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 886 through 888 Processing sheet with id=AE5, first strand: chain 'D' and resid 897 through 899 removed outlier: 4.353A pdb=" N THR D 924 " --> pdb=" O ARG D 963 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 903 through 904 Processing sheet with id=AE7, first strand: chain 'D' and resid 1064 through 1068 removed outlier: 3.584A pdb=" N GLY D1051 " --> pdb=" O VAL D1105 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1180 through 1182 removed outlier: 4.856A pdb=" N ARG D1164 " --> pdb=" O VAL D1206 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL D1206 " --> pdb=" O ARG D1164 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1271 through 1274 Processing sheet with id=AF1, first strand: chain 'J' and resid 39 through 45 removed outlier: 3.770A pdb=" N PHE J 44 " --> pdb=" O GLN J 28 " (cutoff:3.500A) 1260 hydrogen bonds defined for protein. 3573 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 102 hydrogen bonds 204 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 70 stacking parallelities Total time for adding SS restraints: 7.94 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9842 1.35 - 1.49: 7264 1.49 - 1.62: 12711 1.62 - 1.76: 0 1.76 - 1.89: 173 Bond restraints: 29990 Sorted by residual: bond pdb=" C1' DT N 31 " pdb=" N1 DT N 31 " ideal model delta sigma weight residual 1.468 1.530 -0.062 1.40e-02 5.10e+03 1.94e+01 bond pdb=" SD MET D 143 " pdb=" CE MET D 143 " ideal model delta sigma weight residual 1.791 1.890 -0.099 2.50e-02 1.60e+03 1.58e+01 bond pdb=" C1' DT N 60 " pdb=" N1 DT N 60 " ideal model delta sigma weight residual 1.468 1.523 -0.055 1.40e-02 5.10e+03 1.54e+01 bond pdb=" C1' DC N 35 " pdb=" N1 DC N 35 " ideal model delta sigma weight residual 1.468 1.515 -0.047 1.40e-02 5.10e+03 1.11e+01 bond pdb=" C1' DT T 42 " pdb=" N1 DT T 42 " ideal model delta sigma weight residual 1.468 1.514 -0.046 1.40e-02 5.10e+03 1.10e+01 ... (remaining 29985 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.79: 40898 3.79 - 7.59: 143 7.59 - 11.38: 3 11.38 - 15.17: 0 15.17 - 18.96: 1 Bond angle restraints: 41045 Sorted by residual: angle pdb=" P1 POP C2000 " pdb=" O POP C2000 " pdb=" P2 POP C2000 " ideal model delta sigma weight residual 139.66 120.70 18.96 3.00e+00 1.11e-01 4.00e+01 angle pdb=" CA PRO J 77 " pdb=" N PRO J 77 " pdb=" CD PRO J 77 " ideal model delta sigma weight residual 112.00 103.43 8.57 1.40e+00 5.10e-01 3.74e+01 angle pdb=" N3 DT N 31 " pdb=" C4 DT N 31 " pdb=" O4 DT N 31 " ideal model delta sigma weight residual 119.90 123.13 -3.23 6.00e-01 2.78e+00 2.90e+01 angle pdb=" N2 G R 6 " pdb=" C2 G R 6 " pdb=" N3 G R 6 " ideal model delta sigma weight residual 119.90 116.29 3.61 7.00e-01 2.04e+00 2.65e+01 angle pdb=" C PRO M 12 " pdb=" N HIS M 13 " pdb=" CA HIS M 13 " ideal model delta sigma weight residual 121.70 130.64 -8.94 1.80e+00 3.09e-01 2.47e+01 ... (remaining 41040 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.65: 17128 33.65 - 67.31: 935 67.31 - 100.96: 51 100.96 - 134.62: 0 134.62 - 168.27: 1 Dihedral angle restraints: 18115 sinusoidal: 8089 harmonic: 10026 Sorted by residual: dihedral pdb=" CA ASP D1070 " pdb=" C ASP D1070 " pdb=" N GLY D1071 " pdb=" CA GLY D1071 " ideal model delta harmonic sigma weight residual -180.00 -119.25 -60.75 0 5.00e+00 4.00e-02 1.48e+02 dihedral pdb=" CA GLY D 519 " pdb=" C GLY D 519 " pdb=" N LYS D 520 " pdb=" CA LYS D 520 " ideal model delta harmonic sigma weight residual 180.00 150.04 29.96 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA LYS J 76 " pdb=" C LYS J 76 " pdb=" N PRO J 77 " pdb=" CA PRO J 77 " ideal model delta harmonic sigma weight residual -180.00 -151.68 -28.32 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 18112 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 4194 0.076 - 0.153: 471 0.153 - 0.229: 15 0.229 - 0.306: 0 0.306 - 0.382: 1 Chirality restraints: 4681 Sorted by residual: chirality pdb=" CB VAL C 540 " pdb=" CA VAL C 540 " pdb=" CG1 VAL C 540 " pdb=" CG2 VAL C 540 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" C3' DT T 25 " pdb=" C4' DT T 25 " pdb=" O3' DT T 25 " pdb=" C2' DT T 25 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" C3' DC T 20 " pdb=" C4' DC T 20 " pdb=" O3' DC T 20 " pdb=" C2' DC T 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.95e-01 ... (remaining 4678 not shown) Planarity restraints: 5040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS J 76 " -0.093 5.00e-02 4.00e+02 1.35e-01 2.93e+01 pdb=" N PRO J 77 " 0.234 5.00e-02 4.00e+02 pdb=" CA PRO J 77 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO J 77 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG D1231 " 0.347 9.50e-02 1.11e+02 1.55e-01 1.48e+01 pdb=" NE ARG D1231 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG D1231 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG D1231 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D1231 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 69 " 0.333 9.50e-02 1.11e+02 1.49e-01 1.36e+01 pdb=" NE ARG D 69 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG D 69 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG D 69 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 69 " 0.012 2.00e-02 2.50e+03 ... (remaining 5037 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 230 2.53 - 3.12: 23111 3.12 - 3.71: 46253 3.71 - 4.31: 64310 4.31 - 4.90: 107618 Nonbonded interactions: 241522 Sorted by model distance: nonbonded pdb=" O3' A R 5 " pdb="MG MG D2002 " model vdw 1.937 2.170 nonbonded pdb=" OG SER C1050 " pdb=" O THR C1053 " model vdw 1.983 3.040 nonbonded pdb=" OD1 ASP D 539 " pdb=" O2' A R 5 " model vdw 1.998 3.040 nonbonded pdb=" OG SER J 90 " pdb=" OE1 GLU J 92 " model vdw 2.007 3.040 nonbonded pdb=" OG SER B 203 " pdb=" OD1 ASP B 206 " model vdw 2.013 3.040 ... (remaining 241517 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' and (resid 2 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 through 226)) \ selection = (chain 'B' and resid 2 through 226) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.520 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 33.490 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 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 : 0.006 0.349 29998 Z= 0.291 Angle : 0.738 18.963 41057 Z= 0.460 Chirality : 0.047 0.382 4681 Planarity : 0.007 0.155 5040 Dihedral : 18.307 168.269 11663 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.41 % Favored : 93.50 % Rotamer: Outliers : 0.27 % Allowed : 15.94 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.03 % 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: -0.82 (0.14), residues: 3477 helix: 0.80 (0.14), residues: 1372 sheet: -1.29 (0.25), residues: 410 loop : -1.50 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 398 TYR 0.022 0.002 TYR E 56 PHE 0.024 0.002 PHE C 252 TRP 0.012 0.001 TRP M 112 HIS 0.006 0.001 HIS B 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.27 (29990) covalent geometry : angle 0.73841 / 0.46 (41045) hydrogen bonds : bond 0.14188 / 9.63 ( 1356) hydrogen bonds : angle 6.22528 / 4.37 ( 3777) metal coordination : bond 0.19125 / 12.05 ( 8) metal coordination : angle 0.08247 / 0.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 727 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.8142 (tptm) cc_final: 0.7870 (mmtt) REVERT: A 133 LYS cc_start: 0.8828 (pttt) cc_final: 0.8582 (ptmm) REVERT: A 205 ARG cc_start: 0.7856 (ptm-80) cc_final: 0.7445 (ttt90) REVERT: B 3 ILE cc_start: 0.8378 (tt) cc_final: 0.8102 (tt) REVERT: B 24 GLU cc_start: 0.8176 (pt0) cc_final: 0.7880 (pt0) REVERT: B 27 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7393 (mp0) REVERT: B 57 ASP cc_start: 0.8145 (m-30) cc_final: 0.7822 (m-30) REVERT: B 91 GLU cc_start: 0.8075 (pm20) cc_final: 0.7361 (pm20) REVERT: B 109 ASP cc_start: 0.8073 (m-30) cc_final: 0.7632 (m-30) REVERT: B 168 TYR cc_start: 0.9160 (m-80) cc_final: 0.8913 (m-80) REVERT: B 169 SER cc_start: 0.9371 (t) cc_final: 0.9026 (p) REVERT: C 111 ARG cc_start: 0.7681 (ptt90) cc_final: 0.7154 (ptp90) REVERT: C 140 ILE cc_start: 0.7971 (mt) cc_final: 0.7749 (mt) REVERT: C 163 LYS cc_start: 0.8571 (mttm) cc_final: 0.8207 (mtmt) REVERT: C 200 HIS cc_start: 0.8535 (m-70) cc_final: 0.8120 (m-70) REVERT: C 398 ARG cc_start: 0.7199 (ttm110) cc_final: 0.6944 (ttp80) REVERT: C 415 GLN cc_start: 0.7829 (tt0) cc_final: 0.7415 (tt0) REVERT: C 429 GLU cc_start: 0.7961 (pt0) cc_final: 0.7569 (pt0) REVERT: C 490 GLU cc_start: 0.7792 (pt0) cc_final: 0.7254 (pm20) REVERT: C 673 ARG cc_start: 0.8025 (ttp80) cc_final: 0.7795 (ttp-110) REVERT: C 694 ASP cc_start: 0.7603 (m-30) cc_final: 0.7323 (m-30) REVERT: C 748 THR cc_start: 0.9318 (OUTLIER) cc_final: 0.8993 (m) REVERT: C 753 GLU cc_start: 0.8375 (tp30) cc_final: 0.8028 (tp30) REVERT: C 756 GLU cc_start: 0.7714 (tt0) cc_final: 0.7510 (tt0) REVERT: C 797 ARG cc_start: 0.8286 (ttp80) cc_final: 0.8064 (ptm-80) REVERT: C 967 GLN cc_start: 0.7673 (mm110) cc_final: 0.7422 (mm110) REVERT: C 1028 MET cc_start: 0.8857 (ttm) cc_final: 0.8574 (ttp) REVERT: C 1097 VAL cc_start: 0.8877 (t) cc_final: 0.8517 (m) REVERT: D 8 ASP cc_start: 0.7940 (m-30) cc_final: 0.7588 (m-30) REVERT: D 56 ARG cc_start: 0.7867 (ttm-80) cc_final: 0.7609 (ttm-80) REVERT: D 66 LYS cc_start: 0.7466 (mtpt) cc_final: 0.6949 (mttm) REVERT: D 238 GLU cc_start: 0.8173 (pp20) cc_final: 0.7826 (tm-30) REVERT: D 243 GLU cc_start: 0.7233 (tp30) cc_final: 0.6874 (tp30) REVERT: D 400 LYS cc_start: 0.8139 (tppt) cc_final: 0.7933 (tttt) REVERT: D 470 LYS cc_start: 0.8203 (mtpt) cc_final: 0.7755 (mttm) REVERT: D 478 ARG cc_start: 0.7905 (mtm180) cc_final: 0.7684 (mtp-110) REVERT: D 566 LEU cc_start: 0.9147 (mt) cc_final: 0.8927 (mt) REVERT: D 688 MET cc_start: 0.9242 (mmt) cc_final: 0.9032 (mmt) REVERT: D 714 ASP cc_start: 0.8660 (t0) cc_final: 0.8387 (m-30) REVERT: D 772 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7617 (mm-30) REVERT: D 1109 GLN cc_start: 0.8520 (tp40) cc_final: 0.8267 (tp-100) REVERT: D 1112 MET cc_start: 0.7435 (mmt) cc_final: 0.7040 (tpp) REVERT: D 1129 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7468 (mp0) REVERT: D 1140 GLU cc_start: 0.8116 (tt0) cc_final: 0.7902 (tt0) REVERT: D 1167 ILE cc_start: 0.8236 (mm) cc_final: 0.8023 (mm) REVERT: E 103 LEU cc_start: 0.8910 (mt) cc_final: 0.8656 (mt) REVERT: F 218 ASP cc_start: 0.8485 (t0) cc_final: 0.8186 (m-30) REVERT: F 229 ARG cc_start: 0.7540 (ttm170) cc_final: 0.7060 (tpp-160) REVERT: F 282 MET cc_start: 0.8466 (mmp) cc_final: 0.7840 (mmp) REVERT: F 285 CYS cc_start: 0.8136 (p) cc_final: 0.7802 (p) REVERT: F 330 ARG cc_start: 0.8222 (tpp-160) cc_final: 0.7928 (tpp-160) REVERT: F 434 GLN cc_start: 0.7336 (mt0) cc_final: 0.6775 (mt0) REVERT: J 17 GLU cc_start: 0.6845 (tt0) cc_final: 0.6477 (mp0) REVERT: J 64 LEU cc_start: 0.8883 (tp) cc_final: 0.8612 (tp) REVERT: M 94 GLU cc_start: 0.8399 (tm-30) cc_final: 0.7988 (tm-30) REVERT: M 109 ARG cc_start: 0.8222 (ttp80) cc_final: 0.7966 (ttp80) outliers start: 8 outliers final: 3 residues processed: 732 average time/residue: 0.2042 time to fit residues: 228.2299 Evaluate side-chains 562 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 558 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain J residue 5 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.0980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 0.4980 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN A 200 ASN B 119 HIS ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 539 HIS C 679 ASN D 307 ASN D 396 ASN D 689 HIS D 787 GLN D1104 HIS F 505 GLN M 13 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.185128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.123902 restraints weight = 32656.729| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.21 r_work: 0.3091 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2928 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2928 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29998 Z= 0.183 Angle : 0.708 12.607 41057 Z= 0.371 Chirality : 0.047 0.327 4681 Planarity : 0.006 0.099 5040 Dihedral : 15.780 178.526 4983 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.07 % Favored : 93.82 % Rotamer: Outliers : 2.70 % Allowed : 17.17 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.03 % 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: -0.60 (0.14), residues: 3477 helix: 0.88 (0.14), residues: 1408 sheet: -0.93 (0.26), residues: 397 loop : -1.38 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 502 TYR 0.020 0.002 TYR D 749 PHE 0.017 0.002 PHE C 252 TRP 0.023 0.002 TRP J 82 HIS 0.009 0.001 HIS C 539 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (29990) covalent geometry : angle 0.70152 / 0.37 (41045) hydrogen bonds : bond 0.05176 / 3.56 ( 1356) hydrogen bonds : angle 5.02099 / 3.56 ( 3777) metal coordination : bond 0.01516 / 0.85 ( 8) metal coordination : angle 5.60460 / 2.85 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 576 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASP cc_start: 0.8637 (p0) cc_final: 0.8426 (p0) REVERT: A 98 ARG cc_start: 0.7912 (mtp180) cc_final: 0.7471 (mtp-110) REVERT: A 131 LYS cc_start: 0.8738 (mtmm) cc_final: 0.8476 (mtmm) REVERT: A 133 LYS cc_start: 0.8862 (pttt) cc_final: 0.8546 (ptmm) REVERT: A 188 ASP cc_start: 0.7097 (OUTLIER) cc_final: 0.6718 (m-30) REVERT: A 205 ARG cc_start: 0.7654 (ptm-80) cc_final: 0.7147 (ttt90) REVERT: A 223 ARG cc_start: 0.7097 (tmm160) cc_final: 0.6597 (tmm160) REVERT: B 3 ILE cc_start: 0.8282 (tt) cc_final: 0.8011 (tt) REVERT: B 27 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7239 (mp0) REVERT: B 57 ASP cc_start: 0.8265 (m-30) cc_final: 0.7898 (m-30) REVERT: B 169 SER cc_start: 0.9498 (t) cc_final: 0.8993 (p) REVERT: B 232 ILE cc_start: 0.8671 (mm) cc_final: 0.8286 (mt) REVERT: C 111 ARG cc_start: 0.7684 (ptt90) cc_final: 0.6925 (ptp90) REVERT: C 228 ARG cc_start: 0.7444 (mtt90) cc_final: 0.7023 (mtt-85) REVERT: C 398 ARG cc_start: 0.7150 (ttm110) cc_final: 0.6619 (ttp80) REVERT: C 415 GLN cc_start: 0.7847 (tt0) cc_final: 0.7339 (tt0) REVERT: C 429 GLU cc_start: 0.8426 (pt0) cc_final: 0.8118 (pt0) REVERT: C 465 ARG cc_start: 0.7922 (mtm180) cc_final: 0.7659 (mtt90) REVERT: C 488 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8317 (m) REVERT: C 620 ARG cc_start: 0.8530 (mmm160) cc_final: 0.8132 (mmt180) REVERT: C 622 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7792 (tt0) REVERT: C 646 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7642 (tm-30) REVERT: C 673 ARG cc_start: 0.8212 (ttp80) cc_final: 0.7932 (ttp-110) REVERT: C 694 ASP cc_start: 0.7523 (m-30) cc_final: 0.7167 (m-30) REVERT: C 753 GLU cc_start: 0.8383 (tp30) cc_final: 0.7910 (mm-30) REVERT: C 841 HIS cc_start: 0.8455 (t-170) cc_final: 0.8107 (m-70) REVERT: C 866 ASN cc_start: 0.7586 (m-40) cc_final: 0.7243 (m-40) REVERT: C 1015 SER cc_start: 0.9255 (m) cc_final: 0.8823 (p) REVERT: D 8 ASP cc_start: 0.8149 (m-30) cc_final: 0.7788 (m-30) REVERT: D 40 LYS cc_start: 0.8293 (mtpt) cc_final: 0.8071 (tttm) REVERT: D 56 ARG cc_start: 0.7903 (ttm-80) cc_final: 0.7687 (ttm-80) REVERT: D 66 LYS cc_start: 0.7451 (mtpt) cc_final: 0.6963 (mttm) REVERT: D 238 GLU cc_start: 0.8206 (pp20) cc_final: 0.7807 (tm-30) REVERT: D 259 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7729 (pt0) REVERT: D 310 MET cc_start: 0.8857 (mmm) cc_final: 0.8335 (mmm) REVERT: D 470 LYS cc_start: 0.8020 (mtpt) cc_final: 0.7679 (mttm) REVERT: D 566 LEU cc_start: 0.9148 (mt) cc_final: 0.8932 (mt) REVERT: D 762 ARG cc_start: 0.7364 (ptp90) cc_final: 0.7029 (ptp-170) REVERT: D 776 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7602 (mm-30) REVERT: D 946 ASP cc_start: 0.8156 (t0) cc_final: 0.7891 (t0) REVERT: D 948 GLU cc_start: 0.7821 (mp0) cc_final: 0.7512 (mp0) REVERT: D 1109 GLN cc_start: 0.8600 (tp40) cc_final: 0.8340 (tp-100) REVERT: D 1112 MET cc_start: 0.7668 (mmt) cc_final: 0.7440 (mmm) REVERT: D 1167 ILE cc_start: 0.8032 (mm) cc_final: 0.7805 (mm) REVERT: F 217 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.8017 (mmmm) REVERT: F 218 ASP cc_start: 0.8619 (t0) cc_final: 0.8157 (m-30) REVERT: F 229 ARG cc_start: 0.7520 (ttm170) cc_final: 0.6816 (tpp-160) REVERT: F 253 ILE cc_start: 0.8814 (mt) cc_final: 0.8602 (mm) REVERT: F 257 LEU cc_start: 0.8932 (mp) cc_final: 0.8646 (mp) REVERT: F 263 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.8473 (mtp) REVERT: F 282 MET cc_start: 0.8293 (mmp) cc_final: 0.7563 (mmp) REVERT: F 285 CYS cc_start: 0.8341 (p) cc_final: 0.7819 (p) REVERT: F 372 MET cc_start: 0.7963 (mmm) cc_final: 0.7392 (tpp) REVERT: F 402 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8319 (tp30) REVERT: F 403 MET cc_start: 0.8284 (ttm) cc_final: 0.7989 (mmt) REVERT: F 471 GLU cc_start: 0.8503 (mp0) cc_final: 0.8011 (mp0) REVERT: F 507 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8723 (tm-30) REVERT: J 17 GLU cc_start: 0.6911 (tt0) cc_final: 0.6198 (mp0) REVERT: J 64 LEU cc_start: 0.8684 (tp) cc_final: 0.8462 (tp) REVERT: J 88 ARG cc_start: 0.8312 (ptt-90) cc_final: 0.6957 (ptt-90) REVERT: J 96 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8897 (pp20) REVERT: M 87 ARG cc_start: 0.7679 (mtm180) cc_final: 0.7402 (mtt180) REVERT: M 94 GLU cc_start: 0.9028 (tm-30) cc_final: 0.8650 (tm-30) REVERT: M 95 LYS cc_start: 0.8617 (mtpp) cc_final: 0.8135 (tttm) REVERT: M 106 GLU cc_start: 0.9052 (tt0) cc_final: 0.8815 (tm-30) REVERT: M 109 ARG cc_start: 0.8303 (ttp80) cc_final: 0.7694 (ptm160) REVERT: M 141 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9117 (tp) REVERT: M 145 THR cc_start: 0.8310 (OUTLIER) cc_final: 0.8033 (p) outliers start: 79 outliers final: 40 residues processed: 624 average time/residue: 0.1969 time to fit residues: 189.4165 Evaluate side-chains 559 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 512 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 646 GLU Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1038 ASP Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 410 GLN Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 1132 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 217 LYS Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 383 GLN Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 83 ASP Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 145 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 141 optimal weight: 0.0670 chunk 165 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 94 optimal weight: 0.4980 chunk 67 optimal weight: 0.3980 chunk 30 optimal weight: 0.3980 chunk 52 optimal weight: 5.9990 chunk 256 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 266 optimal weight: 0.6980 chunk 179 optimal weight: 1.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 151 GLN C 323 HIS ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 ASN C 451 HIS D 482 GLN D1032 GLN ** D1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 434 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.186856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.123753 restraints weight = 32677.053| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.24 r_work: 0.3098 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29998 Z= 0.137 Angle : 0.646 10.981 41057 Z= 0.339 Chirality : 0.044 0.248 4681 Planarity : 0.005 0.073 5040 Dihedral : 15.733 177.059 4979 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.03 % Favored : 94.88 % Rotamer: Outliers : 2.77 % Allowed : 18.13 % Favored : 79.10 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.03 % 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: -0.37 (0.14), residues: 3477 helix: 1.08 (0.14), residues: 1413 sheet: -0.77 (0.26), residues: 401 loop : -1.29 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 502 TYR 0.016 0.001 TYR E 56 PHE 0.013 0.001 PHE D1186 TRP 0.049 0.002 TRP J 82 HIS 0.005 0.001 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (29990) covalent geometry : angle 0.63985 / 0.34 (41045) hydrogen bonds : bond 0.04500 / 3.09 ( 1356) hydrogen bonds : angle 4.68096 / 3.32 ( 3777) metal coordination : bond 0.00702 / 0.37 ( 8) metal coordination : angle 5.10717 / 2.50 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 557 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.7636 (tm-30) cc_final: 0.7185 (tm-30) REVERT: A 109 ASP cc_start: 0.8784 (m-30) cc_final: 0.8568 (m-30) REVERT: A 131 LYS cc_start: 0.8706 (mtmm) cc_final: 0.8403 (mtmm) REVERT: A 133 LYS cc_start: 0.8827 (pttt) cc_final: 0.8469 (ptmt) REVERT: B 27 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7865 (mm-30) REVERT: B 232 ILE cc_start: 0.8514 (mm) cc_final: 0.8167 (mt) REVERT: C 111 ARG cc_start: 0.7518 (ptt90) cc_final: 0.6867 (ptp90) REVERT: C 225 ARG cc_start: 0.7247 (ttp-170) cc_final: 0.6971 (mtp85) REVERT: C 373 PHE cc_start: 0.8963 (OUTLIER) cc_final: 0.8000 (m-80) REVERT: C 398 ARG cc_start: 0.7104 (ttm110) cc_final: 0.6559 (ttp80) REVERT: C 415 GLN cc_start: 0.7873 (tt0) cc_final: 0.7381 (tt0) REVERT: C 429 GLU cc_start: 0.8431 (pt0) cc_final: 0.8135 (pt0) REVERT: C 465 ARG cc_start: 0.7910 (mtm180) cc_final: 0.7645 (mtt90) REVERT: C 622 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7687 (tt0) REVERT: C 646 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7536 (tm-30) REVERT: C 694 ASP cc_start: 0.7456 (m-30) cc_final: 0.7082 (m-30) REVERT: C 748 THR cc_start: 0.9121 (t) cc_final: 0.8810 (m) REVERT: C 753 GLU cc_start: 0.8335 (tp30) cc_final: 0.7910 (mm-30) REVERT: C 781 LEU cc_start: 0.8515 (mm) cc_final: 0.8297 (mt) REVERT: C 834 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.8031 (p0) REVERT: C 841 HIS cc_start: 0.8440 (t-170) cc_final: 0.8137 (m-70) REVERT: C 866 ASN cc_start: 0.7527 (m-40) cc_final: 0.7196 (m-40) REVERT: C 1015 SER cc_start: 0.9215 (m) cc_final: 0.8759 (p) REVERT: C 1090 THR cc_start: 0.9027 (m) cc_final: 0.8789 (p) REVERT: D 8 ASP cc_start: 0.8144 (m-30) cc_final: 0.7793 (m-30) REVERT: D 56 ARG cc_start: 0.7927 (ttm-80) cc_final: 0.7689 (ttm-80) REVERT: D 66 LYS cc_start: 0.7361 (mtpt) cc_final: 0.6957 (mttm) REVERT: D 155 MET cc_start: 0.8737 (tpt) cc_final: 0.8401 (tpt) REVERT: D 205 MET cc_start: 0.8036 (tpt) cc_final: 0.7247 (mmm) REVERT: D 238 GLU cc_start: 0.8153 (pp20) cc_final: 0.7734 (tm-30) REVERT: D 247 ARG cc_start: 0.8506 (ttm-80) cc_final: 0.7892 (ttm-80) REVERT: D 259 GLU cc_start: 0.8357 (tm-30) cc_final: 0.7753 (pt0) REVERT: D 470 LYS cc_start: 0.8002 (mtpt) cc_final: 0.7693 (mttm) REVERT: D 488 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8232 (pt0) REVERT: D 714 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.8171 (m-30) REVERT: D 762 ARG cc_start: 0.7560 (ptp90) cc_final: 0.7189 (ptp-170) REVERT: D 946 ASP cc_start: 0.8096 (t0) cc_final: 0.7837 (t0) REVERT: D 948 GLU cc_start: 0.7846 (mp0) cc_final: 0.7502 (mp0) REVERT: D 1109 GLN cc_start: 0.8629 (tp40) cc_final: 0.8332 (tp-100) REVERT: D 1112 MET cc_start: 0.7760 (mmt) cc_final: 0.7456 (mmm) REVERT: F 218 ASP cc_start: 0.8541 (t70) cc_final: 0.8130 (m-30) REVERT: F 229 ARG cc_start: 0.7506 (ttm170) cc_final: 0.6772 (tpp-160) REVERT: F 253 ILE cc_start: 0.8819 (mt) cc_final: 0.8595 (mm) REVERT: F 257 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8755 (mp) REVERT: F 262 LEU cc_start: 0.9631 (tt) cc_final: 0.9337 (mm) REVERT: F 285 CYS cc_start: 0.8511 (p) cc_final: 0.7839 (m) REVERT: F 372 MET cc_start: 0.7972 (mmm) cc_final: 0.7589 (tpp) REVERT: F 403 MET cc_start: 0.8206 (ttm) cc_final: 0.7916 (mmm) REVERT: F 424 ASP cc_start: 0.8159 (m-30) cc_final: 0.7840 (m-30) REVERT: F 443 GLU cc_start: 0.7244 (mt-10) cc_final: 0.7041 (mm-30) REVERT: F 507 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8717 (tm-30) REVERT: J 17 GLU cc_start: 0.6862 (tt0) cc_final: 0.6171 (mp0) REVERT: J 103 GLU cc_start: 0.8874 (tp30) cc_final: 0.8235 (tp30) REVERT: J 104 LEU cc_start: 0.9242 (tp) cc_final: 0.9038 (mm) REVERT: M 4 LYS cc_start: 0.8921 (tppt) cc_final: 0.8539 (tppt) REVERT: M 94 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8614 (tm-30) REVERT: M 95 LYS cc_start: 0.8565 (mtpp) cc_final: 0.8201 (tttm) REVERT: M 106 GLU cc_start: 0.8992 (tt0) cc_final: 0.8776 (tm-30) REVERT: M 109 ARG cc_start: 0.8310 (ttp80) cc_final: 0.7791 (ptm160) REVERT: M 141 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9165 (tp) REVERT: M 145 THR cc_start: 0.8308 (OUTLIER) cc_final: 0.8050 (p) outliers start: 81 outliers final: 41 residues processed: 611 average time/residue: 0.1943 time to fit residues: 182.4682 Evaluate side-chains 549 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 501 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 646 GLU Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 834 ASP Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1038 ASP Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 482 GLN Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 714 ASP Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 1132 ILE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 383 GLN Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 46 ASP Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 32 LYS Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 145 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 171 optimal weight: 30.0000 chunk 114 optimal weight: 0.8980 chunk 257 optimal weight: 4.9990 chunk 176 optimal weight: 40.0000 chunk 133 optimal weight: 2.9990 chunk 277 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 170 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 188 optimal weight: 0.5980 chunk 293 optimal weight: 5.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 375 ASN C 419 ASN C 775 ASN C 981 GLN D 307 ASN D 494 HIS ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 787 GLN D1119 HIS ** D1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 377 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.182855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.119114 restraints weight = 32556.338| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.30 r_work: 0.3026 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.2869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 29998 Z= 0.200 Angle : 0.659 10.880 41057 Z= 0.344 Chirality : 0.045 0.242 4681 Planarity : 0.005 0.072 5040 Dihedral : 15.787 177.474 4979 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.58 % Favored : 94.33 % Rotamer: Outliers : 3.46 % Allowed : 19.19 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.03 % 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: -0.38 (0.14), residues: 3477 helix: 1.06 (0.14), residues: 1417 sheet: -0.77 (0.26), residues: 401 loop : -1.29 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 502 TYR 0.018 0.002 TYR D 749 PHE 0.016 0.002 PHE D 252 TRP 0.068 0.002 TRP J 82 HIS 0.007 0.001 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 (29990) covalent geometry : angle 0.65329 / 0.34 (41045) hydrogen bonds : bond 0.04538 / 3.12 ( 1356) hydrogen bonds : angle 4.56644 / 3.24 ( 3777) metal coordination : bond 0.01070 / 0.60 ( 8) metal coordination : angle 5.15016 / 2.45 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 526 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.7775 (tm-30) cc_final: 0.7436 (tm-30) REVERT: A 62 GLU cc_start: 0.8707 (pt0) cc_final: 0.8250 (pm20) REVERT: A 98 ARG cc_start: 0.7651 (mmm-85) cc_final: 0.7370 (mmm-85) REVERT: A 131 LYS cc_start: 0.8760 (mtmm) cc_final: 0.8486 (mtmm) REVERT: A 133 LYS cc_start: 0.8857 (pttt) cc_final: 0.8507 (ptmt) REVERT: A 135 GLU cc_start: 0.7714 (tt0) cc_final: 0.7186 (mt-10) REVERT: A 188 ASP cc_start: 0.7143 (OUTLIER) cc_final: 0.6763 (m-30) REVERT: B 57 ASP cc_start: 0.8334 (m-30) cc_final: 0.7949 (m-30) REVERT: B 98 ARG cc_start: 0.8164 (ptp-170) cc_final: 0.7962 (mtt180) REVERT: B 99 LYS cc_start: 0.8202 (ttmm) cc_final: 0.7784 (ttmt) REVERT: C 111 ARG cc_start: 0.7494 (ptt90) cc_final: 0.6828 (ptp90) REVERT: C 163 LYS cc_start: 0.8507 (mttm) cc_final: 0.7999 (mtmt) REVERT: C 373 PHE cc_start: 0.9057 (OUTLIER) cc_final: 0.7960 (m-80) REVERT: C 383 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.7435 (tm-30) REVERT: C 398 ARG cc_start: 0.7213 (ttm110) cc_final: 0.6582 (ttp80) REVERT: C 415 GLN cc_start: 0.7909 (tt0) cc_final: 0.7389 (tt0) REVERT: C 429 GLU cc_start: 0.8415 (pt0) cc_final: 0.8116 (pt0) REVERT: C 488 THR cc_start: 0.8541 (OUTLIER) cc_final: 0.8310 (m) REVERT: C 538 ARG cc_start: 0.8095 (mtm-85) cc_final: 0.7847 (ttm110) REVERT: C 548 ILE cc_start: 0.7685 (mm) cc_final: 0.7403 (mm) REVERT: C 622 GLU cc_start: 0.8398 (mt-10) cc_final: 0.7852 (tt0) REVERT: C 646 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7600 (tm-30) REVERT: C 673 ARG cc_start: 0.8232 (ttp80) cc_final: 0.7976 (ttp-110) REVERT: C 694 ASP cc_start: 0.7515 (m-30) cc_final: 0.7112 (m-30) REVERT: C 753 GLU cc_start: 0.8474 (tp30) cc_final: 0.8011 (mm-30) REVERT: C 781 LEU cc_start: 0.8562 (mm) cc_final: 0.8335 (mt) REVERT: C 819 ARG cc_start: 0.7814 (ttm-80) cc_final: 0.7572 (ttm110) REVERT: C 857 ASP cc_start: 0.8138 (t0) cc_final: 0.7279 (t0) REVERT: C 858 GLU cc_start: 0.8448 (pm20) cc_final: 0.8228 (pm20) REVERT: C 947 ASP cc_start: 0.8282 (t70) cc_final: 0.7578 (p0) REVERT: C 999 ASP cc_start: 0.6862 (OUTLIER) cc_final: 0.6593 (m-30) REVERT: C 1015 SER cc_start: 0.9222 (m) cc_final: 0.8784 (p) REVERT: C 1101 LYS cc_start: 0.7963 (mmmm) cc_final: 0.7638 (mtmt) REVERT: D 8 ASP cc_start: 0.8163 (m-30) cc_final: 0.7787 (m-30) REVERT: D 40 LYS cc_start: 0.8256 (mtpt) cc_final: 0.8018 (mttm) REVERT: D 56 ARG cc_start: 0.8105 (ttm-80) cc_final: 0.7866 (ttm-80) REVERT: D 66 LYS cc_start: 0.7594 (mtpt) cc_final: 0.7144 (mttp) REVERT: D 155 MET cc_start: 0.8779 (tpt) cc_final: 0.8387 (tpt) REVERT: D 205 MET cc_start: 0.7952 (tpt) cc_final: 0.7265 (mmm) REVERT: D 238 GLU cc_start: 0.8194 (pp20) cc_final: 0.7820 (tm-30) REVERT: D 259 GLU cc_start: 0.8364 (tm-30) cc_final: 0.7782 (pt0) REVERT: D 470 LYS cc_start: 0.7981 (mtpt) cc_final: 0.7678 (mttm) REVERT: D 488 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8298 (pt0) REVERT: D 666 THR cc_start: 0.9025 (p) cc_final: 0.8823 (p) REVERT: D 925 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8122 (mp) REVERT: D 948 GLU cc_start: 0.7890 (mp0) cc_final: 0.7523 (mp0) REVERT: D 1112 MET cc_start: 0.7863 (mmt) cc_final: 0.7547 (mmm) REVERT: F 218 ASP cc_start: 0.8585 (t70) cc_final: 0.8120 (m-30) REVERT: F 229 ARG cc_start: 0.7543 (ttm170) cc_final: 0.6783 (tpp-160) REVERT: F 253 ILE cc_start: 0.8843 (mt) cc_final: 0.8633 (mm) REVERT: F 257 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8762 (mp) REVERT: F 262 LEU cc_start: 0.9674 (tt) cc_final: 0.9234 (mm) REVERT: F 263 MET cc_start: 0.9240 (ttt) cc_final: 0.8981 (ttt) REVERT: F 281 MET cc_start: 0.9171 (ttm) cc_final: 0.8828 (ptp) REVERT: F 285 CYS cc_start: 0.8449 (p) cc_final: 0.7878 (m) REVERT: F 372 MET cc_start: 0.8039 (mmm) cc_final: 0.7320 (tpp) REVERT: F 403 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.8010 (mmm) REVERT: F 424 ASP cc_start: 0.8264 (m-30) cc_final: 0.7847 (m-30) REVERT: F 443 GLU cc_start: 0.7343 (mt-10) cc_final: 0.7133 (mm-30) REVERT: F 507 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8692 (tm-30) REVERT: J 17 GLU cc_start: 0.6801 (tt0) cc_final: 0.6181 (mp0) REVERT: J 96 GLU cc_start: 0.9225 (mm-30) cc_final: 0.8933 (pp20) REVERT: J 103 GLU cc_start: 0.8915 (tp30) cc_final: 0.8305 (tp30) REVERT: J 104 LEU cc_start: 0.9209 (tp) cc_final: 0.8974 (mm) REVERT: M 87 ARG cc_start: 0.7637 (mtm180) cc_final: 0.7216 (mtt180) REVERT: M 94 GLU cc_start: 0.9002 (tm-30) cc_final: 0.8579 (tm-30) REVERT: M 95 LYS cc_start: 0.8765 (mtpp) cc_final: 0.8339 (tttm) REVERT: M 106 GLU cc_start: 0.9038 (tt0) cc_final: 0.8805 (tm-30) REVERT: M 109 ARG cc_start: 0.8307 (ttp80) cc_final: 0.7982 (ptm160) REVERT: M 141 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9087 (pp) REVERT: M 145 THR cc_start: 0.8267 (OUTLIER) cc_final: 0.8033 (p) outliers start: 101 outliers final: 65 residues processed: 590 average time/residue: 0.1890 time to fit residues: 170.8424 Evaluate side-chains 569 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 493 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 646 GLU Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 758 ASP Chi-restraints excluded: chain C residue 779 GLU Chi-restraints excluded: chain C residue 834 ASP Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain C residue 999 ASP Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1038 ASP Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 267 ASN Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 410 GLN Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 925 LEU Chi-restraints excluded: chain D residue 1031 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 383 GLN Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 403 MET Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 46 ASP Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 32 LYS Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 145 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 12 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 126 optimal weight: 0.9990 chunk 205 optimal weight: 0.7980 chunk 189 optimal weight: 5.9990 chunk 196 optimal weight: 1.9990 chunk 290 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 220 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1125 GLN D1227 GLN ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 377 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.183542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.120313 restraints weight = 32547.301| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.29 r_work: 0.3061 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29998 Z= 0.139 Angle : 0.621 14.349 41057 Z= 0.325 Chirality : 0.044 0.497 4681 Planarity : 0.005 0.066 5040 Dihedral : 15.766 176.892 4979 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.98 % Favored : 94.94 % Rotamer: Outliers : 3.18 % Allowed : 19.74 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.03 % 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: -0.24 (0.14), residues: 3477 helix: 1.20 (0.14), residues: 1411 sheet: -0.70 (0.26), residues: 391 loop : -1.22 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J 108 TYR 0.031 0.001 TYR D 248 PHE 0.021 0.001 PHE D 226 TRP 0.081 0.002 TRP J 82 HIS 0.005 0.001 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (29990) covalent geometry : angle 0.61507 / 0.32 (41045) hydrogen bonds : bond 0.04149 / 2.86 ( 1356) hydrogen bonds : angle 4.42817 / 3.15 ( 3777) metal coordination : bond 0.00612 / 0.33 ( 8) metal coordination : angle 5.00263 / 2.41 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 522 time to evaluate : 1.016 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 5 GLN cc_start: 0.7791 (tm-30) cc_final: 0.7570 (tm-30) REVERT: A 62 GLU cc_start: 0.8641 (pt0) cc_final: 0.8252 (pm20) REVERT: A 131 LYS cc_start: 0.8749 (mtmm) cc_final: 0.8433 (mtmm) REVERT: A 133 LYS cc_start: 0.8766 (pttt) cc_final: 0.8390 (ptmt) REVERT: A 135 GLU cc_start: 0.7726 (tt0) cc_final: 0.7330 (mt-10) REVERT: A 188 ASP cc_start: 0.7135 (OUTLIER) cc_final: 0.6783 (m-30) REVERT: B 98 ARG cc_start: 0.8196 (ptp-170) cc_final: 0.7988 (mtt180) REVERT: B 99 LYS cc_start: 0.8175 (ttmm) cc_final: 0.7691 (ttmt) REVERT: B 232 ILE cc_start: 0.8529 (mm) cc_final: 0.8210 (mt) REVERT: C 111 ARG cc_start: 0.7445 (ptt90) cc_final: 0.6782 (ptp90) REVERT: C 160 MET cc_start: 0.9183 (ttm) cc_final: 0.8982 (ttm) REVERT: C 163 LYS cc_start: 0.8487 (mttm) cc_final: 0.7951 (mtmt) REVERT: C 373 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.7976 (m-80) REVERT: C 415 GLN cc_start: 0.7818 (tt0) cc_final: 0.7318 (tt0) REVERT: C 429 GLU cc_start: 0.8355 (pt0) cc_final: 0.8077 (pt0) REVERT: C 435 GLN cc_start: 0.7426 (tt0) cc_final: 0.7175 (tt0) REVERT: C 465 ARG cc_start: 0.7958 (mtm180) cc_final: 0.7635 (mtt90) REVERT: C 488 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8266 (m) REVERT: C 548 ILE cc_start: 0.7685 (mm) cc_final: 0.7395 (mm) REVERT: C 620 ARG cc_start: 0.8544 (mmm160) cc_final: 0.8109 (mmt180) REVERT: C 622 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7827 (tt0) REVERT: C 646 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7615 (tm-30) REVERT: C 673 ARG cc_start: 0.8242 (ttp80) cc_final: 0.7986 (ttp-110) REVERT: C 694 ASP cc_start: 0.7388 (m-30) cc_final: 0.7024 (m-30) REVERT: C 753 GLU cc_start: 0.8419 (tp30) cc_final: 0.8005 (mm-30) REVERT: C 824 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7713 (mp) REVERT: C 857 ASP cc_start: 0.8155 (t0) cc_final: 0.7222 (t0) REVERT: C 947 ASP cc_start: 0.8326 (t70) cc_final: 0.7533 (p0) REVERT: C 1015 SER cc_start: 0.9247 (m) cc_final: 0.8824 (p) REVERT: C 1090 THR cc_start: 0.9057 (m) cc_final: 0.8793 (p) REVERT: C 1101 LYS cc_start: 0.7975 (mmmm) cc_final: 0.7680 (mtmt) REVERT: D 8 ASP cc_start: 0.8132 (m-30) cc_final: 0.7783 (m-30) REVERT: D 40 LYS cc_start: 0.8256 (mtpt) cc_final: 0.8045 (mttm) REVERT: D 56 ARG cc_start: 0.8124 (ttm-80) cc_final: 0.7870 (ttm-80) REVERT: D 66 LYS cc_start: 0.7565 (mtpt) cc_final: 0.7160 (mttm) REVERT: D 155 MET cc_start: 0.8761 (tpt) cc_final: 0.8457 (tpt) REVERT: D 205 MET cc_start: 0.8184 (tpt) cc_final: 0.7444 (mmm) REVERT: D 238 GLU cc_start: 0.8238 (pp20) cc_final: 0.7806 (tm-30) REVERT: D 259 GLU cc_start: 0.8371 (tm-30) cc_final: 0.7787 (pt0) REVERT: D 470 LYS cc_start: 0.7990 (mtpt) cc_final: 0.7691 (mttm) REVERT: D 477 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8185 (mm-30) REVERT: D 488 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8345 (pt0) REVERT: D 948 GLU cc_start: 0.7904 (mp0) cc_final: 0.7527 (mp0) REVERT: D 1112 MET cc_start: 0.7887 (mmt) cc_final: 0.7537 (mmm) REVERT: E 69 ASN cc_start: 0.7817 (m-40) cc_final: 0.7595 (m110) REVERT: F 218 ASP cc_start: 0.8595 (t70) cc_final: 0.8121 (m-30) REVERT: F 220 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8012 (tt0) REVERT: F 229 ARG cc_start: 0.7524 (ttm170) cc_final: 0.6995 (tpp-160) REVERT: F 253 ILE cc_start: 0.8854 (mt) cc_final: 0.8624 (mm) REVERT: F 254 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8561 (mt-10) REVERT: F 262 LEU cc_start: 0.9612 (tt) cc_final: 0.9274 (mm) REVERT: F 273 LEU cc_start: 0.7491 (tp) cc_final: 0.7079 (tp) REVERT: F 281 MET cc_start: 0.9086 (ttm) cc_final: 0.8793 (ptp) REVERT: F 285 CYS cc_start: 0.8443 (p) cc_final: 0.7863 (m) REVERT: F 372 MET cc_start: 0.8040 (mmm) cc_final: 0.7322 (tpp) REVERT: F 403 MET cc_start: 0.8455 (ttm) cc_final: 0.8083 (mmm) REVERT: F 424 ASP cc_start: 0.8256 (m-30) cc_final: 0.7810 (m-30) REVERT: F 443 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7171 (mt-10) REVERT: F 465 ASP cc_start: 0.7845 (m-30) cc_final: 0.7642 (m-30) REVERT: F 507 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8701 (tm-30) REVERT: F 513 LYS cc_start: 0.8093 (tttm) cc_final: 0.7892 (tttt) REVERT: J 17 GLU cc_start: 0.6773 (tt0) cc_final: 0.6172 (mp0) REVERT: J 36 ASN cc_start: 0.8066 (p0) cc_final: 0.7830 (p0) REVERT: M 47 ARG cc_start: 0.7526 (mtt90) cc_final: 0.7252 (mtt90) REVERT: M 94 GLU cc_start: 0.9006 (tm-30) cc_final: 0.8555 (tm-30) REVERT: M 95 LYS cc_start: 0.8719 (mtpp) cc_final: 0.8242 (tttm) REVERT: M 106 GLU cc_start: 0.8846 (tt0) cc_final: 0.8643 (tm-30) REVERT: M 109 ARG cc_start: 0.8341 (ttp80) cc_final: 0.7849 (ptm160) REVERT: M 127 MET cc_start: 0.8267 (tpt) cc_final: 0.8041 (tpt) REVERT: M 141 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9060 (pp) REVERT: M 145 THR cc_start: 0.8233 (OUTLIER) cc_final: 0.7999 (p) outliers start: 93 outliers final: 62 residues processed: 584 average time/residue: 0.1931 time to fit residues: 174.7814 Evaluate side-chains 550 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 481 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 646 GLU Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 758 ASP Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 824 ILE Chi-restraints excluded: chain C residue 834 ASP Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1038 ASP Chi-restraints excluded: chain C residue 1094 ASP Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 1031 VAL Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 383 GLN Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 427 ILE Chi-restraints excluded: chain F residue 466 THR Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 46 ASP Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 32 LYS Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 145 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 141 optimal weight: 2.9990 chunk 264 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 309 optimal weight: 10.0000 chunk 281 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 283 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 272 optimal weight: 7.9990 chunk 168 optimal weight: 0.8980 chunk 299 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.182945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.127802 restraints weight = 32431.963| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.45 r_work: 0.3002 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2816 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2816 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 29998 Z= 0.224 Angle : 0.673 15.931 41057 Z= 0.347 Chirality : 0.046 0.369 4681 Planarity : 0.005 0.073 5040 Dihedral : 15.810 176.774 4979 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.92 % Favored : 94.02 % Rotamer: Outliers : 3.66 % Allowed : 20.32 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.03 % 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: -0.31 (0.14), residues: 3477 helix: 1.06 (0.14), residues: 1418 sheet: -0.72 (0.26), residues: 374 loop : -1.19 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 118 TYR 0.016 0.002 TYR D 749 PHE 0.019 0.002 PHE D 226 TRP 0.095 0.002 TRP J 82 HIS 0.006 0.001 HIS D 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.22 (29990) covalent geometry : angle 0.66471 / 0.35 (41045) hydrogen bonds : bond 0.04493 / 3.09 ( 1356) hydrogen bonds : angle 4.51516 / 3.21 ( 3777) metal coordination : bond 0.01568 / 0.85 ( 8) metal coordination : angle 6.02841 / 3.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 500 time to evaluate : 0.948 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 62 GLU cc_start: 0.8810 (pt0) cc_final: 0.8527 (pm20) REVERT: A 91 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7240 (tm-30) REVERT: A 133 LYS cc_start: 0.8996 (pttt) cc_final: 0.8674 (ptmt) REVERT: A 188 ASP cc_start: 0.7341 (OUTLIER) cc_final: 0.7017 (m-30) REVERT: B 57 ASP cc_start: 0.8374 (m-30) cc_final: 0.8028 (m-30) REVERT: B 99 LYS cc_start: 0.8482 (ttmm) cc_final: 0.7968 (ttmt) REVERT: B 190 ASP cc_start: 0.8607 (p0) cc_final: 0.8405 (p0) REVERT: B 232 ILE cc_start: 0.8715 (mm) cc_final: 0.8372 (mt) REVERT: C 49 GLU cc_start: 0.8286 (pm20) cc_final: 0.7744 (pm20) REVERT: C 111 ARG cc_start: 0.7795 (ptt90) cc_final: 0.7308 (ptp90) REVERT: C 373 PHE cc_start: 0.9242 (OUTLIER) cc_final: 0.8357 (m-80) REVERT: C 398 ARG cc_start: 0.7516 (mtt-85) cc_final: 0.6770 (ttp80) REVERT: C 415 GLN cc_start: 0.7949 (tt0) cc_final: 0.7431 (tt0) REVERT: C 429 GLU cc_start: 0.8432 (pt0) cc_final: 0.8179 (pt0) REVERT: C 440 MET cc_start: 0.9144 (OUTLIER) cc_final: 0.6924 (tpt) REVERT: C 465 ARG cc_start: 0.8142 (mtm180) cc_final: 0.7887 (mtm-85) REVERT: C 488 THR cc_start: 0.8608 (OUTLIER) cc_final: 0.8362 (m) REVERT: C 538 ARG cc_start: 0.8271 (mtm-85) cc_final: 0.8055 (ttm110) REVERT: C 548 ILE cc_start: 0.8268 (mm) cc_final: 0.7990 (mm) REVERT: C 620 ARG cc_start: 0.8622 (mmm160) cc_final: 0.8328 (mmt180) REVERT: C 622 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8146 (tt0) REVERT: C 646 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7930 (tm-30) REVERT: C 673 ARG cc_start: 0.8525 (ttp80) cc_final: 0.8296 (ttp-110) REVERT: C 753 GLU cc_start: 0.8575 (tp30) cc_final: 0.8361 (mm-30) REVERT: C 841 HIS cc_start: 0.8022 (m-70) cc_final: 0.7761 (m-70) REVERT: C 857 ASP cc_start: 0.8128 (t0) cc_final: 0.7526 (t0) REVERT: C 947 ASP cc_start: 0.8320 (t70) cc_final: 0.7777 (p0) REVERT: C 1015 SER cc_start: 0.9382 (m) cc_final: 0.9093 (p) REVERT: C 1044 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.8733 (ttt-90) REVERT: C 1101 LYS cc_start: 0.8525 (mmmm) cc_final: 0.8215 (mtmt) REVERT: D 8 ASP cc_start: 0.8096 (m-30) cc_final: 0.7766 (m-30) REVERT: D 56 ARG cc_start: 0.8503 (ttm-80) cc_final: 0.8273 (ttm-80) REVERT: D 66 LYS cc_start: 0.8045 (mtpt) cc_final: 0.7759 (mttp) REVERT: D 155 MET cc_start: 0.8728 (tpt) cc_final: 0.8340 (tpt) REVERT: D 205 MET cc_start: 0.7739 (tpt) cc_final: 0.7272 (mmm) REVERT: D 238 GLU cc_start: 0.8360 (pp20) cc_final: 0.7978 (tm-30) REVERT: D 259 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8087 (pt0) REVERT: D 397 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7374 (ptt-90) REVERT: D 470 LYS cc_start: 0.8447 (mtpt) cc_final: 0.8156 (mttm) REVERT: D 488 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8517 (tt0) REVERT: D 787 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7751 (mm110) REVERT: D 1112 MET cc_start: 0.8104 (mmt) cc_final: 0.7771 (mmm) REVERT: E 97 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8348 (mtp180) REVERT: F 218 ASP cc_start: 0.8597 (t70) cc_final: 0.8226 (m-30) REVERT: F 220 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8002 (tt0) REVERT: F 229 ARG cc_start: 0.7959 (ttm170) cc_final: 0.7284 (tpp-160) REVERT: F 253 ILE cc_start: 0.9019 (mt) cc_final: 0.8764 (mm) REVERT: F 273 LEU cc_start: 0.7442 (tp) cc_final: 0.7188 (tp) REVERT: F 281 MET cc_start: 0.9006 (ttm) cc_final: 0.8789 (ptp) REVERT: F 285 CYS cc_start: 0.8490 (p) cc_final: 0.8057 (m) REVERT: F 286 ARG cc_start: 0.8441 (mtp85) cc_final: 0.8145 (mmm-85) REVERT: F 372 MET cc_start: 0.8344 (mmm) cc_final: 0.7688 (tpp) REVERT: F 402 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8082 (tp30) REVERT: F 403 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.8129 (mmm) REVERT: F 424 ASP cc_start: 0.8433 (m-30) cc_final: 0.8002 (m-30) REVERT: F 443 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7449 (mp0) REVERT: J 7 ARG cc_start: 0.8265 (ttm-80) cc_final: 0.7752 (mtp85) REVERT: J 17 GLU cc_start: 0.6915 (tt0) cc_final: 0.6444 (mp0) REVERT: J 36 ASN cc_start: 0.8201 (p0) cc_final: 0.7975 (p0) REVERT: J 88 ARG cc_start: 0.8433 (ptt-90) cc_final: 0.6795 (ptt-90) REVERT: J 104 LEU cc_start: 0.9172 (tt) cc_final: 0.8845 (mm) REVERT: M 95 LYS cc_start: 0.8702 (mtpp) cc_final: 0.8210 (tttm) REVERT: M 106 GLU cc_start: 0.8854 (tt0) cc_final: 0.8624 (tm-30) REVERT: M 141 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8998 (pp) REVERT: M 145 THR cc_start: 0.8208 (OUTLIER) cc_final: 0.7958 (p) outliers start: 107 outliers final: 75 residues processed: 580 average time/residue: 0.1926 time to fit residues: 172.8001 Evaluate side-chains 570 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 484 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 646 GLU Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 758 ASP Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1038 ASP Chi-restraints excluded: chain C residue 1044 ARG Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 397 ARG Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 1031 VAL Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 97 ARG Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 383 GLN Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 403 MET Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 427 ILE Chi-restraints excluded: chain F residue 466 THR Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 46 ASP Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 32 LYS Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 130 LYS Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 145 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 250 optimal weight: 4.9990 chunk 287 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 326 optimal weight: 6.9990 chunk 215 optimal weight: 0.4980 chunk 235 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 246 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 184 optimal weight: 0.8980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.181168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.118154 restraints weight = 32859.406| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.28 r_work: 0.3023 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 29998 Z= 0.209 Angle : 0.665 16.836 41057 Z= 0.341 Chirality : 0.045 0.417 4681 Planarity : 0.005 0.071 5040 Dihedral : 15.821 176.091 4979 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.44 % Favored : 94.51 % Rotamer: Outliers : 3.52 % Allowed : 20.90 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.03 % 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: -0.28 (0.14), residues: 3477 helix: 1.07 (0.14), residues: 1421 sheet: -0.69 (0.26), residues: 374 loop : -1.17 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 259 TYR 0.012 0.001 TYR D 749 PHE 0.015 0.002 PHE D1186 TRP 0.066 0.002 TRP J 82 HIS 0.006 0.001 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.21 (29990) covalent geometry : angle 0.65778 / 0.34 (41045) hydrogen bonds : bond 0.04350 / 2.99 ( 1356) hydrogen bonds : angle 4.47225 / 3.19 ( 3777) metal coordination : bond 0.01350 / 0.74 ( 8) metal coordination : angle 5.70733 / 2.85 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 494 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8849 (pt0) cc_final: 0.8450 (pm20) REVERT: A 91 GLU cc_start: 0.7467 (tm-30) cc_final: 0.7251 (tm-30) REVERT: A 98 ARG cc_start: 0.7721 (mmm-85) cc_final: 0.7363 (mmt90) REVERT: A 133 LYS cc_start: 0.8985 (pttt) cc_final: 0.8608 (ptmt) REVERT: A 135 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7764 (mt-10) REVERT: A 188 ASP cc_start: 0.7303 (OUTLIER) cc_final: 0.6931 (m-30) REVERT: B 57 ASP cc_start: 0.8343 (m-30) cc_final: 0.7941 (m-30) REVERT: B 99 LYS cc_start: 0.8344 (ttmm) cc_final: 0.7834 (ttmt) REVERT: B 232 ILE cc_start: 0.8610 (mm) cc_final: 0.8262 (mt) REVERT: C 49 GLU cc_start: 0.8283 (pm20) cc_final: 0.7611 (pm20) REVERT: C 111 ARG cc_start: 0.7678 (ptt90) cc_final: 0.7078 (ptp90) REVERT: C 373 PHE cc_start: 0.9197 (OUTLIER) cc_final: 0.8199 (m-80) REVERT: C 398 ARG cc_start: 0.7257 (mtt-85) cc_final: 0.6477 (ttp80) REVERT: C 415 GLN cc_start: 0.7839 (tt0) cc_final: 0.7308 (tt0) REVERT: C 429 GLU cc_start: 0.8401 (pt0) cc_final: 0.8152 (pt0) REVERT: C 440 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.6823 (tpt) REVERT: C 465 ARG cc_start: 0.7976 (mtm180) cc_final: 0.7688 (mtm-85) REVERT: C 488 THR cc_start: 0.8469 (OUTLIER) cc_final: 0.8232 (m) REVERT: C 538 ARG cc_start: 0.8146 (mtm-85) cc_final: 0.7936 (ttm110) REVERT: C 548 ILE cc_start: 0.8091 (mm) cc_final: 0.7821 (mm) REVERT: C 620 ARG cc_start: 0.8542 (mmm160) cc_final: 0.8155 (mmt180) REVERT: C 646 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7778 (tm-30) REVERT: C 673 ARG cc_start: 0.8319 (ttp80) cc_final: 0.8041 (ttp-110) REVERT: C 753 GLU cc_start: 0.8459 (tp30) cc_final: 0.8087 (mm-30) REVERT: C 824 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7785 (mp) REVERT: C 841 HIS cc_start: 0.8017 (m-70) cc_final: 0.7815 (m-70) REVERT: C 947 ASP cc_start: 0.8365 (t70) cc_final: 0.7660 (p0) REVERT: C 958 ARG cc_start: 0.8630 (ptp90) cc_final: 0.8162 (mtm-85) REVERT: C 985 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8320 (tp) REVERT: C 1015 SER cc_start: 0.9348 (m) cc_final: 0.8968 (p) REVERT: C 1063 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.7158 (t80) REVERT: C 1101 LYS cc_start: 0.8207 (mmmm) cc_final: 0.7865 (mtmt) REVERT: D 8 ASP cc_start: 0.8195 (m-30) cc_final: 0.7807 (m-30) REVERT: D 56 ARG cc_start: 0.8164 (ttm-80) cc_final: 0.7742 (ttm-80) REVERT: D 66 LYS cc_start: 0.7843 (mtpt) cc_final: 0.7516 (mttp) REVERT: D 155 MET cc_start: 0.8796 (tpt) cc_final: 0.8511 (tpt) REVERT: D 205 MET cc_start: 0.8145 (tpt) cc_final: 0.7503 (mmm) REVERT: D 238 GLU cc_start: 0.8291 (pp20) cc_final: 0.7868 (tm-30) REVERT: D 248 TYR cc_start: 0.8523 (m-10) cc_final: 0.8255 (m-80) REVERT: D 259 GLU cc_start: 0.8463 (tm-30) cc_final: 0.7928 (pt0) REVERT: D 312 MET cc_start: 0.8916 (mtt) cc_final: 0.8607 (mtt) REVERT: D 470 LYS cc_start: 0.8155 (mtpt) cc_final: 0.7852 (mttm) REVERT: D 477 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8203 (mm-30) REVERT: D 488 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8344 (pt0) REVERT: D 787 GLN cc_start: 0.7627 (mm-40) cc_final: 0.7397 (mm110) REVERT: D 928 ASP cc_start: 0.7993 (m-30) cc_final: 0.7747 (t0) REVERT: D 1112 MET cc_start: 0.7974 (mmt) cc_final: 0.7636 (mmm) REVERT: D 1182 ASP cc_start: 0.7764 (t0) cc_final: 0.7560 (t0) REVERT: F 218 ASP cc_start: 0.8631 (t70) cc_final: 0.8204 (m-30) REVERT: F 220 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7992 (tt0) REVERT: F 229 ARG cc_start: 0.7689 (ttm170) cc_final: 0.7163 (tpp-160) REVERT: F 280 ASP cc_start: 0.8739 (m-30) cc_final: 0.8026 (t0) REVERT: F 285 CYS cc_start: 0.8440 (p) cc_final: 0.7929 (m) REVERT: F 286 ARG cc_start: 0.8414 (mtp85) cc_final: 0.8122 (mmm-85) REVERT: F 372 MET cc_start: 0.8186 (mmm) cc_final: 0.7502 (tpp) REVERT: F 402 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8341 (tp30) REVERT: F 403 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8151 (mmt) REVERT: F 440 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7994 (pt0) REVERT: J 7 ARG cc_start: 0.8154 (ttm-80) cc_final: 0.7561 (mmm-85) REVERT: J 17 GLU cc_start: 0.6836 (tt0) cc_final: 0.6247 (mp0) REVERT: J 36 ASN cc_start: 0.8287 (p0) cc_final: 0.8045 (p0) REVERT: M 90 LYS cc_start: 0.9382 (mmtp) cc_final: 0.8994 (mppt) REVERT: M 95 LYS cc_start: 0.8686 (mtpp) cc_final: 0.8375 (tttm) REVERT: M 106 GLU cc_start: 0.8929 (tt0) cc_final: 0.8636 (tm-30) REVERT: M 141 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.8996 (pp) REVERT: M 145 THR cc_start: 0.8308 (OUTLIER) cc_final: 0.8053 (p) outliers start: 103 outliers final: 83 residues processed: 574 average time/residue: 0.1903 time to fit residues: 168.0093 Evaluate side-chains 568 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 473 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 646 GLU Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 652 GLU Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 758 ASP Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 824 ILE Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain C residue 885 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1038 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 407 LYS Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 700 LEU Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 1031 VAL Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 383 GLN Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 403 MET Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 427 ILE Chi-restraints excluded: chain F residue 440 GLU Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 46 ASP Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 32 LYS Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 145 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 101 optimal weight: 2.9990 chunk 348 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 334 optimal weight: 6.9990 chunk 223 optimal weight: 0.8980 chunk 274 optimal weight: 10.0000 chunk 215 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 ASN B 152 ASN C 443 ASN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.181781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.117346 restraints weight = 32908.524| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.34 r_work: 0.3024 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 29998 Z= 0.174 Angle : 0.643 17.169 41057 Z= 0.331 Chirality : 0.044 0.362 4681 Planarity : 0.005 0.070 5040 Dihedral : 15.806 175.758 4979 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.78 % Favored : 94.16 % Rotamer: Outliers : 3.83 % Allowed : 20.73 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.03 % 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: -0.21 (0.14), residues: 3477 helix: 1.12 (0.14), residues: 1421 sheet: -0.65 (0.26), residues: 374 loop : -1.11 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 108 TYR 0.015 0.001 TYR D 251 PHE 0.022 0.001 PHE D 226 TRP 0.054 0.002 TRP J 82 HIS 0.006 0.001 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (29990) covalent geometry : angle 0.63679 / 0.33 (41045) hydrogen bonds : bond 0.04153 / 2.86 ( 1356) hydrogen bonds : angle 4.42693 / 3.16 ( 3777) metal coordination : bond 0.01035 / 0.56 ( 8) metal coordination : angle 5.36314 / 2.64 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 490 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8857 (pt0) cc_final: 0.8441 (pm20) REVERT: A 91 GLU cc_start: 0.7519 (tm-30) cc_final: 0.7266 (tm-30) REVERT: A 98 ARG cc_start: 0.7750 (mmm-85) cc_final: 0.7466 (mmt90) REVERT: A 133 LYS cc_start: 0.8980 (pttt) cc_final: 0.8599 (ptmt) REVERT: A 188 ASP cc_start: 0.7312 (OUTLIER) cc_final: 0.6937 (m-30) REVERT: B 57 ASP cc_start: 0.8387 (m-30) cc_final: 0.8003 (m-30) REVERT: B 99 LYS cc_start: 0.8355 (ttmm) cc_final: 0.7920 (ttmt) REVERT: B 232 ILE cc_start: 0.8593 (mm) cc_final: 0.8248 (mt) REVERT: C 49 GLU cc_start: 0.8250 (pm20) cc_final: 0.7585 (pm20) REVERT: C 67 SER cc_start: 0.8505 (m) cc_final: 0.8193 (p) REVERT: C 373 PHE cc_start: 0.9172 (OUTLIER) cc_final: 0.8233 (m-80) REVERT: C 398 ARG cc_start: 0.7263 (mtt-85) cc_final: 0.6443 (ttp80) REVERT: C 415 GLN cc_start: 0.7818 (tt0) cc_final: 0.7320 (tt0) REVERT: C 429 GLU cc_start: 0.8389 (pt0) cc_final: 0.8134 (pt0) REVERT: C 440 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.6921 (tpt) REVERT: C 465 ARG cc_start: 0.7973 (mtm180) cc_final: 0.7693 (mtm-85) REVERT: C 488 THR cc_start: 0.8456 (OUTLIER) cc_final: 0.8221 (m) REVERT: C 548 ILE cc_start: 0.8164 (mm) cc_final: 0.7887 (mm) REVERT: C 620 ARG cc_start: 0.8571 (mmm160) cc_final: 0.8178 (mmt180) REVERT: C 673 ARG cc_start: 0.8365 (ttp80) cc_final: 0.8089 (ttp-110) REVERT: C 753 GLU cc_start: 0.8470 (tp30) cc_final: 0.8104 (mm-30) REVERT: C 824 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7820 (mp) REVERT: C 857 ASP cc_start: 0.8338 (t0) cc_final: 0.7040 (t0) REVERT: C 947 ASP cc_start: 0.8404 (t70) cc_final: 0.7653 (p0) REVERT: C 958 ARG cc_start: 0.8636 (ptp90) cc_final: 0.8172 (mtm-85) REVERT: C 985 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8302 (tp) REVERT: C 1015 SER cc_start: 0.9349 (m) cc_final: 0.8993 (p) REVERT: C 1063 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7061 (t80) REVERT: C 1101 LYS cc_start: 0.8169 (mmmm) cc_final: 0.7868 (mtmt) REVERT: D 8 ASP cc_start: 0.8166 (m-30) cc_final: 0.7794 (m-30) REVERT: D 56 ARG cc_start: 0.8188 (ttm-80) cc_final: 0.7881 (ttm-80) REVERT: D 66 LYS cc_start: 0.7844 (mtpt) cc_final: 0.7534 (mttp) REVERT: D 155 MET cc_start: 0.8828 (tpt) cc_final: 0.8538 (tpt) REVERT: D 205 MET cc_start: 0.8134 (tpt) cc_final: 0.7553 (mmm) REVERT: D 238 GLU cc_start: 0.8298 (pp20) cc_final: 0.7866 (tm-30) REVERT: D 248 TYR cc_start: 0.8448 (m-10) cc_final: 0.8247 (m-80) REVERT: D 259 GLU cc_start: 0.8518 (tm-30) cc_final: 0.7993 (pt0) REVERT: D 312 MET cc_start: 0.8893 (mtt) cc_final: 0.8496 (mtt) REVERT: D 435 GLN cc_start: 0.8849 (pm20) cc_final: 0.8629 (pm20) REVERT: D 470 LYS cc_start: 0.8164 (mtpt) cc_final: 0.7864 (mttm) REVERT: D 477 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8043 (mm-30) REVERT: D 488 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8305 (pt0) REVERT: D 787 GLN cc_start: 0.7616 (mm-40) cc_final: 0.7410 (mm110) REVERT: D 928 ASP cc_start: 0.7982 (m-30) cc_final: 0.7714 (t0) REVERT: D 1112 MET cc_start: 0.7989 (mmt) cc_final: 0.7668 (mmm) REVERT: D 1182 ASP cc_start: 0.7829 (t0) cc_final: 0.7612 (t0) REVERT: E 97 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8122 (mtp180) REVERT: F 218 ASP cc_start: 0.8623 (t70) cc_final: 0.8198 (m-30) REVERT: F 220 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8034 (tt0) REVERT: F 229 ARG cc_start: 0.7714 (ttm170) cc_final: 0.7197 (tpp-160) REVERT: F 285 CYS cc_start: 0.8400 (p) cc_final: 0.7942 (m) REVERT: F 286 ARG cc_start: 0.8414 (mtp85) cc_final: 0.8113 (mmm-85) REVERT: F 372 MET cc_start: 0.8203 (mmm) cc_final: 0.7526 (tpp) REVERT: F 402 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8340 (tm-30) REVERT: F 403 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.8152 (mmt) REVERT: F 440 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7907 (pt0) REVERT: J 7 ARG cc_start: 0.8133 (ttm-80) cc_final: 0.7518 (mmm-85) REVERT: J 17 GLU cc_start: 0.6815 (tt0) cc_final: 0.6218 (mp0) REVERT: J 36 ASN cc_start: 0.8303 (p0) cc_final: 0.8077 (p0) REVERT: J 84 MET cc_start: 0.8259 (mtp) cc_final: 0.7935 (mtp) REVERT: J 88 ARG cc_start: 0.8648 (ptt-90) cc_final: 0.7503 (ptt-90) REVERT: M 95 LYS cc_start: 0.8677 (mtpp) cc_final: 0.8277 (tttm) REVERT: M 106 GLU cc_start: 0.8916 (tt0) cc_final: 0.8608 (tm-30) REVERT: M 127 MET cc_start: 0.8138 (tpt) cc_final: 0.7933 (tpt) REVERT: M 141 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8958 (pp) REVERT: M 145 THR cc_start: 0.8293 (OUTLIER) cc_final: 0.8035 (p) outliers start: 112 outliers final: 83 residues processed: 580 average time/residue: 0.1829 time to fit residues: 164.3024 Evaluate side-chains 566 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 471 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 758 ASP Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 824 ILE Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1038 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 397 ARG Chi-restraints excluded: chain D residue 407 LYS Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 700 LEU Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 1031 VAL Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 97 ARG Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 383 GLN Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 403 MET Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 427 ILE Chi-restraints excluded: chain F residue 440 GLU Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 46 ASP Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 32 LYS Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 145 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 19 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 246 optimal weight: 2.9990 chunk 254 optimal weight: 5.9990 chunk 16 optimal weight: 0.0970 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 317 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 HIS A 200 ASN B 152 ASN C 443 ASN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.182875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.118981 restraints weight = 32734.766| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.29 r_work: 0.3049 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 29998 Z= 0.146 Angle : 0.636 17.738 41057 Z= 0.328 Chirality : 0.043 0.311 4681 Planarity : 0.005 0.069 5040 Dihedral : 15.771 175.418 4979 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.41 % Favored : 94.54 % Rotamer: Outliers : 3.39 % Allowed : 21.45 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.03 % 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: 3477 helix: 1.15 (0.14), residues: 1422 sheet: -0.58 (0.27), residues: 372 loop : -1.06 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C1044 TYR 0.020 0.001 TYR C1029 PHE 0.013 0.001 PHE D 252 TRP 0.046 0.002 TRP J 82 HIS 0.006 0.001 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (29990) covalent geometry : angle 0.62997 / 0.33 (41045) hydrogen bonds : bond 0.03983 / 2.74 ( 1356) hydrogen bonds : angle 4.37290 / 3.13 ( 3777) metal coordination : bond 0.00808 / 0.43 ( 8) metal coordination : angle 5.12343 / 2.49 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 483 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8839 (pt0) cc_final: 0.8431 (pm20) REVERT: A 91 GLU cc_start: 0.7531 (tm-30) cc_final: 0.7281 (tm-30) REVERT: A 98 ARG cc_start: 0.7750 (mmm-85) cc_final: 0.7409 (mmt90) REVERT: A 133 LYS cc_start: 0.8937 (pttt) cc_final: 0.8524 (ptmt) REVERT: A 188 ASP cc_start: 0.7361 (OUTLIER) cc_final: 0.6992 (m-30) REVERT: B 57 ASP cc_start: 0.8393 (m-30) cc_final: 0.8017 (m-30) REVERT: B 99 LYS cc_start: 0.8368 (ttmm) cc_final: 0.7847 (ttmt) REVERT: C 67 SER cc_start: 0.8494 (m) cc_final: 0.8187 (p) REVERT: C 162 GLU cc_start: 0.8610 (pm20) cc_final: 0.8372 (pm20) REVERT: C 373 PHE cc_start: 0.9128 (OUTLIER) cc_final: 0.8181 (m-80) REVERT: C 415 GLN cc_start: 0.7812 (tt0) cc_final: 0.7394 (mt0) REVERT: C 429 GLU cc_start: 0.8341 (pt0) cc_final: 0.8063 (pt0) REVERT: C 440 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.6983 (tpt) REVERT: C 465 ARG cc_start: 0.7928 (mtm180) cc_final: 0.7673 (mtm-85) REVERT: C 488 THR cc_start: 0.8479 (OUTLIER) cc_final: 0.8241 (m) REVERT: C 620 ARG cc_start: 0.8571 (mmm160) cc_final: 0.8182 (mmt180) REVERT: C 622 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8021 (tt0) REVERT: C 673 ARG cc_start: 0.8384 (ttp80) cc_final: 0.8112 (ttp-110) REVERT: C 753 GLU cc_start: 0.8452 (tp30) cc_final: 0.8109 (mm-30) REVERT: C 824 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.7835 (mp) REVERT: C 857 ASP cc_start: 0.7715 (t0) cc_final: 0.7107 (t0) REVERT: C 947 ASP cc_start: 0.8410 (t70) cc_final: 0.7665 (p0) REVERT: C 958 ARG cc_start: 0.8653 (ptp90) cc_final: 0.8182 (mtm-85) REVERT: C 985 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8493 (tp) REVERT: C 1015 SER cc_start: 0.9345 (m) cc_final: 0.9000 (p) REVERT: C 1063 PHE cc_start: 0.8254 (OUTLIER) cc_final: 0.7363 (t80) REVERT: C 1090 THR cc_start: 0.9080 (m) cc_final: 0.8861 (p) REVERT: C 1101 LYS cc_start: 0.8157 (mmmm) cc_final: 0.7860 (mtmt) REVERT: D 8 ASP cc_start: 0.8130 (m-30) cc_final: 0.7755 (m-30) REVERT: D 56 ARG cc_start: 0.8191 (ttm-80) cc_final: 0.7887 (ttm-80) REVERT: D 66 LYS cc_start: 0.7797 (mtpt) cc_final: 0.7516 (mttp) REVERT: D 155 MET cc_start: 0.8825 (tpt) cc_final: 0.8530 (tpt) REVERT: D 205 MET cc_start: 0.8150 (tpt) cc_final: 0.7556 (mmm) REVERT: D 238 GLU cc_start: 0.8315 (pp20) cc_final: 0.7896 (tm-30) REVERT: D 259 GLU cc_start: 0.8537 (tm-30) cc_final: 0.7977 (pt0) REVERT: D 312 MET cc_start: 0.9045 (mtt) cc_final: 0.8737 (mtt) REVERT: D 435 GLN cc_start: 0.8819 (pm20) cc_final: 0.8609 (pm20) REVERT: D 470 LYS cc_start: 0.8154 (mtpt) cc_final: 0.7851 (mttm) REVERT: D 477 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8072 (mm-30) REVERT: D 488 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8281 (pt0) REVERT: D 928 ASP cc_start: 0.7989 (m-30) cc_final: 0.7706 (t0) REVERT: D 1112 MET cc_start: 0.7974 (mmt) cc_final: 0.7650 (mmm) REVERT: E 97 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8085 (mtp180) REVERT: F 218 ASP cc_start: 0.8626 (t70) cc_final: 0.8199 (m-30) REVERT: F 220 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8030 (tt0) REVERT: F 229 ARG cc_start: 0.7719 (ttm170) cc_final: 0.6976 (tpp-160) REVERT: F 263 MET cc_start: 0.9290 (tpp) cc_final: 0.9018 (ttt) REVERT: F 280 ASP cc_start: 0.8736 (m-30) cc_final: 0.8034 (t0) REVERT: F 281 MET cc_start: 0.9071 (ttm) cc_final: 0.8843 (ptp) REVERT: F 285 CYS cc_start: 0.8450 (p) cc_final: 0.7961 (m) REVERT: F 286 ARG cc_start: 0.8404 (mtp85) cc_final: 0.8099 (mmm-85) REVERT: F 372 MET cc_start: 0.8178 (mmm) cc_final: 0.7522 (tpp) REVERT: F 402 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8264 (tm-30) REVERT: F 403 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8161 (mmt) REVERT: F 440 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7824 (pt0) REVERT: F 458 ASP cc_start: 0.7540 (m-30) cc_final: 0.7329 (m-30) REVERT: F 465 ASP cc_start: 0.8445 (m-30) cc_final: 0.7989 (m-30) REVERT: J 7 ARG cc_start: 0.8072 (ttm-80) cc_final: 0.7633 (mmm-85) REVERT: J 17 GLU cc_start: 0.6874 (tt0) cc_final: 0.6285 (mp0) REVERT: J 36 ASN cc_start: 0.8306 (p0) cc_final: 0.8068 (p0) REVERT: J 84 MET cc_start: 0.8122 (mtp) cc_final: 0.7754 (mtp) REVERT: J 88 ARG cc_start: 0.8622 (ptt-90) cc_final: 0.7048 (ptt-90) REVERT: M 95 LYS cc_start: 0.8689 (mtpp) cc_final: 0.8202 (tttm) REVERT: M 106 GLU cc_start: 0.8796 (tt0) cc_final: 0.8511 (tm-30) REVERT: M 145 THR cc_start: 0.8248 (OUTLIER) cc_final: 0.8036 (p) outliers start: 99 outliers final: 78 residues processed: 562 average time/residue: 0.1820 time to fit residues: 158.3276 Evaluate side-chains 560 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 471 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 646 GLU Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 758 ASP Chi-restraints excluded: chain C residue 824 ILE Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1038 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 397 ARG Chi-restraints excluded: chain D residue 407 LYS Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 700 LEU Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 1031 VAL Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 97 ARG Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 383 GLN Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 403 MET Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 427 ILE Chi-restraints excluded: chain F residue 440 GLU Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 46 ASP Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 32 LYS Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 145 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 247 optimal weight: 3.9990 chunk 159 optimal weight: 0.1980 chunk 319 optimal weight: 20.0000 chunk 323 optimal weight: 6.9990 chunk 225 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 260 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 138 optimal weight: 0.7980 chunk 305 optimal weight: 0.5980 chunk 320 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 443 ASN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 787 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.183838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.120164 restraints weight = 32520.023| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.29 r_work: 0.3063 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 29998 Z= 0.132 Angle : 0.631 17.703 41057 Z= 0.324 Chirality : 0.043 0.395 4681 Planarity : 0.005 0.063 5040 Dihedral : 15.737 175.088 4979 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.35 % Favored : 94.62 % Rotamer: Outliers : 2.94 % Allowed : 21.69 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.03 % 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: 3477 helix: 1.20 (0.14), residues: 1421 sheet: -0.48 (0.27), residues: 364 loop : -1.04 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 819 TYR 0.011 0.001 TYR C 344 PHE 0.031 0.001 PHE D 226 TRP 0.043 0.002 TRP J 82 HIS 0.005 0.001 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (29990) covalent geometry : angle 0.62547 / 0.32 (41045) hydrogen bonds : bond 0.03836 / 2.63 ( 1356) hydrogen bonds : angle 4.31767 / 3.08 ( 3777) metal coordination : bond 0.00703 / 0.37 ( 8) metal coordination : angle 4.88945 / 2.37 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 492 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8787 (pt0) cc_final: 0.8412 (pm20) REVERT: A 91 GLU cc_start: 0.7529 (tm-30) cc_final: 0.7248 (tm-30) REVERT: A 98 ARG cc_start: 0.7796 (mmm-85) cc_final: 0.7438 (mmt90) REVERT: A 133 LYS cc_start: 0.8926 (pttt) cc_final: 0.8511 (ptmt) REVERT: A 135 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7702 (mt-10) REVERT: A 188 ASP cc_start: 0.7369 (OUTLIER) cc_final: 0.7001 (m-30) REVERT: B 57 ASP cc_start: 0.8372 (m-30) cc_final: 0.8010 (m-30) REVERT: B 76 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8591 (tt) REVERT: B 99 LYS cc_start: 0.8402 (ttmm) cc_final: 0.7857 (ttmt) REVERT: C 49 GLU cc_start: 0.8181 (pm20) cc_final: 0.7536 (pm20) REVERT: C 67 SER cc_start: 0.8522 (m) cc_final: 0.8206 (p) REVERT: C 138 GLU cc_start: 0.7976 (tt0) cc_final: 0.7612 (tp30) REVERT: C 162 GLU cc_start: 0.8645 (pm20) cc_final: 0.8405 (pm20) REVERT: C 373 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8113 (m-80) REVERT: C 398 ARG cc_start: 0.7248 (mtt-85) cc_final: 0.6425 (ttp80) REVERT: C 415 GLN cc_start: 0.7820 (tt0) cc_final: 0.7416 (mt0) REVERT: C 429 GLU cc_start: 0.8317 (pt0) cc_final: 0.8061 (pt0) REVERT: C 465 ARG cc_start: 0.7899 (mtm180) cc_final: 0.7628 (mtm-85) REVERT: C 488 THR cc_start: 0.8447 (OUTLIER) cc_final: 0.8198 (m) REVERT: C 673 ARG cc_start: 0.8420 (ttp80) cc_final: 0.8153 (ttp-110) REVERT: C 753 GLU cc_start: 0.8446 (tp30) cc_final: 0.8115 (mm-30) REVERT: C 824 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7849 (mp) REVERT: C 857 ASP cc_start: 0.8233 (t0) cc_final: 0.7384 (t0) REVERT: C 947 ASP cc_start: 0.8422 (t70) cc_final: 0.7684 (p0) REVERT: C 985 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8492 (tp) REVERT: C 1015 SER cc_start: 0.9333 (m) cc_final: 0.8986 (p) REVERT: C 1063 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7457 (t80) REVERT: C 1090 THR cc_start: 0.9077 (m) cc_final: 0.8870 (p) REVERT: C 1101 LYS cc_start: 0.8154 (mmmm) cc_final: 0.7886 (mtmt) REVERT: D 8 ASP cc_start: 0.8101 (m-30) cc_final: 0.7797 (m-30) REVERT: D 56 ARG cc_start: 0.8191 (ttm-80) cc_final: 0.7878 (ttm-80) REVERT: D 66 LYS cc_start: 0.7772 (mtpt) cc_final: 0.7478 (mttp) REVERT: D 155 MET cc_start: 0.8850 (tpt) cc_final: 0.8574 (tpt) REVERT: D 205 MET cc_start: 0.8164 (tpt) cc_final: 0.7568 (mmm) REVERT: D 238 GLU cc_start: 0.8326 (pp20) cc_final: 0.7881 (tm-30) REVERT: D 259 GLU cc_start: 0.8435 (tm-30) cc_final: 0.7862 (pt0) REVERT: D 312 MET cc_start: 0.9051 (mtt) cc_final: 0.8747 (mtt) REVERT: D 470 LYS cc_start: 0.8151 (mtpt) cc_final: 0.7833 (mttm) REVERT: D 477 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8041 (mm-30) REVERT: D 488 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8356 (tt0) REVERT: D 762 ARG cc_start: 0.7438 (ptp-170) cc_final: 0.7191 (mtm-85) REVERT: D 928 ASP cc_start: 0.8011 (m-30) cc_final: 0.7706 (t0) REVERT: D 991 ILE cc_start: 0.9112 (mm) cc_final: 0.8834 (mm) REVERT: D 1112 MET cc_start: 0.7975 (mmt) cc_final: 0.7650 (mmm) REVERT: E 97 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8079 (mtp85) REVERT: F 218 ASP cc_start: 0.8628 (t70) cc_final: 0.8198 (m-30) REVERT: F 220 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8046 (tt0) REVERT: F 229 ARG cc_start: 0.7722 (ttm170) cc_final: 0.7179 (tpp-160) REVERT: F 263 MET cc_start: 0.9265 (tpp) cc_final: 0.8912 (ttt) REVERT: F 280 ASP cc_start: 0.8816 (m-30) cc_final: 0.8088 (t0) REVERT: F 281 MET cc_start: 0.9027 (ttm) cc_final: 0.8797 (ptp) REVERT: F 285 CYS cc_start: 0.8378 (p) cc_final: 0.7942 (m) REVERT: F 286 ARG cc_start: 0.8388 (mtp85) cc_final: 0.8087 (mmm-85) REVERT: F 372 MET cc_start: 0.8206 (mmm) cc_final: 0.7535 (tpp) REVERT: F 402 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8250 (tm-30) REVERT: F 403 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8117 (mmt) REVERT: F 440 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7920 (pt0) REVERT: F 458 ASP cc_start: 0.7522 (m-30) cc_final: 0.7311 (m-30) REVERT: J 7 ARG cc_start: 0.8071 (ttm-80) cc_final: 0.7657 (mmm-85) REVERT: J 17 GLU cc_start: 0.6878 (tt0) cc_final: 0.6294 (mp0) REVERT: J 36 ASN cc_start: 0.8300 (p0) cc_final: 0.8083 (p0) REVERT: J 84 MET cc_start: 0.8175 (mtp) cc_final: 0.7730 (mtp) REVERT: J 88 ARG cc_start: 0.8626 (ptt-90) cc_final: 0.7165 (ptt-90) REVERT: M 95 LYS cc_start: 0.8626 (mtpp) cc_final: 0.7868 (tttm) REVERT: M 106 GLU cc_start: 0.8806 (tt0) cc_final: 0.8502 (tm-30) REVERT: M 145 THR cc_start: 0.8140 (OUTLIER) cc_final: 0.7927 (p) outliers start: 86 outliers final: 71 residues processed: 558 average time/residue: 0.1964 time to fit residues: 169.9895 Evaluate side-chains 557 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 475 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 646 GLU Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 758 ASP Chi-restraints excluded: chain C residue 824 ILE Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1038 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 397 ARG Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 1031 VAL Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 97 ARG Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 383 GLN Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 403 MET Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 427 ILE Chi-restraints excluded: chain F residue 440 GLU Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 46 ASP Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 32 LYS Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 145 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 265 optimal weight: 9.9990 chunk 123 optimal weight: 0.5980 chunk 118 optimal weight: 8.9990 chunk 221 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 251 optimal weight: 2.9990 chunk 138 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 8 optimal weight: 0.2980 chunk 333 optimal weight: 50.0000 chunk 272 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 ASN B 152 ASN C 443 ASN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 787 GLN ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.184766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.121260 restraints weight = 32868.383| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.36 r_work: 0.3073 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 29998 Z= 0.128 Angle : 0.622 18.132 41057 Z= 0.319 Chirality : 0.043 0.542 4681 Planarity : 0.005 0.062 5040 Dihedral : 15.698 174.572 4979 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.09 % Favored : 94.88 % Rotamer: Outliers : 2.94 % Allowed : 22.00 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.03 % 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: 0.05 (0.14), residues: 3477 helix: 1.31 (0.14), residues: 1420 sheet: -0.29 (0.27), residues: 364 loop : -1.00 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 259 TYR 0.031 0.001 TYR D 248 PHE 0.021 0.001 PHE D 226 TRP 0.038 0.001 TRP J 82 HIS 0.005 0.001 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (29990) covalent geometry : angle 0.61732 / 0.32 (41045) hydrogen bonds : bond 0.03724 / 2.56 ( 1356) hydrogen bonds : angle 4.26655 / 3.04 ( 3777) metal coordination : bond 0.00621 / 0.33 ( 8) metal coordination : angle 4.70661 / 2.27 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9452.35 seconds wall clock time: 161 minutes 25.97 seconds (9685.97 seconds total)