Starting phenix.real_space_refine on Thu Mar 5 07:17:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uiq_64201/03_2026/9uiq_64201.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uiq_64201/03_2026/9uiq_64201.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uiq_64201/03_2026/9uiq_64201.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uiq_64201/03_2026/9uiq_64201.map" model { file = "/net/cci-nas-00/data/ceres_data/9uiq_64201/03_2026/9uiq_64201.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uiq_64201/03_2026/9uiq_64201.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians P 11 5.49 5 Mg 2 5.21 5 S 130 5.16 5 C 12466 2.51 5 N 3409 2.21 5 O 3760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19778 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3660 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 29, 'TRANS': 431} Chain breaks: 5 Chain: "B" Number of atoms: 2493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2493 Classifications: {'peptide': 316} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 303} Chain: "C" Number of atoms: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2534 Classifications: {'peptide': 318} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 305} Chain breaks: 1 Chain: "D" Number of atoms: 2311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2311 Classifications: {'peptide': 297} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 285} Chain breaks: 4 Chain: "E" Number of atoms: 2751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2751 Classifications: {'peptide': 345} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 330} Chain breaks: 1 Chain: "F" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1954 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain breaks: 1 Chain: "G" Number of atoms: 1981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1981 Classifications: {'peptide': 257} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 249} Chain: "H" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1972 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.15, per 1000 atoms: 0.21 Number of scatterers: 19778 At special positions: 0 Unit cell: (119.97, 118.11, 132.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 130 16.00 P 11 15.00 Mg 2 11.99 O 3760 8.00 N 3409 7.00 C 12466 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: 1.88 Conformation dependent library (CDL) restraints added in 909.3 milliseconds 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4764 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 14 sheets defined 53.4% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 290 through 294 removed outlier: 3.516A pdb=" N LEU A 294 " --> pdb=" O TYR A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 308 removed outlier: 4.202A pdb=" N LEU A 305 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LYS A 306 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TRP A 307 " --> pdb=" O CYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 392 removed outlier: 4.161A pdb=" N ALA A 384 " --> pdb=" O LYS A 380 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N HIS A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 419 removed outlier: 3.994A pdb=" N ALA A 415 " --> pdb=" O THR A 411 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA A 416 " --> pdb=" O ARG A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 428 Processing helix chain 'A' and resid 471 through 479 removed outlier: 3.565A pdb=" N GLU A 478 " --> pdb=" O ARG A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 503 removed outlier: 3.964A pdb=" N GLN A 500 " --> pdb=" O PRO A 496 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU A 501 " --> pdb=" O SER A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 530 removed outlier: 3.651A pdb=" N LEU A 527 " --> pdb=" O GLN A 523 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 545 Processing helix chain 'A' and resid 548 through 556 removed outlier: 3.907A pdb=" N ASN A 554 " --> pdb=" O ARG A 550 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A 556 " --> pdb=" O CYS A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 595 removed outlier: 4.290A pdb=" N VAL A 589 " --> pdb=" O GLY A 585 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TRP A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 639 removed outlier: 3.701A pdb=" N HIS A 637 " --> pdb=" O TYR A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 656 Processing helix chain 'A' and resid 665 through 689 removed outlier: 3.562A pdb=" N HIS A 687 " --> pdb=" O ALA A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 698 removed outlier: 3.775A pdb=" N ARG A 696 " --> pdb=" O GLN A 693 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TYR A 697 " --> pdb=" O LEU A 694 " (cutoff:3.500A) Proline residue: A 698 - end of helix Processing helix chain 'A' and resid 699 through 709 removed outlier: 4.227A pdb=" N VAL A 703 " --> pdb=" O PRO A 699 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL A 707 " --> pdb=" O VAL A 703 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU A 708 " --> pdb=" O ALA A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 743 removed outlier: 4.083A pdb=" N GLY A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 760 Processing helix chain 'A' and resid 761 through 767 removed outlier: 3.741A pdb=" N LEU A 765 " --> pdb=" O ALA A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 787 Processing helix chain 'A' and resid 788 through 799 Processing helix chain 'A' and resid 821 through 826 Processing helix chain 'A' and resid 837 through 855 removed outlier: 3.512A pdb=" N MET A 853 " --> pdb=" O GLU A 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 42 Processing helix chain 'B' and resid 46 through 50 removed outlier: 3.660A pdb=" N ILE B 50 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 67 Processing helix chain 'B' and resid 81 through 95 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.825A pdb=" N ILE B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LYS B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.693A pdb=" N MET B 146 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 161 removed outlier: 4.191A pdb=" N ARG B 156 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 177 Processing helix chain 'B' and resid 178 through 184 Processing helix chain 'B' and resid 194 through 210 Processing helix chain 'B' and resid 214 through 226 Processing helix chain 'B' and resid 228 through 244 Processing helix chain 'B' and resid 247 through 255 Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 274 through 288 Processing helix chain 'B' and resid 291 through 306 removed outlier: 4.066A pdb=" N THR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 329 Processing helix chain 'B' and resid 333 through 348 removed outlier: 3.687A pdb=" N MET B 337 " --> pdb=" O SER B 333 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 26 Processing helix chain 'C' and resid 30 through 34 Processing helix chain 'C' and resid 37 through 50 Processing helix chain 'C' and resid 65 through 78 Processing helix chain 'C' and resid 79 through 86 removed outlier: 4.156A pdb=" N GLY C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N SER C 85 " --> pdb=" O LYS C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 95 No H-bonds generated for 'chain 'C' and resid 93 through 95' Processing helix chain 'C' and resid 99 through 103 Processing helix chain 'C' and resid 103 through 110 Processing helix chain 'C' and resid 126 through 130 Processing helix chain 'C' and resid 131 through 145 Processing helix chain 'C' and resid 157 through 161 Processing helix chain 'C' and resid 164 through 168 Processing helix chain 'C' and resid 178 through 193 Proline residue: C 184 - end of helix Processing helix chain 'C' and resid 198 through 210 Processing helix chain 'C' and resid 212 through 228 Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 243 through 257 Processing helix chain 'C' and resid 258 through 274 Processing helix chain 'C' and resid 276 through 291 Processing helix chain 'C' and resid 294 through 314 removed outlier: 3.658A pdb=" N SER C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL C 314 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 338 removed outlier: 4.181A pdb=" N THR C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG C 333 " --> pdb=" O PHE C 329 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASP C 334 " --> pdb=" O GLN C 330 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU C 335 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 45 Processing helix chain 'D' and resid 56 through 65 removed outlier: 3.979A pdb=" N ALA D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 82 Processing helix chain 'D' and resid 83 through 97 Processing helix chain 'D' and resid 116 through 129 removed outlier: 3.778A pdb=" N LEU D 129 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 155 Processing helix chain 'D' and resid 156 through 168 Processing helix chain 'D' and resid 181 through 185 removed outlier: 3.667A pdb=" N SER D 184 " --> pdb=" O ASN D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 191 removed outlier: 3.642A pdb=" N LEU D 190 " --> pdb=" O ILE D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'D' and resid 223 through 234 Processing helix chain 'D' and resid 239 through 253 removed outlier: 3.651A pdb=" N THR D 243 " --> pdb=" O ARG D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 267 Processing helix chain 'D' and resid 270 through 284 removed outlier: 3.581A pdb=" N ILE D 274 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY D 284 " --> pdb=" O ALA D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 299 removed outlier: 3.535A pdb=" N LEU D 289 " --> pdb=" O SER D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 316 removed outlier: 3.909A pdb=" N GLU D 316 " --> pdb=" O ASP D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 340 Processing helix chain 'D' and resid 343 through 360 Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 12 through 16 Processing helix chain 'E' and resid 19 through 32 Processing helix chain 'E' and resid 47 through 60 Processing helix chain 'E' and resid 61 through 66 Processing helix chain 'E' and resid 96 through 102 removed outlier: 6.725A pdb=" N ASN E 102 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 120 removed outlier: 3.852A pdb=" N GLN E 120 " --> pdb=" O ALA E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 140 Processing helix chain 'E' and resid 141 through 155 Processing helix chain 'E' and resid 172 through 177 Processing helix chain 'E' and resid 188 through 203 Processing helix chain 'E' and resid 208 through 220 Processing helix chain 'E' and resid 222 through 237 Processing helix chain 'E' and resid 249 through 265 Processing helix chain 'E' and resid 267 through 284 removed outlier: 3.645A pdb=" N HIS E 284 " --> pdb=" O GLU E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 301 removed outlier: 3.729A pdb=" N HIS E 301 " --> pdb=" O SER E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 306 No H-bonds generated for 'chain 'E' and resid 304 through 306' Processing helix chain 'E' and resid 307 through 325 Processing helix chain 'E' and resid 327 through 348 removed outlier: 4.025A pdb=" N HIS E 331 " --> pdb=" O LYS E 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 21 removed outlier: 4.358A pdb=" N LEU F 12 " --> pdb=" O GLN F 8 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP F 21 " --> pdb=" O GLU F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 57 No H-bonds generated for 'chain 'F' and resid 55 through 57' Processing helix chain 'F' and resid 72 through 81 removed outlier: 3.965A pdb=" N CYS F 81 " --> pdb=" O LYS F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 155 removed outlier: 3.654A pdb=" N HIS F 153 " --> pdb=" O ARG F 149 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE F 154 " --> pdb=" O ASP F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 217 through 222 Proline residue: F 220 - end of helix No H-bonds generated for 'chain 'F' and resid 217 through 222' Processing helix chain 'G' and resid 9 through 21 removed outlier: 3.847A pdb=" N LYS G 13 " --> pdb=" O GLY G 9 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU G 19 " --> pdb=" O VAL G 15 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASP G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 57 No H-bonds generated for 'chain 'G' and resid 55 through 57' Processing helix chain 'G' and resid 72 through 80 Processing helix chain 'G' and resid 141 through 155 removed outlier: 3.865A pdb=" N HIS G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE G 154 " --> pdb=" O ASP G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 216 Processing helix chain 'G' and resid 217 through 222 Proline residue: G 220 - end of helix No H-bonds generated for 'chain 'G' and resid 217 through 222' Processing helix chain 'H' and resid 8 through 20 removed outlier: 4.453A pdb=" N LEU H 12 " --> pdb=" O GLN H 8 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU H 16 " --> pdb=" O LEU H 12 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU H 17 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA H 18 " --> pdb=" O LYS H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 57 No H-bonds generated for 'chain 'H' and resid 55 through 57' Processing helix chain 'H' and resid 72 through 80 removed outlier: 3.599A pdb=" N LYS H 80 " --> pdb=" O SER H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 155 removed outlier: 3.819A pdb=" N HIS H 153 " --> pdb=" O ARG H 149 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE H 154 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 216 Processing helix chain 'H' and resid 217 through 219 No H-bonds generated for 'chain 'H' and resid 217 through 219' Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 180 Processing sheet with id=AA2, first strand: chain 'A' and resid 394 through 397 Processing sheet with id=AA3, first strand: chain 'A' and resid 803 through 807 Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.381A pdb=" N LEU B 103 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LYS B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ALA B 168 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE B 138 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ALA B 170 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU B 140 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE B 72 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N CYS B 171 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ILE B 74 " --> pdb=" O CYS B 171 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE B 73 " --> pdb=" O LEU B 188 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 87 through 91 removed outlier: 6.494A pdb=" N LEU C 88 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ASP C 125 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU C 90 " --> pdb=" O ASP C 125 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LYS C 120 " --> pdb=" O ARG C 150 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N CYS C 152 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL C 122 " --> pdb=" O CYS C 152 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ILE C 154 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU C 124 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU C 56 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N CYS C 155 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU C 58 " --> pdb=" O CYS C 155 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU C 57 " --> pdb=" O PHE C 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 196 through 197 removed outlier: 6.637A pdb=" N ASP C 196 " --> pdb=" O VAL C 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 145 through 147 removed outlier: 6.297A pdb=" N LEU D 75 " --> pdb=" O PHE D 197 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 68 through 74 removed outlier: 6.604A pdb=" N LEU E 93 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N THR E 135 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL E 95 " --> pdb=" O THR E 135 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LYS E 130 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE E 162 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL E 132 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N CYS E 164 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU E 134 " --> pdb=" O CYS E 164 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 59 through 62 removed outlier: 3.592A pdb=" N THR F 59 " --> pdb=" O ARG F 5 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER G 172 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ALA G 157 " --> pdb=" O SER G 172 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL G 203 " --> pdb=" O CYS G 162 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 66 through 71 removed outlier: 8.211A pdb=" N GLU F 25 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N MET F 40 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N CYS F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLN F 38 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY F 245 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LYS F 240 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N THR F 224 " --> pdb=" O LYS F 240 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 204 through 208 removed outlier: 5.275A pdb=" N ALA F 157 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER F 172 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN F 177 " --> pdb=" O GLU H 115 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU H 115 " --> pdb=" O ASN F 177 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS F 181 " --> pdb=" O VAL H 111 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL H 111 " --> pdb=" O LYS F 181 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER H 112 " --> pdb=" O PHE H 103 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL H 102 " --> pdb=" O THR H 89 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR H 59 " --> pdb=" O ARG H 5 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 59 through 60 removed outlier: 3.730A pdb=" N ASN H 177 " --> pdb=" O GLU G 115 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER H 172 " --> pdb=" O ALA H 157 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ALA H 157 " --> pdb=" O SER H 172 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 66 through 71 removed outlier: 7.494A pdb=" N GLU G 25 " --> pdb=" O MET G 40 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N MET G 40 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N CYS G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLN G 38 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N SER G 230 " --> pdb=" O PRO G 234 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 69 through 71 removed outlier: 6.657A pdb=" N GLU H 25 " --> pdb=" O MET H 40 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N MET H 40 " --> pdb=" O GLU H 25 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N CYS H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN H 38 " --> pdb=" O CYS H 27 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER H 39 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL H 48 " --> pdb=" O SER H 39 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY H 245 " --> pdb=" O ILE H 241 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N SER H 230 " --> pdb=" O PRO H 234 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS H 240 " --> pdb=" O THR H 224 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N THR H 224 " --> pdb=" O LYS H 240 " (cutoff:3.500A) 1076 hydrogen bonds defined for protein. 3063 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.57 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6543 1.34 - 1.46: 3008 1.46 - 1.58: 10320 1.58 - 1.69: 19 1.69 - 1.81: 200 Bond restraints: 20090 Sorted by residual: bond pdb=" CB PRO A 771 " pdb=" CG PRO A 771 " ideal model delta sigma weight residual 1.492 1.602 -0.110 5.00e-02 4.00e+02 4.85e+00 bond pdb=" CG1 ILE C 284 " pdb=" CD1 ILE C 284 " ideal model delta sigma weight residual 1.513 1.443 0.070 3.90e-02 6.57e+02 3.18e+00 bond pdb=" CB GLU A 847 " pdb=" CG GLU A 847 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.07e+00 bond pdb=" CG GLU A 847 " pdb=" CD GLU A 847 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.65e+00 bond pdb=" CB ARG D 105 " pdb=" CG ARG D 105 " ideal model delta sigma weight residual 1.520 1.483 0.037 3.00e-02 1.11e+03 1.53e+00 ... (remaining 20085 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 26532 1.70 - 3.39: 503 3.39 - 5.09: 106 5.09 - 6.78: 26 6.78 - 8.48: 7 Bond angle restraints: 27174 Sorted by residual: angle pdb=" N GLU A 847 " pdb=" CA GLU A 847 " pdb=" CB GLU A 847 " ideal model delta sigma weight residual 110.22 116.77 -6.55 1.54e+00 4.22e-01 1.81e+01 angle pdb=" CA GLU A 847 " pdb=" CB GLU A 847 " pdb=" CG GLU A 847 " ideal model delta sigma weight residual 114.10 122.16 -8.06 2.00e+00 2.50e-01 1.62e+01 angle pdb=" CA PRO A 771 " pdb=" N PRO A 771 " pdb=" CD PRO A 771 " ideal model delta sigma weight residual 112.00 106.58 5.42 1.40e+00 5.10e-01 1.50e+01 angle pdb=" CB GLU A 847 " pdb=" CG GLU A 847 " pdb=" CD GLU A 847 " ideal model delta sigma weight residual 112.60 119.16 -6.56 1.70e+00 3.46e-01 1.49e+01 angle pdb=" C GLU D 168 " pdb=" N LYS D 169 " pdb=" CA LYS D 169 " ideal model delta sigma weight residual 121.54 128.27 -6.73 1.91e+00 2.74e-01 1.24e+01 ... (remaining 27169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.30: 12031 27.30 - 54.60: 375 54.60 - 81.90: 28 81.90 - 109.19: 7 109.19 - 136.49: 1 Dihedral angle restraints: 12442 sinusoidal: 5128 harmonic: 7314 Sorted by residual: dihedral pdb=" O2A ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PA ADP E 401 " pdb=" PB ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 76.49 -136.49 1 2.00e+01 2.50e-03 4.14e+01 dihedral pdb=" CA ILE D 186 " pdb=" C ILE D 186 " pdb=" N ILE D 187 " pdb=" CA ILE D 187 " ideal model delta harmonic sigma weight residual -180.00 -156.17 -23.83 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA MET F 119 " pdb=" C MET F 119 " pdb=" N ASP F 120 " pdb=" CA ASP F 120 " ideal model delta harmonic sigma weight residual 180.00 158.63 21.37 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 12439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2449 0.045 - 0.089: 544 0.089 - 0.134: 166 0.134 - 0.178: 9 0.178 - 0.223: 2 Chirality restraints: 3170 Sorted by residual: chirality pdb=" CB ILE G 128 " pdb=" CA ILE G 128 " pdb=" CG1 ILE G 128 " pdb=" CG2 ILE G 128 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA GLU A 847 " pdb=" N GLU A 847 " pdb=" C GLU A 847 " pdb=" CB GLU A 847 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.64e-01 chirality pdb=" CA GLU D 188 " pdb=" N GLU D 188 " pdb=" C GLU D 188 " pdb=" CB GLU D 188 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.30e-01 ... (remaining 3167 not shown) Planarity restraints: 3461 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 279 " 0.017 2.00e-02 2.50e+03 1.82e-02 6.64e+00 pdb=" CG TYR B 279 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR B 279 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR B 279 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR B 279 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 279 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 279 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 279 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 188 " -0.038 5.00e-02 4.00e+02 5.71e-02 5.21e+00 pdb=" N PRO D 189 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 189 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 189 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 126 " -0.019 2.00e-02 2.50e+03 1.65e-02 4.78e+00 pdb=" CG PHE D 126 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE D 126 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE D 126 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE D 126 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 126 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE D 126 " -0.000 2.00e-02 2.50e+03 ... (remaining 3458 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 272 2.58 - 3.16: 17360 3.16 - 3.74: 32271 3.74 - 4.32: 42889 4.32 - 4.90: 70729 Nonbonded interactions: 163521 Sorted by model distance: nonbonded pdb="MG MG C 401 " pdb=" O3G ATP C 402 " model vdw 2.005 2.170 nonbonded pdb="MG MG B 401 " pdb=" O1B ATP B 402 " model vdw 2.046 2.170 nonbonded pdb="MG MG C 401 " pdb=" O1B ATP C 402 " model vdw 2.089 2.170 nonbonded pdb="MG MG C 401 " pdb=" O1A ATP C 402 " model vdw 2.093 2.170 nonbonded pdb=" OG1 THR C 67 " pdb="MG MG C 401 " model vdw 2.137 2.170 ... (remaining 163516 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 'F' selection = (chain 'G' and (resid 1 through 189 or resid 191 through 255)) selection = (chain 'H' and (resid 1 through 189 or resid 191 through 255)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.220 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 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 : 0.003 0.110 20090 Z= 0.140 Angle : 0.612 8.475 27174 Z= 0.321 Chirality : 0.041 0.223 3170 Planarity : 0.004 0.057 3461 Dihedral : 12.637 136.494 7678 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.33 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.18), residues: 2464 helix: 1.62 (0.16), residues: 1139 sheet: 0.59 (0.24), residues: 478 loop : -0.07 (0.23), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 146 TYR 0.045 0.002 TYR B 279 PHE 0.037 0.001 PHE D 126 TRP 0.025 0.001 TRP H 28 HIS 0.012 0.001 HIS E 194 Details of bonding type rmsd covalent geometry : bond 0.00314 (20090) covalent geometry : angle 0.61180 (27174) hydrogen bonds : bond 0.19739 ( 1076) hydrogen bonds : angle 7.02996 ( 3063) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 HIS cc_start: 0.7791 (t70) cc_final: 0.7568 (t70) REVERT: A 473 ARG cc_start: 0.9081 (ptt90) cc_final: 0.8846 (ppt90) REVERT: A 730 MET cc_start: 0.9233 (tpp) cc_final: 0.8889 (tpp) REVERT: A 847 GLU cc_start: 0.8885 (mp0) cc_final: 0.8653 (mp0) REVERT: B 175 ASP cc_start: 0.8689 (p0) cc_final: 0.8347 (p0) REVERT: B 176 LYS cc_start: 0.9297 (mmtp) cc_final: 0.9016 (mmmm) REVERT: C 90 LEU cc_start: 0.9131 (mt) cc_final: 0.8762 (mp) REVERT: D 229 TYR cc_start: 0.8908 (t80) cc_final: 0.8531 (t80) REVERT: E 110 GLU cc_start: 0.9465 (mm-30) cc_final: 0.9104 (mm-30) REVERT: E 111 MET cc_start: 0.9485 (mmp) cc_final: 0.9175 (mmm) REVERT: F 17 GLU cc_start: 0.8820 (tp30) cc_final: 0.8560 (tp30) REVERT: F 38 GLN cc_start: 0.7980 (tt0) cc_final: 0.7728 (tt0) REVERT: G 1 MET cc_start: 0.8355 (tpp) cc_final: 0.7255 (tpp) REVERT: G 38 GLN cc_start: 0.9016 (tt0) cc_final: 0.8700 (tt0) REVERT: G 119 MET cc_start: 0.8231 (mmm) cc_final: 0.8012 (mmm) REVERT: H 2 PHE cc_start: 0.8773 (t80) cc_final: 0.8559 (t80) REVERT: H 90 LEU cc_start: 0.9028 (tp) cc_final: 0.8692 (tp) REVERT: H 204 GLN cc_start: 0.8944 (tm-30) cc_final: 0.8699 (mp-120) REVERT: H 214 PHE cc_start: 0.9313 (m-10) cc_final: 0.8844 (m-80) REVERT: H 244 MET cc_start: 0.8857 (ppp) cc_final: 0.8087 (tmm) REVERT: H 250 TYR cc_start: 0.8967 (m-80) cc_final: 0.8606 (m-80) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.1522 time to fit residues: 58.2190 Evaluate side-chains 196 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 50.0000 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 GLN A 713 HIS A 738 GLN B 118 ASN B 182 GLN B 298 ASN ** C 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN D 361 GLN ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.081673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.055515 restraints weight = 76208.171| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 4.93 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 20090 Z= 0.282 Angle : 0.690 10.422 27174 Z= 0.357 Chirality : 0.044 0.184 3170 Planarity : 0.005 0.052 3461 Dihedral : 7.899 141.819 2808 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.02 % Favored : 95.94 % Rotamer: Outliers : 0.69 % Allowed : 7.90 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.18), residues: 2464 helix: 1.44 (0.15), residues: 1155 sheet: 0.23 (0.23), residues: 510 loop : -0.18 (0.24), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 634 TYR 0.034 0.002 TYR B 279 PHE 0.019 0.002 PHE G 169 TRP 0.012 0.002 TRP A 282 HIS 0.010 0.001 HIS E 194 Details of bonding type rmsd covalent geometry : bond 0.00606 (20090) covalent geometry : angle 0.68974 (27174) hydrogen bonds : bond 0.04637 ( 1076) hydrogen bonds : angle 5.55048 ( 3063) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 206 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 HIS cc_start: 0.7802 (t70) cc_final: 0.7594 (t70) REVERT: A 473 ARG cc_start: 0.9133 (ptt90) cc_final: 0.8916 (ppt90) REVERT: A 524 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7761 (pm20) REVERT: B 175 ASP cc_start: 0.9016 (p0) cc_final: 0.8666 (p0) REVERT: B 176 LYS cc_start: 0.9541 (mmtp) cc_final: 0.9171 (mmmm) REVERT: B 308 MET cc_start: 0.8559 (ppp) cc_final: 0.8201 (ppp) REVERT: C 90 LEU cc_start: 0.9156 (mt) cc_final: 0.8867 (mp) REVERT: D 172 LYS cc_start: 0.9258 (ptmm) cc_final: 0.8870 (tmtt) REVERT: E 106 VAL cc_start: 0.9657 (m) cc_final: 0.9041 (p) REVERT: E 110 GLU cc_start: 0.9511 (mm-30) cc_final: 0.9113 (mm-30) REVERT: F 17 GLU cc_start: 0.9249 (tp30) cc_final: 0.9003 (tp30) REVERT: F 68 MET cc_start: 0.8926 (ppp) cc_final: 0.8517 (ppp) REVERT: G 1 MET cc_start: 0.8388 (tpp) cc_final: 0.7472 (tpp) REVERT: G 38 GLN cc_start: 0.9091 (tt0) cc_final: 0.8665 (tt0) REVERT: G 45 VAL cc_start: 0.9201 (OUTLIER) cc_final: 0.8876 (m) REVERT: G 117 LYS cc_start: 0.8253 (mttt) cc_final: 0.8005 (mttt) REVERT: G 146 ARG cc_start: 0.8852 (mmm-85) cc_final: 0.8517 (mmm-85) REVERT: H 1 MET cc_start: 0.8998 (tpt) cc_final: 0.8703 (tpp) REVERT: H 2 PHE cc_start: 0.8736 (t80) cc_final: 0.8367 (t80) REVERT: H 91 ARG cc_start: 0.8586 (mmm-85) cc_final: 0.8366 (mmm-85) REVERT: H 204 GLN cc_start: 0.8888 (tm-30) cc_final: 0.8605 (tm-30) REVERT: H 214 PHE cc_start: 0.9324 (m-10) cc_final: 0.8849 (m-80) REVERT: H 244 MET cc_start: 0.9093 (ppp) cc_final: 0.8504 (tmm) outliers start: 15 outliers final: 6 residues processed: 216 average time/residue: 0.1544 time to fit residues: 48.8338 Evaluate side-chains 189 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 181 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 73 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 54 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 chunk 239 optimal weight: 8.9990 chunk 135 optimal weight: 2.9990 chunk 198 optimal weight: 8.9990 chunk 183 optimal weight: 40.0000 chunk 226 optimal weight: 20.0000 chunk 225 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 HIS B 336 GLN C 132 GLN D 125 ASN ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 HIS E 265 GLN F 49 GLN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.083589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.057261 restraints weight = 75621.939| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 4.99 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20090 Z= 0.132 Angle : 0.594 9.068 27174 Z= 0.303 Chirality : 0.042 0.158 3170 Planarity : 0.004 0.052 3461 Dihedral : 7.657 142.400 2808 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.49 % Favored : 96.47 % Rotamer: Outliers : 1.23 % Allowed : 8.95 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.17), residues: 2464 helix: 1.52 (0.15), residues: 1155 sheet: 0.13 (0.22), residues: 509 loop : -0.21 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 185 TYR 0.032 0.001 TYR B 279 PHE 0.020 0.001 PHE G 215 TRP 0.010 0.001 TRP F 28 HIS 0.010 0.001 HIS E 194 Details of bonding type rmsd covalent geometry : bond 0.00283 (20090) covalent geometry : angle 0.59435 (27174) hydrogen bonds : bond 0.03845 ( 1076) hydrogen bonds : angle 5.12442 ( 3063) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 221 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 HIS cc_start: 0.7803 (t70) cc_final: 0.7567 (t70) REVERT: A 473 ARG cc_start: 0.9146 (ptt90) cc_final: 0.8884 (ppt90) REVERT: A 509 HIS cc_start: 0.8281 (t70) cc_final: 0.7308 (m-70) REVERT: A 730 MET cc_start: 0.9440 (tpp) cc_final: 0.8976 (tpp) REVERT: B 175 ASP cc_start: 0.8985 (p0) cc_final: 0.8654 (p0) REVERT: B 176 LYS cc_start: 0.9552 (mmtp) cc_final: 0.9147 (mmmm) REVERT: B 308 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8170 (ppp) REVERT: C 90 LEU cc_start: 0.9200 (mt) cc_final: 0.8892 (mp) REVERT: C 213 MET cc_start: 0.8414 (tpt) cc_final: 0.8026 (tpp) REVERT: D 172 LYS cc_start: 0.9236 (ptmm) cc_final: 0.8883 (tmtt) REVERT: E 106 VAL cc_start: 0.9628 (m) cc_final: 0.9030 (p) REVERT: E 110 GLU cc_start: 0.9500 (mm-30) cc_final: 0.9089 (mm-30) REVERT: E 111 MET cc_start: 0.9429 (mmm) cc_final: 0.9219 (mmm) REVERT: F 17 GLU cc_start: 0.9217 (tp30) cc_final: 0.8941 (tp30) REVERT: F 68 MET cc_start: 0.8766 (ppp) cc_final: 0.8334 (ppp) REVERT: F 244 MET cc_start: 0.8825 (mmm) cc_final: 0.8394 (mmm) REVERT: G 1 MET cc_start: 0.8440 (tpp) cc_final: 0.8239 (tpp) REVERT: G 38 GLN cc_start: 0.9065 (tt0) cc_final: 0.8628 (tt0) REVERT: G 49 GLN cc_start: 0.8305 (tm-30) cc_final: 0.7794 (tm-30) REVERT: G 211 TYR cc_start: 0.9262 (m-80) cc_final: 0.8900 (m-80) REVERT: H 1 MET cc_start: 0.9001 (tpt) cc_final: 0.8749 (tpp) REVERT: H 153 HIS cc_start: 0.9383 (m170) cc_final: 0.8991 (m-70) REVERT: H 214 PHE cc_start: 0.9310 (m-10) cc_final: 0.8781 (m-80) REVERT: H 244 MET cc_start: 0.9193 (ppp) cc_final: 0.8808 (tmm) outliers start: 27 outliers final: 11 residues processed: 237 average time/residue: 0.1504 time to fit residues: 53.5209 Evaluate side-chains 204 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 192 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 679 ASP Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 125 GLN Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 68 MET Chi-restraints excluded: chain H residue 219 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 70 optimal weight: 1.9990 chunk 240 optimal weight: 30.0000 chunk 119 optimal weight: 8.9990 chunk 217 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 192 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 226 optimal weight: 8.9990 chunk 40 optimal weight: 30.0000 chunk 153 optimal weight: 0.9980 chunk 171 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 HIS B 298 ASN ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.083970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.057710 restraints weight = 75753.331| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 4.96 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20090 Z= 0.127 Angle : 0.590 10.192 27174 Z= 0.298 Chirality : 0.041 0.155 3170 Planarity : 0.004 0.053 3461 Dihedral : 7.447 139.859 2808 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.73 % Favored : 96.23 % Rotamer: Outliers : 1.14 % Allowed : 10.46 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.17), residues: 2464 helix: 1.58 (0.15), residues: 1161 sheet: 0.13 (0.22), residues: 510 loop : -0.22 (0.24), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 149 TYR 0.033 0.001 TYR B 279 PHE 0.022 0.001 PHE G 215 TRP 0.009 0.001 TRP F 28 HIS 0.004 0.001 HIS E 37 Details of bonding type rmsd covalent geometry : bond 0.00276 (20090) covalent geometry : angle 0.59040 (27174) hydrogen bonds : bond 0.03487 ( 1076) hydrogen bonds : angle 4.86141 ( 3063) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 216 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 HIS cc_start: 0.7851 (t70) cc_final: 0.7611 (t70) REVERT: A 473 ARG cc_start: 0.9185 (ptt90) cc_final: 0.8891 (ppt90) REVERT: A 509 HIS cc_start: 0.8293 (t70) cc_final: 0.7373 (m-70) REVERT: B 175 ASP cc_start: 0.9020 (p0) cc_final: 0.8685 (p0) REVERT: B 176 LYS cc_start: 0.9571 (mmtp) cc_final: 0.9150 (mmmm) REVERT: B 229 MET cc_start: 0.8902 (tpp) cc_final: 0.8618 (tpp) REVERT: C 90 LEU cc_start: 0.9221 (mt) cc_final: 0.8908 (mp) REVERT: C 213 MET cc_start: 0.8397 (tpt) cc_final: 0.8082 (tpp) REVERT: C 225 MET cc_start: 0.8740 (tmm) cc_final: 0.8495 (tmm) REVERT: D 172 LYS cc_start: 0.9266 (ptmm) cc_final: 0.8895 (tmtt) REVERT: E 106 VAL cc_start: 0.9630 (m) cc_final: 0.8973 (p) REVERT: E 110 GLU cc_start: 0.9492 (mm-30) cc_final: 0.9064 (mm-30) REVERT: E 194 HIS cc_start: 0.8904 (t70) cc_final: 0.8656 (t-90) REVERT: E 201 LYS cc_start: 0.9628 (tppt) cc_final: 0.9350 (mmtm) REVERT: E 213 HIS cc_start: 0.9135 (m-70) cc_final: 0.8760 (m90) REVERT: F 17 GLU cc_start: 0.9237 (tp30) cc_final: 0.8931 (tp30) REVERT: F 68 MET cc_start: 0.8696 (ppp) cc_final: 0.8408 (ppp) REVERT: G 38 GLN cc_start: 0.9061 (tt0) cc_final: 0.8558 (tt0) REVERT: G 49 GLN cc_start: 0.8316 (tm-30) cc_final: 0.7793 (tm-30) REVERT: G 80 LYS cc_start: 0.9311 (mppt) cc_final: 0.8975 (mptt) REVERT: G 211 TYR cc_start: 0.9241 (m-80) cc_final: 0.8925 (m-80) REVERT: H 1 MET cc_start: 0.8982 (tpt) cc_final: 0.8525 (tpp) REVERT: H 61 ARG cc_start: 0.9005 (ppt170) cc_final: 0.8526 (ptm-80) REVERT: H 153 HIS cc_start: 0.9372 (m170) cc_final: 0.8977 (m-70) REVERT: H 214 PHE cc_start: 0.9281 (m-10) cc_final: 0.8758 (m-80) REVERT: H 235 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.8999 (pp) REVERT: H 244 MET cc_start: 0.9165 (ppp) cc_final: 0.8870 (tmm) outliers start: 25 outliers final: 12 residues processed: 231 average time/residue: 0.1462 time to fit residues: 50.9028 Evaluate side-chains 209 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 196 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain H residue 2 PHE Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 68 MET Chi-restraints excluded: chain H residue 235 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 14 optimal weight: 50.0000 chunk 168 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 HIS B 298 ASN ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 HIS ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 125 GLN ** H 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 204 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.083278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.057028 restraints weight = 74767.546| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 4.92 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20090 Z= 0.152 Angle : 0.596 10.105 27174 Z= 0.298 Chirality : 0.041 0.198 3170 Planarity : 0.004 0.052 3461 Dihedral : 7.342 139.361 2808 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.81 % Favored : 96.14 % Rotamer: Outliers : 1.42 % Allowed : 11.51 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.17), residues: 2464 helix: 1.64 (0.15), residues: 1161 sheet: 0.09 (0.22), residues: 510 loop : -0.23 (0.23), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 64 TYR 0.033 0.001 TYR B 279 PHE 0.020 0.001 PHE G 215 TRP 0.007 0.001 TRP F 28 HIS 0.005 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00329 (20090) covalent geometry : angle 0.59594 (27174) hydrogen bonds : bond 0.03414 ( 1076) hydrogen bonds : angle 4.74836 ( 3063) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: A 390 HIS cc_start: 0.7841 (t70) cc_final: 0.7579 (t70) REVERT: A 473 ARG cc_start: 0.9181 (ptt90) cc_final: 0.8898 (ppt90) REVERT: A 524 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8099 (pm20) REVERT: B 175 ASP cc_start: 0.9038 (p0) cc_final: 0.8724 (p0) REVERT: B 176 LYS cc_start: 0.9568 (mmtp) cc_final: 0.9154 (mmmm) REVERT: B 229 MET cc_start: 0.9007 (tpp) cc_final: 0.8781 (tpp) REVERT: B 308 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8247 (ppp) REVERT: C 90 LEU cc_start: 0.9214 (mt) cc_final: 0.8998 (mp) REVERT: C 213 MET cc_start: 0.8626 (tpt) cc_final: 0.8381 (tpp) REVERT: C 225 MET cc_start: 0.8731 (tmm) cc_final: 0.8465 (tmm) REVERT: D 172 LYS cc_start: 0.9239 (ptmm) cc_final: 0.8883 (tmtt) REVERT: E 106 VAL cc_start: 0.9644 (m) cc_final: 0.8971 (p) REVERT: E 110 GLU cc_start: 0.9496 (mm-30) cc_final: 0.9076 (mm-30) REVERT: E 111 MET cc_start: 0.9432 (mmm) cc_final: 0.9230 (mmm) REVERT: E 194 HIS cc_start: 0.8937 (t70) cc_final: 0.8671 (t70) REVERT: E 201 LYS cc_start: 0.9634 (tppt) cc_final: 0.9360 (mmtm) REVERT: E 213 HIS cc_start: 0.9078 (m-70) cc_final: 0.8718 (m90) REVERT: F 44 HIS cc_start: 0.8488 (t-90) cc_final: 0.8215 (t70) REVERT: G 1 MET cc_start: 0.8507 (tpp) cc_final: 0.8048 (tpp) REVERT: G 38 GLN cc_start: 0.8996 (tt0) cc_final: 0.8406 (tt0) REVERT: G 49 GLN cc_start: 0.8380 (tm-30) cc_final: 0.7858 (tm-30) REVERT: G 64 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7480 (pmt-80) REVERT: G 211 TYR cc_start: 0.9259 (m-80) cc_final: 0.8940 (m-80) REVERT: H 1 MET cc_start: 0.9006 (tpt) cc_final: 0.8551 (tpp) REVERT: H 40 MET cc_start: 0.7788 (tpp) cc_final: 0.7466 (tpp) REVERT: H 61 ARG cc_start: 0.9004 (ppt170) cc_final: 0.8665 (ptm-80) REVERT: H 79 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9290 (mm) REVERT: H 91 ARG cc_start: 0.8564 (mmm-85) cc_final: 0.8254 (mmm-85) REVERT: H 153 HIS cc_start: 0.9358 (m170) cc_final: 0.8992 (m-70) REVERT: H 214 PHE cc_start: 0.9292 (m-10) cc_final: 0.8772 (m-80) REVERT: H 229 MET cc_start: 0.8322 (pmm) cc_final: 0.8071 (pmm) REVERT: H 232 ASP cc_start: 0.8703 (m-30) cc_final: 0.8155 (t0) REVERT: H 235 LEU cc_start: 0.9428 (tp) cc_final: 0.8740 (pp) REVERT: H 244 MET cc_start: 0.9130 (ppp) cc_final: 0.8841 (tmm) outliers start: 31 outliers final: 18 residues processed: 224 average time/residue: 0.1435 time to fit residues: 48.8549 Evaluate side-chains 211 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 679 ASP Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 68 MET Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 219 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 229 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 19 optimal weight: 0.3980 chunk 181 optimal weight: 8.9990 chunk 180 optimal weight: 9.9990 chunk 16 optimal weight: 0.3980 chunk 52 optimal weight: 0.0000 chunk 209 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 222 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 ASN A 713 HIS B 298 ASN ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.084300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.057920 restraints weight = 74698.667| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 4.97 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20090 Z= 0.113 Angle : 0.583 10.205 27174 Z= 0.291 Chirality : 0.041 0.150 3170 Planarity : 0.004 0.052 3461 Dihedral : 7.257 139.008 2808 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.37 % Favored : 96.59 % Rotamer: Outliers : 1.23 % Allowed : 12.29 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.17), residues: 2464 helix: 1.62 (0.16), residues: 1165 sheet: 0.10 (0.22), residues: 506 loop : -0.31 (0.23), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 64 TYR 0.036 0.001 TYR B 279 PHE 0.034 0.001 PHE F 215 TRP 0.007 0.001 TRP E 251 HIS 0.004 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00247 (20090) covalent geometry : angle 0.58294 (27174) hydrogen bonds : bond 0.03268 ( 1076) hydrogen bonds : angle 4.60148 ( 3063) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 214 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 390 HIS cc_start: 0.7844 (t70) cc_final: 0.7598 (t70) REVERT: A 473 ARG cc_start: 0.9175 (ptt90) cc_final: 0.8878 (ppt90) REVERT: A 524 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8014 (pm20) REVERT: B 175 ASP cc_start: 0.9046 (p0) cc_final: 0.8697 (p0) REVERT: B 176 LYS cc_start: 0.9573 (mmtp) cc_final: 0.9157 (mmmm) REVERT: B 308 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8260 (ppp) REVERT: C 90 LEU cc_start: 0.9246 (mt) cc_final: 0.9031 (mp) REVERT: C 213 MET cc_start: 0.8593 (tpt) cc_final: 0.8088 (tpp) REVERT: C 225 MET cc_start: 0.8744 (tmm) cc_final: 0.8528 (tmm) REVERT: D 117 GLN cc_start: 0.8573 (tm-30) cc_final: 0.8072 (tm-30) REVERT: D 121 GLU cc_start: 0.8985 (pp20) cc_final: 0.8688 (pp20) REVERT: D 172 LYS cc_start: 0.9248 (ptmm) cc_final: 0.8880 (tmtt) REVERT: E 106 VAL cc_start: 0.9638 (m) cc_final: 0.8960 (p) REVERT: E 110 GLU cc_start: 0.9498 (mm-30) cc_final: 0.9074 (mm-30) REVERT: E 111 MET cc_start: 0.9444 (mmm) cc_final: 0.9217 (mmm) REVERT: E 194 HIS cc_start: 0.8952 (t70) cc_final: 0.8721 (t70) REVERT: E 213 HIS cc_start: 0.9073 (m-70) cc_final: 0.8705 (m90) REVERT: F 17 GLU cc_start: 0.9190 (tp30) cc_final: 0.8768 (tp30) REVERT: F 75 MET cc_start: 0.9640 (mmm) cc_final: 0.8978 (tpp) REVERT: F 125 GLN cc_start: 0.9164 (tt0) cc_final: 0.8783 (tm-30) REVERT: F 244 MET cc_start: 0.8826 (tpp) cc_final: 0.8486 (tpp) REVERT: G 1 MET cc_start: 0.8505 (tpp) cc_final: 0.8024 (tpp) REVERT: G 38 GLN cc_start: 0.8955 (tt0) cc_final: 0.8331 (tt0) REVERT: G 49 GLN cc_start: 0.8358 (tm-30) cc_final: 0.7827 (tm-30) REVERT: G 199 MET cc_start: 0.8408 (tmm) cc_final: 0.7812 (tmm) REVERT: G 211 TYR cc_start: 0.9222 (m-80) cc_final: 0.8943 (m-80) REVERT: H 1 MET cc_start: 0.9045 (tpt) cc_final: 0.8660 (tpp) REVERT: H 40 MET cc_start: 0.7938 (tpp) cc_final: 0.7550 (tpp) REVERT: H 61 ARG cc_start: 0.9083 (ppt170) cc_final: 0.8642 (ptm-80) REVERT: H 79 LEU cc_start: 0.9532 (OUTLIER) cc_final: 0.9282 (mm) REVERT: H 91 ARG cc_start: 0.8569 (mmm-85) cc_final: 0.8310 (mmm-85) REVERT: H 153 HIS cc_start: 0.9364 (m170) cc_final: 0.9012 (m-70) REVERT: H 214 PHE cc_start: 0.9294 (m-10) cc_final: 0.8768 (m-80) REVERT: H 232 ASP cc_start: 0.8685 (m-30) cc_final: 0.8100 (t0) REVERT: H 235 LEU cc_start: 0.9446 (tp) cc_final: 0.8754 (pp) REVERT: H 244 MET cc_start: 0.9070 (ppp) cc_final: 0.8862 (tmm) outliers start: 27 outliers final: 18 residues processed: 231 average time/residue: 0.1395 time to fit residues: 49.4454 Evaluate side-chains 218 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 197 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 679 ASP Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 68 MET Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 219 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 59 optimal weight: 9.9990 chunk 174 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 95 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 128 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 214 optimal weight: 0.4980 chunk 109 optimal weight: 50.0000 chunk 240 optimal weight: 5.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 HIS B 298 ASN C 76 GLN ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.082547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.056245 restraints weight = 75726.678| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 4.88 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20090 Z= 0.204 Angle : 0.625 9.946 27174 Z= 0.313 Chirality : 0.042 0.223 3170 Planarity : 0.004 0.051 3461 Dihedral : 7.229 138.991 2808 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.90 % Favored : 96.06 % Rotamer: Outliers : 1.46 % Allowed : 12.75 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.17), residues: 2464 helix: 1.76 (0.16), residues: 1147 sheet: 0.04 (0.22), residues: 507 loop : -0.20 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 149 TYR 0.036 0.002 TYR B 279 PHE 0.039 0.001 PHE G 215 TRP 0.005 0.001 TRP E 251 HIS 0.006 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00439 (20090) covalent geometry : angle 0.62467 (27174) hydrogen bonds : bond 0.03455 ( 1076) hydrogen bonds : angle 4.67040 ( 3063) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 HIS cc_start: 0.7867 (t70) cc_final: 0.7595 (t70) REVERT: A 473 ARG cc_start: 0.9164 (ptt90) cc_final: 0.8852 (ppt90) REVERT: A 524 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7983 (pm20) REVERT: B 175 ASP cc_start: 0.9099 (p0) cc_final: 0.8787 (p0) REVERT: B 176 LYS cc_start: 0.9590 (mmtp) cc_final: 0.9183 (mmmm) REVERT: C 90 LEU cc_start: 0.9217 (mt) cc_final: 0.8903 (mp) REVERT: C 213 MET cc_start: 0.8605 (tpt) cc_final: 0.8289 (tpp) REVERT: C 225 MET cc_start: 0.8792 (tmm) cc_final: 0.8512 (tmm) REVERT: D 117 GLN cc_start: 0.8573 (tm-30) cc_final: 0.8080 (tm-30) REVERT: D 121 GLU cc_start: 0.9014 (pp20) cc_final: 0.8683 (pp20) REVERT: D 172 LYS cc_start: 0.9250 (ptmm) cc_final: 0.8887 (tmtt) REVERT: E 106 VAL cc_start: 0.9634 (m) cc_final: 0.8964 (p) REVERT: E 110 GLU cc_start: 0.9503 (mm-30) cc_final: 0.9090 (mm-30) REVERT: E 194 HIS cc_start: 0.8979 (t70) cc_final: 0.8711 (t70) REVERT: E 213 HIS cc_start: 0.9081 (m-70) cc_final: 0.8777 (m-70) REVERT: F 17 GLU cc_start: 0.9214 (tp30) cc_final: 0.8860 (tp30) REVERT: F 125 GLN cc_start: 0.9138 (tt0) cc_final: 0.8767 (tm-30) REVERT: G 1 MET cc_start: 0.8601 (tpp) cc_final: 0.8153 (tpp) REVERT: G 38 GLN cc_start: 0.8919 (tt0) cc_final: 0.8424 (tt0) REVERT: G 40 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7985 (tmm) REVERT: G 49 GLN cc_start: 0.8395 (tm-30) cc_final: 0.7860 (tm-30) REVERT: G 211 TYR cc_start: 0.9254 (m-80) cc_final: 0.8970 (m-80) REVERT: H 1 MET cc_start: 0.9114 (tpt) cc_final: 0.8561 (tpp) REVERT: H 40 MET cc_start: 0.8052 (tpp) cc_final: 0.7736 (tpp) REVERT: H 61 ARG cc_start: 0.9130 (ppt170) cc_final: 0.8818 (ptm-80) REVERT: H 79 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.9341 (mm) REVERT: H 91 ARG cc_start: 0.8589 (mmm-85) cc_final: 0.8184 (mmm-85) REVERT: H 153 HIS cc_start: 0.9376 (m170) cc_final: 0.9022 (m-70) REVERT: H 214 PHE cc_start: 0.9308 (m-10) cc_final: 0.8901 (m-80) REVERT: H 244 MET cc_start: 0.9083 (ppp) cc_final: 0.8830 (tmm) outliers start: 32 outliers final: 19 residues processed: 221 average time/residue: 0.1401 time to fit residues: 47.5747 Evaluate side-chains 212 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 68 MET Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 219 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 16 optimal weight: 7.9990 chunk 172 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 152 optimal weight: 8.9990 chunk 130 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 140 optimal weight: 8.9990 chunk 3 optimal weight: 50.0000 chunk 109 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 HIS ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN ** H 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.081729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.055259 restraints weight = 76446.511| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 5.00 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 20090 Z= 0.243 Angle : 0.655 10.476 27174 Z= 0.329 Chirality : 0.043 0.242 3170 Planarity : 0.004 0.050 3461 Dihedral : 7.351 142.197 2808 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.26 % Favored : 95.70 % Rotamer: Outliers : 1.51 % Allowed : 13.11 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.17), residues: 2464 helix: 1.58 (0.15), residues: 1161 sheet: -0.10 (0.22), residues: 504 loop : -0.27 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 149 TYR 0.037 0.002 TYR B 279 PHE 0.041 0.002 PHE G 215 TRP 0.005 0.001 TRP F 28 HIS 0.006 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00520 (20090) covalent geometry : angle 0.65547 (27174) hydrogen bonds : bond 0.03618 ( 1076) hydrogen bonds : angle 4.78955 ( 3063) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 198 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 390 HIS cc_start: 0.7866 (t70) cc_final: 0.7629 (t-170) REVERT: A 473 ARG cc_start: 0.9146 (ptt90) cc_final: 0.8832 (ppt90) REVERT: A 524 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7962 (pm20) REVERT: B 176 LYS cc_start: 0.9594 (mmtp) cc_final: 0.9251 (mmmm) REVERT: C 225 MET cc_start: 0.8729 (tmm) cc_final: 0.8444 (tmm) REVERT: D 117 GLN cc_start: 0.8583 (tm-30) cc_final: 0.8202 (tm-30) REVERT: D 121 GLU cc_start: 0.9060 (pp20) cc_final: 0.8722 (pp20) REVERT: D 172 LYS cc_start: 0.9261 (ptmm) cc_final: 0.8909 (tmtt) REVERT: E 106 VAL cc_start: 0.9638 (m) cc_final: 0.8999 (p) REVERT: E 110 GLU cc_start: 0.9515 (mm-30) cc_final: 0.9092 (mm-30) REVERT: E 111 MET cc_start: 0.9436 (mmm) cc_final: 0.9052 (mmm) REVERT: E 194 HIS cc_start: 0.9010 (t70) cc_final: 0.8743 (t70) REVERT: E 213 HIS cc_start: 0.9108 (m-70) cc_final: 0.8802 (m-70) REVERT: F 17 GLU cc_start: 0.9219 (tp30) cc_final: 0.8878 (tp30) REVERT: F 68 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8304 (ppp) REVERT: F 125 GLN cc_start: 0.9174 (tt0) cc_final: 0.8773 (tm-30) REVERT: G 38 GLN cc_start: 0.8941 (tt0) cc_final: 0.8419 (tt0) REVERT: G 40 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.8061 (tmm) REVERT: G 49 GLN cc_start: 0.8475 (tm-30) cc_final: 0.7921 (tm-30) REVERT: G 57 PHE cc_start: 0.8658 (m-80) cc_final: 0.8101 (t80) REVERT: G 99 LEU cc_start: 0.9017 (tt) cc_final: 0.8723 (tp) REVERT: G 199 MET cc_start: 0.8315 (tmm) cc_final: 0.7819 (tmm) REVERT: G 211 TYR cc_start: 0.9263 (m-80) cc_final: 0.8996 (m-80) REVERT: H 153 HIS cc_start: 0.9360 (m170) cc_final: 0.9007 (m-70) REVERT: H 214 PHE cc_start: 0.9309 (m-10) cc_final: 0.8944 (m-80) REVERT: H 244 MET cc_start: 0.9084 (ppp) cc_final: 0.8838 (tmm) outliers start: 33 outliers final: 25 residues processed: 221 average time/residue: 0.1432 time to fit residues: 48.4194 Evaluate side-chains 214 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 679 ASP Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 38 GLN Chi-restraints excluded: chain H residue 68 MET Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 235 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 81 optimal weight: 2.9990 chunk 221 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 245 optimal weight: 3.9990 chunk 219 optimal weight: 10.0000 chunk 88 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 232 optimal weight: 0.1980 chunk 91 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 HIS ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 ASN H 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.083383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.057180 restraints weight = 74777.977| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 4.90 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20090 Z= 0.127 Angle : 0.636 10.255 27174 Z= 0.313 Chirality : 0.042 0.284 3170 Planarity : 0.004 0.053 3461 Dihedral : 7.269 142.786 2808 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.49 % Favored : 96.47 % Rotamer: Outliers : 1.23 % Allowed : 13.66 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.17), residues: 2464 helix: 1.66 (0.16), residues: 1161 sheet: -0.03 (0.22), residues: 500 loop : -0.25 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 210 TYR 0.038 0.001 TYR B 279 PHE 0.032 0.001 PHE G 215 TRP 0.007 0.001 TRP E 251 HIS 0.004 0.001 HIS F 44 Details of bonding type rmsd covalent geometry : bond 0.00280 (20090) covalent geometry : angle 0.63573 (27174) hydrogen bonds : bond 0.03341 ( 1076) hydrogen bonds : angle 4.63238 ( 3063) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 203 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 HIS cc_start: 0.7853 (t70) cc_final: 0.7604 (t-170) REVERT: A 473 ARG cc_start: 0.9155 (ptt90) cc_final: 0.8846 (ppt90) REVERT: A 524 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7967 (pm20) REVERT: B 175 ASP cc_start: 0.9107 (p0) cc_final: 0.8885 (p0) REVERT: B 176 LYS cc_start: 0.9570 (mmtp) cc_final: 0.9259 (mmmm) REVERT: B 304 LYS cc_start: 0.8840 (tppp) cc_final: 0.8606 (tppp) REVERT: C 213 MET cc_start: 0.8451 (tpt) cc_final: 0.8195 (tpp) REVERT: C 225 MET cc_start: 0.8802 (tmm) cc_final: 0.8511 (tmm) REVERT: D 117 GLN cc_start: 0.8601 (tm-30) cc_final: 0.8056 (tm-30) REVERT: D 121 GLU cc_start: 0.9009 (pp20) cc_final: 0.8690 (pp20) REVERT: D 172 LYS cc_start: 0.9265 (ptmm) cc_final: 0.8882 (tmtt) REVERT: E 106 VAL cc_start: 0.9629 (m) cc_final: 0.8964 (p) REVERT: E 110 GLU cc_start: 0.9504 (mm-30) cc_final: 0.9067 (mm-30) REVERT: E 111 MET cc_start: 0.9441 (mmm) cc_final: 0.9045 (mmm) REVERT: E 194 HIS cc_start: 0.8997 (t70) cc_final: 0.8743 (t70) REVERT: E 213 HIS cc_start: 0.9117 (m-70) cc_final: 0.8742 (m90) REVERT: F 17 GLU cc_start: 0.9215 (tp30) cc_final: 0.8837 (tp30) REVERT: F 68 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8236 (ppp) REVERT: F 249 TYR cc_start: 0.8975 (m-10) cc_final: 0.8733 (m-10) REVERT: G 1 MET cc_start: 0.8586 (tpp) cc_final: 0.7431 (tpp) REVERT: G 38 GLN cc_start: 0.8915 (tt0) cc_final: 0.8375 (tt0) REVERT: G 49 GLN cc_start: 0.8390 (tm-30) cc_final: 0.7830 (tm-30) REVERT: G 57 PHE cc_start: 0.8634 (m-80) cc_final: 0.8087 (t80) REVERT: G 199 MET cc_start: 0.8257 (tmm) cc_final: 0.7697 (tmm) REVERT: H 149 ARG cc_start: 0.9216 (ttp-110) cc_final: 0.8819 (ttp-110) REVERT: H 153 HIS cc_start: 0.9347 (m170) cc_final: 0.8980 (m-70) REVERT: H 156 ASP cc_start: 0.9487 (p0) cc_final: 0.8746 (t0) REVERT: H 214 PHE cc_start: 0.9314 (m-10) cc_final: 0.8933 (m-80) REVERT: H 244 MET cc_start: 0.9032 (ppp) cc_final: 0.8808 (tmm) outliers start: 27 outliers final: 21 residues processed: 220 average time/residue: 0.1407 time to fit residues: 47.4724 Evaluate side-chains 216 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 193 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 38 GLN Chi-restraints excluded: chain H residue 68 MET Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 86 optimal weight: 9.9990 chunk 182 optimal weight: 6.9990 chunk 52 optimal weight: 0.2980 chunk 0 optimal weight: 40.0000 chunk 197 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 151 optimal weight: 20.0000 chunk 103 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 HIS ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN F 44 HIS H 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.083090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.056847 restraints weight = 75370.257| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 4.91 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20090 Z= 0.143 Angle : 0.649 10.965 27174 Z= 0.318 Chirality : 0.042 0.274 3170 Planarity : 0.004 0.055 3461 Dihedral : 7.197 139.978 2808 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.73 % Favored : 96.23 % Rotamer: Outliers : 1.23 % Allowed : 13.98 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.17), residues: 2464 helix: 1.67 (0.16), residues: 1161 sheet: -0.08 (0.22), residues: 505 loop : -0.26 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 210 TYR 0.038 0.001 TYR B 279 PHE 0.056 0.001 PHE F 215 TRP 0.011 0.001 TRP F 28 HIS 0.009 0.001 HIS F 44 Details of bonding type rmsd covalent geometry : bond 0.00317 (20090) covalent geometry : angle 0.64890 (27174) hydrogen bonds : bond 0.03340 ( 1076) hydrogen bonds : angle 4.63527 ( 3063) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 HIS cc_start: 0.7846 (t70) cc_final: 0.7589 (t-170) REVERT: A 473 ARG cc_start: 0.9132 (ptt90) cc_final: 0.8816 (ppt90) REVERT: A 524 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7957 (pm20) REVERT: B 175 ASP cc_start: 0.9095 (p0) cc_final: 0.8879 (p0) REVERT: B 176 LYS cc_start: 0.9568 (mmtp) cc_final: 0.9259 (mmmm) REVERT: B 304 LYS cc_start: 0.8820 (tppp) cc_final: 0.8573 (tppp) REVERT: C 213 MET cc_start: 0.8469 (tpt) cc_final: 0.8223 (tpp) REVERT: C 225 MET cc_start: 0.8774 (tmm) cc_final: 0.8497 (tmm) REVERT: D 117 GLN cc_start: 0.8592 (tm-30) cc_final: 0.8183 (tm-30) REVERT: D 121 GLU cc_start: 0.9038 (pp20) cc_final: 0.8710 (pp20) REVERT: D 172 LYS cc_start: 0.9263 (ptmm) cc_final: 0.8882 (tmtt) REVERT: D 356 MET cc_start: 0.8587 (tpt) cc_final: 0.8134 (tpt) REVERT: E 106 VAL cc_start: 0.9635 (m) cc_final: 0.8965 (p) REVERT: E 110 GLU cc_start: 0.9503 (mm-30) cc_final: 0.9067 (mm-30) REVERT: E 111 MET cc_start: 0.9438 (mmm) cc_final: 0.9040 (mmm) REVERT: E 194 HIS cc_start: 0.9012 (t70) cc_final: 0.8756 (t70) REVERT: E 213 HIS cc_start: 0.9046 (m-70) cc_final: 0.8758 (m-70) REVERT: F 17 GLU cc_start: 0.9190 (tp30) cc_final: 0.8814 (tp30) REVERT: F 68 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8265 (ppp) REVERT: G 1 MET cc_start: 0.8661 (tpp) cc_final: 0.7572 (tpp) REVERT: G 38 GLN cc_start: 0.8874 (tt0) cc_final: 0.8306 (tt0) REVERT: G 49 GLN cc_start: 0.8401 (tm-30) cc_final: 0.7856 (tm-30) REVERT: G 57 PHE cc_start: 0.8672 (m-80) cc_final: 0.8129 (t80) REVERT: H 149 ARG cc_start: 0.9213 (ttp-110) cc_final: 0.8805 (ttp-110) REVERT: H 153 HIS cc_start: 0.9355 (m170) cc_final: 0.8985 (m-70) REVERT: H 156 ASP cc_start: 0.9452 (p0) cc_final: 0.8733 (t0) REVERT: H 214 PHE cc_start: 0.9314 (m-10) cc_final: 0.8942 (m-80) REVERT: H 249 TYR cc_start: 0.8914 (m-80) cc_final: 0.8477 (m-80) REVERT: H 251 LEU cc_start: 0.8388 (tp) cc_final: 0.7839 (pp) outliers start: 27 outliers final: 23 residues processed: 213 average time/residue: 0.1453 time to fit residues: 47.1627 Evaluate side-chains 216 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 38 GLN Chi-restraints excluded: chain H residue 68 MET Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 107 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 238 optimal weight: 30.0000 chunk 191 optimal weight: 40.0000 chunk 159 optimal weight: 10.0000 chunk 227 optimal weight: 0.8980 chunk 224 optimal weight: 40.0000 chunk 192 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 HIS ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN H 38 GLN ** H 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 204 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.082123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.055888 restraints weight = 76006.397| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 4.91 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20090 Z= 0.205 Angle : 0.675 10.978 27174 Z= 0.331 Chirality : 0.043 0.275 3170 Planarity : 0.004 0.053 3461 Dihedral : 7.208 140.270 2808 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.98 % Favored : 95.98 % Rotamer: Outliers : 1.46 % Allowed : 13.80 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.17), residues: 2464 helix: 1.64 (0.15), residues: 1161 sheet: -0.11 (0.22), residues: 504 loop : -0.27 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 210 TYR 0.038 0.002 TYR B 279 PHE 0.047 0.001 PHE F 215 TRP 0.010 0.001 TRP F 28 HIS 0.005 0.001 HIS F 44 Details of bonding type rmsd covalent geometry : bond 0.00444 (20090) covalent geometry : angle 0.67482 (27174) hydrogen bonds : bond 0.03416 ( 1076) hydrogen bonds : angle 4.72454 ( 3063) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3932.22 seconds wall clock time: 68 minutes 32.57 seconds (4112.57 seconds total)