Starting phenix.real_space_refine on Sun Oct 12 03:28:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8umt_42383/10_2025/8umt_42383.cif Found real_map, /net/cci-nas-00/data/ceres_data/8umt_42383/10_2025/8umt_42383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8umt_42383/10_2025/8umt_42383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8umt_42383/10_2025/8umt_42383.map" model { file = "/net/cci-nas-00/data/ceres_data/8umt_42383/10_2025/8umt_42383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8umt_42383/10_2025/8umt_42383.cif" } resolution = 3.33 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= 0.045 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 3 5.21 5 S 135 5.16 5 C 13022 2.51 5 N 3568 2.21 5 O 3958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20697 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4255 Classifications: {'peptide': 537} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 32, 'TRANS': 504} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2492 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 12, 'TRANS': 303} Chain: "C" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2563 Classifications: {'peptide': 322} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 309} Chain: "D" Number of atoms: 2512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2512 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain: "E" Number of atoms: 2745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2745 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 15, 'TRANS': 329} Chain: "F" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1989 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 7, 'TRANS': 250} Chain: "G" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2009 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "H" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2009 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 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, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 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: 4.69, per 1000 atoms: 0.23 Number of scatterers: 20697 At special positions: 0 Unit cell: (115.92, 120.888, 147.384, 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 135 16.00 P 11 15.00 Mg 3 11.99 O 3958 8.00 N 3568 7.00 C 13022 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: 1.75 Conformation dependent library (CDL) restraints added in 945.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4994 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 15 sheets defined 50.4% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 297 through 310 Processing helix chain 'A' and resid 311 through 314 Processing helix chain 'A' and resid 347 through 355 Processing helix chain 'A' and resid 379 through 391 Processing helix chain 'A' and resid 405 through 414 Processing helix chain 'A' and resid 441 through 453 Processing helix chain 'A' and resid 495 through 499 Processing helix chain 'A' and resid 501 through 505 removed outlier: 3.542A pdb=" N ALA A 505 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 530 removed outlier: 3.780A pdb=" N GLN A 529 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 545 Processing helix chain 'A' and resid 549 through 563 Processing helix chain 'A' and resid 568 through 573 removed outlier: 3.584A pdb=" N VAL A 572 " --> pdb=" O SER A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 595 removed outlier: 3.571A pdb=" N GLN A 591 " --> pdb=" O PHE A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 642 Processing helix chain 'A' and resid 645 through 656 Processing helix chain 'A' and resid 668 through 690 Processing helix chain 'A' and resid 699 through 709 removed outlier: 4.734A pdb=" N VAL A 703 " --> pdb=" O PRO A 699 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A 704 " --> pdb=" O PHE A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 744 Processing helix chain 'A' and resid 745 through 750 removed outlier: 3.697A pdb=" N SER A 750 " --> pdb=" O PRO A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 760 Processing helix chain 'A' and resid 761 through 769 Processing helix chain 'A' and resid 782 through 800 Processing helix chain 'A' and resid 820 through 825 removed outlier: 3.971A pdb=" N LEU A 824 " --> pdb=" O ASN A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 863 Processing helix chain 'B' and resid 37 through 42 removed outlier: 3.628A pdb=" N TYR B 42 " --> pdb=" O TRP B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 50 Processing helix chain 'B' and resid 54 through 67 removed outlier: 3.687A pdb=" N ARG B 65 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 67 " --> pdb=" O PHE B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 94 Processing helix chain 'B' and resid 95 through 98 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.889A pdb=" N VAL B 116 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 161 removed outlier: 4.204A pdb=" N ARG B 156 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 184 removed outlier: 3.743A pdb=" N ARG B 184 " --> pdb=" O PRO B 180 " (cutoff:3.500A) 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 243 Processing helix chain 'B' and resid 247 through 256 removed outlier: 4.029A pdb=" N PHE B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS B 253 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL B 254 " --> pdb=" O ASN B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 275 through 287 Processing helix chain 'B' and resid 291 through 305 removed outlier: 3.968A pdb=" N THR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 330 Processing helix chain 'B' and resid 333 through 348 removed outlier: 3.759A pdb=" N MET B 337 " --> pdb=" O SER B 333 " (cutoff:3.500A) removed outlier: 3.712A 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 37 through 50 removed outlier: 3.580A pdb=" N GLU C 50 " --> pdb=" O LYS C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 78 removed outlier: 3.624A pdb=" N ILE C 70 " --> pdb=" O LYS C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 110 Processing helix chain 'C' and resid 127 through 130 removed outlier: 3.607A pdb=" N MET C 130 " --> pdb=" O ALA C 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 127 through 130' Processing helix chain 'C' and resid 131 through 145 Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.666A pdb=" N LYS C 160 " --> pdb=" O TYR C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 169 Processing helix chain 'C' and resid 178 through 193 Proline residue: C 184 - end of helix Processing helix chain 'C' and resid 198 through 209 Processing helix chain 'C' and resid 212 through 227 removed outlier: 3.527A pdb=" N ALA C 216 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 243 through 256 Processing helix chain 'C' and resid 258 through 274 Processing helix chain 'C' and resid 276 through 288 Processing helix chain 'C' and resid 294 through 314 Processing helix chain 'C' and resid 317 through 340 removed outlier: 4.024A pdb=" N GLN C 321 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 55 through 69 removed outlier: 3.701A pdb=" N ALA D 69 " --> pdb=" O SER D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 104 Proline residue: D 98 - end of helix removed outlier: 4.345A pdb=" N ARG D 102 " --> pdb=" O PRO D 98 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 128 removed outlier: 3.947A pdb=" N VAL D 119 " --> pdb=" O GLY D 115 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL D 123 " --> pdb=" O VAL D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 155 removed outlier: 3.627A pdb=" N MET D 155 " --> pdb=" O ALA D 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 152 through 155' Processing helix chain 'D' and resid 156 through 170 Processing helix chain 'D' and resid 182 through 186 removed outlier: 3.603A pdb=" N ARG D 185 " --> pdb=" O TYR D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 193 removed outlier: 3.663A pdb=" N ARG D 193 " --> pdb=" O PRO D 189 " (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 237 through 253 Processing helix chain 'D' and resid 258 through 266 removed outlier: 3.788A pdb=" N ILE D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 283 removed outlier: 3.577A pdb=" N ILE D 274 " --> pdb=" O PRO D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 299 Processing helix chain 'D' and resid 302 through 315 Processing helix chain 'D' and resid 320 through 341 Processing helix chain 'D' and resid 343 through 360 Processing helix chain 'E' and resid 12 through 16 removed outlier: 3.624A pdb=" N LEU E 16 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 Processing helix chain 'E' and resid 47 through 60 Processing helix chain 'E' and resid 62 through 66 removed outlier: 3.850A pdb=" N GLU E 65 " --> pdb=" O VAL E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 100 removed outlier: 3.847A pdb=" N ASP E 99 " --> pdb=" O ASN E 96 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA E 100 " --> pdb=" O PRO E 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 96 through 100' Processing helix chain 'E' and resid 103 through 117 removed outlier: 3.837A pdb=" N LEU E 112 " --> pdb=" O ILE E 108 " (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 167 through 171 Processing helix chain 'E' and resid 172 through 177 Processing helix chain 'E' and resid 188 through 202 Processing helix chain 'E' and resid 208 through 219 Processing helix chain 'E' and resid 222 through 237 removed outlier: 3.654A pdb=" N CYS E 230 " --> pdb=" O ALA E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 265 removed outlier: 3.948A pdb=" N GLN E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 284 Processing helix chain 'E' and resid 287 through 301 Processing helix chain 'E' and resid 306 through 323 removed outlier: 4.165A pdb=" N GLU E 310 " --> pdb=" O GLN E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 349 removed outlier: 4.248A pdb=" N HIS E 331 " --> pdb=" O LYS E 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 19 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 80 Processing helix chain 'F' and resid 141 through 155 removed outlier: 3.859A pdb=" N ILE F 154 " --> pdb=" O ASP F 150 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY F 155 " --> pdb=" O LEU F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 218 through 222 removed outlier: 3.838A pdb=" N SER F 222 " --> pdb=" O THR F 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 20 removed outlier: 4.510A pdb=" N LEU G 12 " --> pdb=" O GLN G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 80 Processing helix chain 'G' and resid 141 through 152 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 10 No H-bonds generated for 'chain 'H' and resid 8 through 10' Processing helix chain 'H' and resid 11 through 16 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 79 removed outlier: 3.568A pdb=" N LYS H 77 " --> pdb=" O THR H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 152 Processing helix chain 'H' and resid 190 through 194 removed outlier: 4.012A pdb=" N GLU H 193 " --> pdb=" O LYS H 190 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA H 194 " --> pdb=" O GLU H 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 190 through 194' Processing helix chain 'H' and resid 209 through 217 Processing helix chain 'H' and resid 218 through 222 removed outlier: 3.857A pdb=" N LEU H 221 " --> pdb=" O ALA H 218 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER H 222 " --> pdb=" O THR H 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 218 through 222' 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 399 removed outlier: 5.888A pdb=" N SER A 394 " --> pdb=" O CYS A 431 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL A 433 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL A 396 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N ASP A 435 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N MET A 398 " --> pdb=" O ASP A 435 " (cutoff:3.500A) removed outlier: 9.677A pdb=" N ILE A 487 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LEU A 432 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ILE A 489 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE A 434 " --> pdb=" O ILE A 489 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 532 through 533 removed outlier: 7.933A pdb=" N ARG A 532 " --> pdb=" O LEU A 567 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 803 through 807 Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.227A pdb=" N LYS B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ALA B 168 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE B 138 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ALA B 170 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU B 140 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE B 73 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 87 through 90 removed outlier: 6.566A pdb=" N LEU C 88 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ASP C 125 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU C 90 " --> pdb=" O ASP C 125 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL C 122 " --> pdb=" O ARG C 150 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU C 56 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N CYS C 155 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 6.309A 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) Processing sheet with id=AA7, first strand: chain 'C' and resid 196 through 197 removed outlier: 6.183A pdb=" N ASP C 196 " --> pdb=" O VAL C 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 75 through 77 removed outlier: 5.673A pdb=" N LYS D 145 " --> pdb=" O ARG D 175 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N CYS D 177 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N VAL D 147 " --> pdb=" O CYS D 177 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE D 179 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LEU D 149 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU D 106 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ASP D 150 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU D 108 " --> pdb=" O ASP D 150 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 68 through 75 removed outlier: 6.192A pdb=" N VAL E 132 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N CYS E 164 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU E 134 " --> pdb=" O CYS E 164 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU E 38 " --> pdb=" O LEU E 163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 59 through 62 removed outlier: 4.212A pdb=" N THR F 59 " --> pdb=" O ARG F 5 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN G 177 " --> pdb=" O GLU F 115 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N SER G 172 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA G 157 " --> pdb=" O SER G 172 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 66 through 71 removed outlier: 7.260A pdb=" N GLU F 25 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N MET F 40 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N CYS F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN F 38 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N SER F 230 " --> pdb=" O PRO F 234 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS F 240 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N THR F 224 " --> pdb=" O LYS F 240 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 204 through 208 removed outlier: 5.483A pdb=" N ALA F 157 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N SER F 172 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N VAL F 167 " --> pdb=" O LEU F 182 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR H 59 " --> pdb=" O ARG H 5 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 60 through 61 removed outlier: 3.860A pdb=" N VAL G 111 " --> pdb=" O LYS H 181 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS H 181 " --> pdb=" O VAL G 111 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 66 through 71 removed outlier: 5.969A pdb=" N GLU G 25 " --> pdb=" O MET G 40 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N MET G 40 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N CYS G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLN G 38 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 66 through 71 removed outlier: 3.592A pdb=" N LEU H 66 " --> pdb=" O ILE H 30 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLU H 25 " --> pdb=" O MET H 40 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N MET H 40 " --> pdb=" O GLU H 25 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N CYS H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN H 38 " --> pdb=" O CYS H 27 " (cutoff:3.500A) 1103 hydrogen bonds defined for protein. 3177 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: 3.78 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 6966 1.36 - 1.51: 5077 1.51 - 1.65: 8779 1.65 - 1.80: 120 1.80 - 1.95: 85 Bond restraints: 21027 Sorted by residual: bond pdb=" CA LYS H 217 " pdb=" C LYS H 217 " ideal model delta sigma weight residual 1.522 1.583 -0.061 1.43e-02 4.89e+03 1.83e+01 bond pdb=" N PHE D 54 " pdb=" CA PHE D 54 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.29e-02 6.01e+03 1.09e+01 bond pdb=" N LEU G 12 " pdb=" CA LEU G 12 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.23e-02 6.61e+03 8.05e+00 bond pdb=" N VAL A 180 " pdb=" CA VAL A 180 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.89e+00 bond pdb=" N GLU H 85 " pdb=" CA GLU H 85 " ideal model delta sigma weight residual 1.458 1.490 -0.031 1.14e-02 7.69e+03 7.58e+00 ... (remaining 21022 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 27693 1.97 - 3.94: 648 3.94 - 5.91: 70 5.91 - 7.89: 35 7.89 - 9.86: 8 Bond angle restraints: 28454 Sorted by residual: angle pdb=" N TYR E 343 " pdb=" CA TYR E 343 " pdb=" C TYR E 343 " ideal model delta sigma weight residual 111.14 106.05 5.09 1.08e+00 8.57e-01 2.22e+01 angle pdb=" N ASP F 156 " pdb=" CA ASP F 156 " pdb=" C ASP F 156 " ideal model delta sigma weight residual 114.31 108.23 6.08 1.29e+00 6.01e-01 2.22e+01 angle pdb=" C THR A 417 " pdb=" N GLN A 418 " pdb=" CA GLN A 418 " ideal model delta sigma weight residual 122.61 129.22 -6.61 1.56e+00 4.11e-01 1.80e+01 angle pdb=" C GLY E 33 " pdb=" N ASP E 34 " pdb=" CA ASP E 34 " ideal model delta sigma weight residual 122.82 128.83 -6.01 1.42e+00 4.96e-01 1.79e+01 angle pdb=" N GLU D 188 " pdb=" CA GLU D 188 " pdb=" C GLU D 188 " ideal model delta sigma weight residual 113.25 118.71 -5.46 1.30e+00 5.92e-01 1.76e+01 ... (remaining 28449 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.19: 12342 26.19 - 52.37: 576 52.37 - 78.56: 71 78.56 - 104.75: 6 104.75 - 130.93: 2 Dihedral angle restraints: 12997 sinusoidal: 5323 harmonic: 7674 Sorted by residual: dihedral pdb=" C5' ADP E2000 " pdb=" O5' ADP E2000 " pdb=" PA ADP E2000 " pdb=" O2A ADP E2000 " ideal model delta sinusoidal sigma weight residual 300.00 169.07 130.93 1 2.00e+01 2.50e-03 3.97e+01 dihedral pdb=" O1B ADP E2000 " pdb=" O3A ADP E2000 " pdb=" PB ADP E2000 " pdb=" PA ADP E2000 " ideal model delta sinusoidal sigma weight residual -60.00 -163.80 103.80 1 2.00e+01 2.50e-03 2.97e+01 dihedral pdb=" CA VAL F 236 " pdb=" C VAL F 236 " pdb=" N VAL F 237 " pdb=" CA VAL F 237 " ideal model delta harmonic sigma weight residual 180.00 159.34 20.66 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 12994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2532 0.051 - 0.103: 608 0.103 - 0.154: 156 0.154 - 0.206: 19 0.206 - 0.257: 2 Chirality restraints: 3317 Sorted by residual: 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 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA LEU H 50 " pdb=" N LEU H 50 " pdb=" C LEU H 50 " pdb=" CB LEU H 50 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CB ILE H 241 " pdb=" CA ILE H 241 " pdb=" CG1 ILE H 241 " pdb=" CG2 ILE H 241 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.06e-01 ... (remaining 3314 not shown) Planarity restraints: 3643 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 698 " -0.065 5.00e-02 4.00e+02 9.76e-02 1.52e+01 pdb=" N PRO A 699 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO A 699 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 699 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 293 " -0.018 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C GLU A 293 " 0.065 2.00e-02 2.50e+03 pdb=" O GLU A 293 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU A 294 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR E 76 " 0.051 5.00e-02 4.00e+02 7.63e-02 9.32e+00 pdb=" N PRO E 77 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO E 77 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 77 " 0.043 5.00e-02 4.00e+02 ... (remaining 3640 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 214 2.62 - 3.19: 16863 3.19 - 3.76: 32679 3.76 - 4.33: 43253 4.33 - 4.90: 71982 Nonbonded interactions: 164991 Sorted by model distance: nonbonded pdb="MG MG B 401 " pdb=" O1B AGS B 402 " model vdw 2.048 2.170 nonbonded pdb="MG MG B 401 " pdb=" O2G AGS B 402 " model vdw 2.071 2.170 nonbonded pdb=" OG1 THR B 83 " pdb="MG MG B 401 " model vdw 2.080 2.170 nonbonded pdb="MG MG D 401 " pdb=" O3G AGS D 402 " model vdw 2.082 2.170 nonbonded pdb="MG MG B 401 " pdb=" O1A AGS B 402 " model vdw 2.107 2.170 ... (remaining 164986 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 258) selection = (chain 'H' and resid 1 through 258) } 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: 0.010 Normalize map: mean=0, sd=1: 2.140 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.120 Find NCS groups from input model: 0.320 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: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 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 : 0.004 0.064 21027 Z= 0.212 Angle : 0.750 9.857 28454 Z= 0.424 Chirality : 0.048 0.257 3317 Planarity : 0.007 0.098 3643 Dihedral : 14.616 130.935 8003 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.61 % Favored : 96.35 % Rotamer: Outliers : 4.14 % Allowed : 11.52 % Favored : 84.34 % 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 aren not related in a simple way. whole: -2.12 (0.15), residues: 2601 helix: -1.46 (0.12), residues: 1208 sheet: -0.65 (0.23), residues: 513 loop : -1.46 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 311 TYR 0.012 0.001 TYR D 77 PHE 0.015 0.002 PHE F 169 TRP 0.009 0.001 TRP H 28 HIS 0.005 0.001 HIS C 55 Details of bonding type rmsd covalent geometry : bond 0.00372 (21027) covalent geometry : angle 0.74968 (28454) hydrogen bonds : bond 0.13946 ( 1103) hydrogen bonds : angle 6.43190 ( 3177) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 473 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 531 MET cc_start: 0.5988 (tpp) cc_final: 0.5635 (tpp) REVERT: A 843 LEU cc_start: 0.8676 (tp) cc_final: 0.8456 (tp) REVERT: B 38 TRP cc_start: 0.7185 (m-10) cc_final: 0.6967 (m-10) REVERT: B 245 PHE cc_start: 0.7011 (t80) cc_final: 0.6804 (t80) REVERT: D 238 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8210 (tt) REVERT: E 155 TYR cc_start: 0.5786 (m-80) cc_final: 0.5361 (m-80) REVERT: F 1 MET cc_start: 0.4277 (ppp) cc_final: 0.3350 (ppp) REVERT: F 14 LYS cc_start: 0.8759 (mmtt) cc_final: 0.8115 (ttpp) REVERT: G 87 ILE cc_start: 0.7059 (OUTLIER) cc_final: 0.6516 (pp) REVERT: G 143 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6758 (mp0) REVERT: G 154 ILE cc_start: 0.5604 (OUTLIER) cc_final: 0.5277 (tp) outliers start: 95 outliers final: 19 residues processed: 545 average time/residue: 0.1664 time to fit residues: 135.3312 Evaluate side-chains 337 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 314 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain B residue 247 ASN Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain H residue 235 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 0.0970 chunk 258 optimal weight: 3.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN A 655 ASN A 690 GLN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 GLN ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 GLN E 194 HIS E 213 HIS ** E 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 177 ASN G 36 ASN G 65 ASN G 246 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.190021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.154867 restraints weight = 34278.191| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 2.81 r_work: 0.3973 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 21027 Z= 0.199 Angle : 0.678 11.270 28454 Z= 0.346 Chirality : 0.045 0.172 3317 Planarity : 0.006 0.081 3643 Dihedral : 8.296 129.603 2937 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.80 % Allowed : 16.19 % Favored : 80.02 % 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 aren not related in a simple way. whole: -0.99 (0.16), residues: 2601 helix: -0.24 (0.14), residues: 1225 sheet: -0.52 (0.23), residues: 516 loop : -1.10 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 164 TYR 0.029 0.002 TYR F 133 PHE 0.024 0.002 PHE H 207 TRP 0.013 0.002 TRP H 28 HIS 0.014 0.001 HIS F 153 Details of bonding type rmsd covalent geometry : bond 0.00461 (21027) covalent geometry : angle 0.67825 (28454) hydrogen bonds : bond 0.04221 ( 1103) hydrogen bonds : angle 5.01102 ( 3177) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 346 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 843 LEU cc_start: 0.9268 (tp) cc_final: 0.9032 (tp) REVERT: A 847 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8964 (mm-30) REVERT: D 193 ARG cc_start: 0.7333 (mmm160) cc_final: 0.6363 (ttp80) REVERT: F 1 MET cc_start: 0.6184 (ppp) cc_final: 0.4901 (ppp) REVERT: F 14 LYS cc_start: 0.9259 (mmtt) cc_final: 0.8708 (mtpp) REVERT: F 60 TYR cc_start: 0.3845 (t80) cc_final: 0.3550 (t80) REVERT: F 99 LEU cc_start: 0.8344 (pp) cc_final: 0.7994 (tp) REVERT: F 148 CYS cc_start: 0.8984 (m) cc_final: 0.8708 (m) REVERT: G 13 LYS cc_start: 0.8292 (ttmm) cc_final: 0.7753 (mttp) REVERT: G 87 ILE cc_start: 0.7363 (OUTLIER) cc_final: 0.7085 (pp) REVERT: H 184 GLN cc_start: 0.6209 (tm-30) cc_final: 0.5769 (tm-30) outliers start: 87 outliers final: 53 residues processed: 401 average time/residue: 0.1626 time to fit residues: 97.5257 Evaluate side-chains 348 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 294 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 247 ASN Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 302 ASN Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 64 ARG Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 246 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 235 optimal weight: 2.9990 chunk 159 optimal weight: 30.0000 chunk 20 optimal weight: 7.9990 chunk 194 optimal weight: 8.9990 chunk 179 optimal weight: 1.9990 chunk 178 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 chunk 238 optimal weight: 8.9990 chunk 126 optimal weight: 4.9990 chunk 240 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 ASN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 HIS E 244 GLN F 184 GLN G 125 GLN H 131 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.184539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.141301 restraints weight = 34102.434| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 3.37 r_work: 0.3780 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21027 Z= 0.171 Angle : 0.641 11.672 28454 Z= 0.324 Chirality : 0.043 0.229 3317 Planarity : 0.005 0.078 3643 Dihedral : 7.764 124.857 2917 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.80 % Allowed : 16.71 % Favored : 79.49 % 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 aren not related in a simple way. whole: -0.60 (0.16), residues: 2601 helix: 0.20 (0.15), residues: 1232 sheet: -0.53 (0.23), residues: 516 loop : -0.97 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 93 TYR 0.016 0.002 TYR B 279 PHE 0.019 0.002 PHE A 506 TRP 0.025 0.002 TRP A 307 HIS 0.012 0.001 HIS F 153 Details of bonding type rmsd covalent geometry : bond 0.00397 (21027) covalent geometry : angle 0.64068 (28454) hydrogen bonds : bond 0.03896 ( 1103) hydrogen bonds : angle 4.84745 ( 3177) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 335 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 PHE cc_start: 0.8066 (t80) cc_final: 0.7769 (t80) REVERT: A 843 LEU cc_start: 0.9332 (tp) cc_final: 0.9087 (tp) REVERT: A 847 GLU cc_start: 0.9222 (mm-30) cc_final: 0.9014 (mm-30) REVERT: B 176 LYS cc_start: 0.7319 (mtmt) cc_final: 0.6979 (mtmm) REVERT: B 199 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7907 (mm) REVERT: D 117 GLN cc_start: 0.8038 (tp40) cc_final: 0.7696 (tp-100) REVERT: E 119 GLN cc_start: 0.6686 (OUTLIER) cc_final: 0.5888 (pm20) REVERT: F 1 MET cc_start: 0.6472 (ppp) cc_final: 0.5202 (ppp) REVERT: F 14 LYS cc_start: 0.9215 (mmtt) cc_final: 0.8553 (mtpp) REVERT: F 40 MET cc_start: 0.6395 (tpp) cc_final: 0.6076 (tpt) REVERT: F 60 TYR cc_start: 0.4115 (t80) cc_final: 0.3871 (t80) REVERT: F 99 LEU cc_start: 0.8473 (pp) cc_final: 0.8179 (tp) REVERT: F 112 SER cc_start: 0.8331 (m) cc_final: 0.7332 (p) REVERT: F 148 CYS cc_start: 0.9015 (m) cc_final: 0.8704 (m) REVERT: G 13 LYS cc_start: 0.8263 (ttmm) cc_final: 0.7683 (mttp) REVERT: G 87 ILE cc_start: 0.7357 (OUTLIER) cc_final: 0.7061 (pp) REVERT: H 153 HIS cc_start: 0.7275 (m90) cc_final: 0.7065 (m170) REVERT: H 184 GLN cc_start: 0.6506 (tm-30) cc_final: 0.6121 (tm-30) outliers start: 87 outliers final: 57 residues processed: 392 average time/residue: 0.1653 time to fit residues: 97.8915 Evaluate side-chains 365 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 305 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 560 TYR Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 799 TYR Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 64 ARG Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 246 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 147 optimal weight: 0.7980 chunk 231 optimal weight: 10.0000 chunk 160 optimal weight: 0.0970 chunk 248 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 171 optimal weight: 10.0000 chunk 29 optimal weight: 0.0370 chunk 13 optimal weight: 5.9990 chunk 157 optimal weight: 10.0000 chunk 106 optimal weight: 0.7980 chunk 213 optimal weight: 4.9990 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 ASN A 655 ASN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN D 301 HIS E 194 HIS E 213 HIS ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 GLN H 36 ASN H 44 HIS H 131 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.190395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.154174 restraints weight = 34309.124| |-----------------------------------------------------------------------------| r_work (start): 0.4200 rms_B_bonded: 2.74 r_work: 0.3957 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21027 Z= 0.114 Angle : 0.597 10.167 28454 Z= 0.301 Chirality : 0.042 0.173 3317 Planarity : 0.005 0.075 3643 Dihedral : 7.232 126.848 2913 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.18 % Allowed : 18.85 % Favored : 77.97 % 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 aren not related in a simple way. whole: -0.21 (0.17), residues: 2601 helix: 0.62 (0.15), residues: 1233 sheet: -0.46 (0.22), residues: 528 loop : -0.88 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 5 TYR 0.022 0.001 TYR B 213 PHE 0.029 0.001 PHE E 339 TRP 0.028 0.001 TRP A 307 HIS 0.010 0.001 HIS F 153 Details of bonding type rmsd covalent geometry : bond 0.00254 (21027) covalent geometry : angle 0.59747 (28454) hydrogen bonds : bond 0.03403 ( 1103) hydrogen bonds : angle 4.61623 ( 3177) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 340 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 839 GLN cc_start: 0.7645 (pm20) cc_final: 0.7302 (pm20) REVERT: A 843 LEU cc_start: 0.9297 (tp) cc_final: 0.9029 (tp) REVERT: A 853 MET cc_start: 0.9092 (mmm) cc_final: 0.8852 (mmp) REVERT: E 21 GLU cc_start: 0.8025 (pt0) cc_final: 0.7609 (pm20) REVERT: F 1 MET cc_start: 0.6233 (ppp) cc_final: 0.4853 (ppp) REVERT: F 14 LYS cc_start: 0.9159 (mmtt) cc_final: 0.8912 (mmtp) REVERT: F 40 MET cc_start: 0.6451 (tpp) cc_final: 0.6168 (tpt) REVERT: F 53 ARG cc_start: 0.8872 (ptp-110) cc_final: 0.8320 (mtm110) REVERT: F 144 PHE cc_start: 0.8603 (t80) cc_final: 0.8020 (t80) REVERT: F 148 CYS cc_start: 0.8869 (m) cc_final: 0.8388 (m) REVERT: G 13 LYS cc_start: 0.8225 (ttmm) cc_final: 0.7713 (mttp) REVERT: G 87 ILE cc_start: 0.7376 (OUTLIER) cc_final: 0.6983 (pp) outliers start: 73 outliers final: 50 residues processed: 388 average time/residue: 0.1596 time to fit residues: 94.1995 Evaluate side-chains 362 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 311 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 799 TYR Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 235 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 44 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 240 optimal weight: 0.9990 chunk 177 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 229 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 ASN A 655 ASN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 22 GLN E 213 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.187356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.151267 restraints weight = 34350.607| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 2.84 r_work: 0.3909 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21027 Z= 0.164 Angle : 0.624 10.630 28454 Z= 0.316 Chirality : 0.043 0.251 3317 Planarity : 0.005 0.073 3643 Dihedral : 6.991 127.466 2906 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.97 % Allowed : 18.63 % Favored : 77.40 % 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 aren not related in a simple way. whole: -0.21 (0.17), residues: 2601 helix: 0.61 (0.15), residues: 1233 sheet: -0.47 (0.22), residues: 526 loop : -0.85 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 61 TYR 0.016 0.002 TYR F 60 PHE 0.029 0.002 PHE E 339 TRP 0.024 0.002 TRP A 307 HIS 0.008 0.001 HIS F 153 Details of bonding type rmsd covalent geometry : bond 0.00383 (21027) covalent geometry : angle 0.62402 (28454) hydrogen bonds : bond 0.03596 ( 1103) hydrogen bonds : angle 4.66332 ( 3177) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 328 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6558 (pm20) REVERT: A 409 PHE cc_start: 0.8165 (OUTLIER) cc_final: 0.7650 (m-80) REVERT: A 853 MET cc_start: 0.9179 (mmm) cc_final: 0.8961 (mmp) REVERT: B 102 MET cc_start: 0.7784 (tpp) cc_final: 0.7572 (tpp) REVERT: B 210 ARG cc_start: 0.6974 (ttp80) cc_final: 0.6410 (ttp80) REVERT: B 229 MET cc_start: 0.7055 (tpp) cc_final: 0.6854 (tpp) REVERT: C 182 MET cc_start: 0.5440 (ttt) cc_final: 0.5214 (ttt) REVERT: D 240 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8363 (mtpp) REVERT: E 105 ARG cc_start: 0.7827 (ptp-170) cc_final: 0.7208 (ptp-170) REVERT: E 119 GLN cc_start: 0.6745 (OUTLIER) cc_final: 0.5921 (pm20) REVERT: E 343 TYR cc_start: 0.7914 (t80) cc_final: 0.7373 (t80) REVERT: F 14 LYS cc_start: 0.9150 (mmtt) cc_final: 0.8907 (mmtp) REVERT: F 40 MET cc_start: 0.6519 (tpp) cc_final: 0.6216 (tpt) REVERT: F 60 TYR cc_start: 0.5267 (t80) cc_final: 0.4925 (t80) REVERT: F 61 ARG cc_start: 0.8585 (ptp90) cc_final: 0.8364 (ptp90) REVERT: F 90 LEU cc_start: 0.8655 (tp) cc_final: 0.8267 (tp) REVERT: F 99 LEU cc_start: 0.7905 (tp) cc_final: 0.7693 (pp) REVERT: F 144 PHE cc_start: 0.8725 (t80) cc_final: 0.8138 (t80) REVERT: F 148 CYS cc_start: 0.8845 (m) cc_final: 0.8389 (m) REVERT: F 149 ARG cc_start: 0.9330 (mtp-110) cc_final: 0.8952 (mtm-85) REVERT: G 13 LYS cc_start: 0.8244 (ttmm) cc_final: 0.7730 (mttp) REVERT: G 87 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.6913 (pp) REVERT: H 116 MET cc_start: 0.7281 (ttm) cc_final: 0.7053 (ttt) outliers start: 91 outliers final: 67 residues processed: 386 average time/residue: 0.1632 time to fit residues: 95.8623 Evaluate side-chains 375 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 303 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 409 PHE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 799 TYR Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 302 ASN Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 246 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 189 optimal weight: 0.3980 chunk 140 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 235 optimal weight: 8.9990 chunk 194 optimal weight: 50.0000 chunk 179 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 181 optimal weight: 2.9990 chunk 200 optimal weight: 0.0060 overall best weight: 1.0600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 194 HIS E 213 HIS H 36 ASN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.189079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.152968 restraints weight = 34279.174| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 2.77 r_work: 0.3912 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21027 Z= 0.127 Angle : 0.616 12.294 28454 Z= 0.309 Chirality : 0.042 0.188 3317 Planarity : 0.004 0.073 3643 Dihedral : 6.773 127.350 2906 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.93 % Allowed : 18.85 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.17), residues: 2601 helix: 0.77 (0.15), residues: 1230 sheet: -0.43 (0.22), residues: 523 loop : -0.71 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 91 TYR 0.012 0.001 TYR B 279 PHE 0.034 0.002 PHE E 339 TRP 0.027 0.001 TRP A 307 HIS 0.007 0.001 HIS F 153 Details of bonding type rmsd covalent geometry : bond 0.00292 (21027) covalent geometry : angle 0.61607 (28454) hydrogen bonds : bond 0.03354 ( 1103) hydrogen bonds : angle 4.52029 ( 3177) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 339 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 PHE cc_start: 0.8158 (t80) cc_final: 0.7588 (m-80) REVERT: A 853 MET cc_start: 0.9251 (mmm) cc_final: 0.9025 (mmp) REVERT: B 102 MET cc_start: 0.7899 (tpp) cc_final: 0.7191 (tpt) REVERT: B 199 LEU cc_start: 0.8178 (mm) cc_final: 0.7949 (mm) REVERT: B 210 ARG cc_start: 0.7061 (ttp80) cc_final: 0.6540 (ttp80) REVERT: D 240 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8344 (mtpp) REVERT: D 246 GLN cc_start: 0.6930 (tp40) cc_final: 0.6631 (tp-100) REVERT: E 21 GLU cc_start: 0.8130 (pt0) cc_final: 0.7651 (pm20) REVERT: E 105 ARG cc_start: 0.7873 (ptp-170) cc_final: 0.7194 (ptp-170) REVERT: E 119 GLN cc_start: 0.6793 (OUTLIER) cc_final: 0.5992 (pm20) REVERT: E 343 TYR cc_start: 0.7955 (t80) cc_final: 0.7374 (t80) REVERT: F 14 LYS cc_start: 0.9147 (mmtt) cc_final: 0.8918 (mmtp) REVERT: F 53 ARG cc_start: 0.8863 (ptp-110) cc_final: 0.8295 (mtm110) REVERT: F 60 TYR cc_start: 0.5360 (t80) cc_final: 0.5086 (t80) REVERT: F 61 ARG cc_start: 0.8594 (ptp90) cc_final: 0.8104 (ptm-80) REVERT: F 144 PHE cc_start: 0.8792 (t80) cc_final: 0.8131 (t80) REVERT: F 148 CYS cc_start: 0.8904 (m) cc_final: 0.8432 (m) REVERT: G 13 LYS cc_start: 0.8182 (ttmm) cc_final: 0.7653 (mttp) REVERT: G 87 ILE cc_start: 0.7431 (OUTLIER) cc_final: 0.6919 (pp) REVERT: H 131 GLN cc_start: 0.6590 (tm-30) cc_final: 0.6055 (tm-30) outliers start: 90 outliers final: 67 residues processed: 399 average time/residue: 0.1626 time to fit residues: 98.5600 Evaluate side-chains 382 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 312 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 799 TYR Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 246 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 248 optimal weight: 3.9990 chunk 191 optimal weight: 30.0000 chunk 98 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 156 optimal weight: 20.0000 chunk 152 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 232 optimal weight: 9.9990 chunk 138 optimal weight: 0.8980 chunk 183 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 213 HIS G 177 ASN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.188682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.154010 restraints weight = 34212.359| |-----------------------------------------------------------------------------| r_work (start): 0.4220 rms_B_bonded: 2.53 r_work: 0.3974 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21027 Z= 0.183 Angle : 0.663 10.485 28454 Z= 0.334 Chirality : 0.044 0.284 3317 Planarity : 0.005 0.072 3643 Dihedral : 6.876 127.346 2906 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.41 % Allowed : 19.20 % Favored : 76.40 % 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 aren not related in a simple way. whole: -0.16 (0.17), residues: 2601 helix: 0.62 (0.15), residues: 1232 sheet: -0.39 (0.23), residues: 520 loop : -0.79 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 140 TYR 0.018 0.002 TYR G 211 PHE 0.030 0.002 PHE E 339 TRP 0.029 0.002 TRP A 307 HIS 0.007 0.001 HIS F 153 Details of bonding type rmsd covalent geometry : bond 0.00428 (21027) covalent geometry : angle 0.66331 (28454) hydrogen bonds : bond 0.03660 ( 1103) hydrogen bonds : angle 4.66840 ( 3177) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 318 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6546 (pm20) REVERT: A 409 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7650 (m-80) REVERT: B 102 MET cc_start: 0.7819 (tpp) cc_final: 0.6922 (tpt) REVERT: B 210 ARG cc_start: 0.6907 (ttp80) cc_final: 0.6412 (ttp80) REVERT: B 229 MET cc_start: 0.7217 (tpp) cc_final: 0.6936 (tpp) REVERT: D 108 LEU cc_start: 0.8582 (mm) cc_final: 0.8382 (mm) REVERT: D 240 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8395 (mtpp) REVERT: D 246 GLN cc_start: 0.6765 (tp40) cc_final: 0.6489 (tp40) REVERT: E 105 ARG cc_start: 0.7632 (ptp-170) cc_final: 0.7132 (ptp-170) REVERT: E 119 GLN cc_start: 0.6673 (OUTLIER) cc_final: 0.5840 (pm20) REVERT: E 343 TYR cc_start: 0.7895 (t80) cc_final: 0.7392 (t80) REVERT: F 14 LYS cc_start: 0.9116 (mmtt) cc_final: 0.8906 (mmtp) REVERT: F 53 ARG cc_start: 0.8805 (ptp-110) cc_final: 0.8273 (mtm110) REVERT: F 60 TYR cc_start: 0.5339 (t80) cc_final: 0.4610 (t80) REVERT: F 61 ARG cc_start: 0.8569 (ptp90) cc_final: 0.8162 (ptp90) REVERT: F 99 LEU cc_start: 0.8260 (pp) cc_final: 0.7992 (tp) REVERT: F 144 PHE cc_start: 0.8806 (t80) cc_final: 0.8143 (t80) REVERT: F 148 CYS cc_start: 0.8777 (m) cc_final: 0.8280 (m) REVERT: F 149 ARG cc_start: 0.9244 (mtp-110) cc_final: 0.8895 (mtm-85) REVERT: G 13 LYS cc_start: 0.8150 (ttmm) cc_final: 0.7696 (mttp) REVERT: G 87 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.6944 (pp) outliers start: 101 outliers final: 80 residues processed: 385 average time/residue: 0.1640 time to fit residues: 95.6811 Evaluate side-chains 390 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 305 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 409 PHE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 799 TYR Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 177 CYS Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 302 ASN Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 246 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 44 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 196 optimal weight: 7.9990 chunk 125 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 chunk 162 optimal weight: 4.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 194 HIS E 213 HIS H 36 ASN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.184728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.148362 restraints weight = 34483.394| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 2.99 r_work: 0.3846 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 21027 Z= 0.228 Angle : 0.725 10.999 28454 Z= 0.366 Chirality : 0.046 0.282 3317 Planarity : 0.005 0.073 3643 Dihedral : 7.196 129.209 2906 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.49 % Allowed : 19.94 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.16), residues: 2601 helix: 0.36 (0.14), residues: 1226 sheet: -0.52 (0.23), residues: 502 loop : -0.86 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 140 TYR 0.016 0.002 TYR E 318 PHE 0.040 0.002 PHE E 339 TRP 0.030 0.002 TRP A 307 HIS 0.008 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00537 (21027) covalent geometry : angle 0.72514 (28454) hydrogen bonds : bond 0.04026 ( 1103) hydrogen bonds : angle 4.85471 ( 3177) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 327 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6483 (pm20) REVERT: A 307 TRP cc_start: 0.6823 (t60) cc_final: 0.6602 (t60) REVERT: A 409 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.7704 (m-80) REVERT: B 102 MET cc_start: 0.8017 (tpp) cc_final: 0.7156 (tpt) REVERT: B 210 ARG cc_start: 0.7083 (ttp80) cc_final: 0.6537 (ttp80) REVERT: D 255 LYS cc_start: 0.8046 (tptt) cc_final: 0.7776 (mmtm) REVERT: E 105 ARG cc_start: 0.7849 (ptp-170) cc_final: 0.7262 (ptp-170) REVERT: E 119 GLN cc_start: 0.6820 (OUTLIER) cc_final: 0.6014 (pm20) REVERT: E 194 HIS cc_start: 0.7211 (OUTLIER) cc_final: 0.6990 (t-90) REVERT: E 343 TYR cc_start: 0.8025 (t80) cc_final: 0.7492 (t80) REVERT: F 14 LYS cc_start: 0.9119 (mmtt) cc_final: 0.8835 (mtmt) REVERT: F 53 ARG cc_start: 0.8902 (ptp-110) cc_final: 0.8313 (mtm110) REVERT: F 61 ARG cc_start: 0.8659 (ptp90) cc_final: 0.8136 (ptm-80) REVERT: F 91 ARG cc_start: 0.7104 (ptm-80) cc_final: 0.6464 (ptm-80) REVERT: F 144 PHE cc_start: 0.8775 (t80) cc_final: 0.8063 (t80) REVERT: F 148 CYS cc_start: 0.8878 (m) cc_final: 0.8421 (m) REVERT: F 149 ARG cc_start: 0.9320 (mtp-110) cc_final: 0.8925 (mtm-85) REVERT: G 13 LYS cc_start: 0.8277 (ttmm) cc_final: 0.7783 (mttp) REVERT: G 87 ILE cc_start: 0.7652 (OUTLIER) cc_final: 0.7148 (pp) REVERT: H 27 CYS cc_start: 0.8363 (t) cc_final: 0.7987 (p) REVERT: H 131 GLN cc_start: 0.6712 (tm130) cc_final: 0.6145 (tm-30) outliers start: 103 outliers final: 78 residues processed: 402 average time/residue: 0.1702 time to fit residues: 104.1979 Evaluate side-chains 386 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 303 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 409 PHE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 177 CYS Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 302 ASN Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 246 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 114 optimal weight: 0.5980 chunk 167 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 184 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 233 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 194 HIS E 213 HIS F 38 GLN F 65 ASN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.190027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.155947 restraints weight = 34070.232| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 2.51 r_work: 0.4001 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21027 Z= 0.136 Angle : 0.683 13.637 28454 Z= 0.341 Chirality : 0.044 0.282 3317 Planarity : 0.005 0.077 3643 Dihedral : 6.948 129.149 2906 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.45 % Allowed : 21.25 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.17), residues: 2601 helix: 0.63 (0.15), residues: 1228 sheet: -0.46 (0.23), residues: 502 loop : -0.75 (0.22), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 140 TYR 0.022 0.001 TYR E 330 PHE 0.034 0.002 PHE E 339 TRP 0.026 0.002 TRP A 307 HIS 0.035 0.001 HIS E 194 Details of bonding type rmsd covalent geometry : bond 0.00312 (21027) covalent geometry : angle 0.68328 (28454) hydrogen bonds : bond 0.03520 ( 1103) hydrogen bonds : angle 4.61986 ( 3177) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 327 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 PHE cc_start: 0.8255 (t80) cc_final: 0.7675 (m-80) REVERT: B 210 ARG cc_start: 0.6962 (ttp80) cc_final: 0.6477 (ttp80) REVERT: B 229 MET cc_start: 0.7120 (tpp) cc_final: 0.6793 (tpp) REVERT: D 54 PHE cc_start: 0.6055 (OUTLIER) cc_final: 0.5689 (t80) REVERT: D 255 LYS cc_start: 0.8068 (tptt) cc_final: 0.7790 (mmtm) REVERT: E 21 GLU cc_start: 0.7969 (pt0) cc_final: 0.7627 (pm20) REVERT: E 105 ARG cc_start: 0.7647 (ptp-170) cc_final: 0.7374 (ptp-170) REVERT: E 119 GLN cc_start: 0.6713 (OUTLIER) cc_final: 0.5891 (pm20) REVERT: E 343 TYR cc_start: 0.7877 (t80) cc_final: 0.7401 (t80) REVERT: F 5 ARG cc_start: 0.7571 (ptm-80) cc_final: 0.7347 (ptm160) REVERT: F 14 LYS cc_start: 0.9077 (mmtt) cc_final: 0.8777 (ptpp) REVERT: F 53 ARG cc_start: 0.8817 (ptp-110) cc_final: 0.8279 (mtm110) REVERT: F 61 ARG cc_start: 0.8562 (ptp90) cc_final: 0.8291 (ptp90) REVERT: F 91 ARG cc_start: 0.7130 (ptm-80) cc_final: 0.6717 (ptm-80) REVERT: F 99 LEU cc_start: 0.7810 (tp) cc_final: 0.7572 (pp) REVERT: F 139 MET cc_start: 0.2662 (OUTLIER) cc_final: 0.2296 (ppp) REVERT: F 144 PHE cc_start: 0.8741 (t80) cc_final: 0.7980 (t80) REVERT: F 148 CYS cc_start: 0.8818 (m) cc_final: 0.8320 (m) REVERT: G 13 LYS cc_start: 0.8149 (ttmm) cc_final: 0.7707 (mttp) REVERT: G 87 ILE cc_start: 0.7459 (OUTLIER) cc_final: 0.6959 (pp) REVERT: G 199 MET cc_start: 0.2913 (ptt) cc_final: 0.2347 (ptt) REVERT: H 27 CYS cc_start: 0.8291 (t) cc_final: 0.7897 (p) REVERT: H 131 GLN cc_start: 0.6754 (tm130) cc_final: 0.6091 (tm-30) outliers start: 79 outliers final: 64 residues processed: 381 average time/residue: 0.1593 time to fit residues: 92.6340 Evaluate side-chains 372 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 304 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 246 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 17 optimal weight: 8.9990 chunk 237 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 30 optimal weight: 0.0980 chunk 102 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 233 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 239 optimal weight: 0.0040 overall best weight: 1.2198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 HIS E 213 HIS F 38 GLN H 36 ASN ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.189728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.155022 restraints weight = 34167.475| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 2.55 r_work: 0.4004 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21027 Z= 0.141 Angle : 0.683 11.508 28454 Z= 0.338 Chirality : 0.044 0.289 3317 Planarity : 0.005 0.075 3643 Dihedral : 6.818 128.075 2906 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.18 % Allowed : 21.73 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.17), residues: 2601 helix: 0.72 (0.15), residues: 1227 sheet: -0.41 (0.23), residues: 502 loop : -0.74 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 140 TYR 0.011 0.001 TYR E 318 PHE 0.041 0.002 PHE E 339 TRP 0.015 0.002 TRP A 307 HIS 0.010 0.001 HIS E 194 Details of bonding type rmsd covalent geometry : bond 0.00329 (21027) covalent geometry : angle 0.68274 (28454) hydrogen bonds : bond 0.03463 ( 1103) hydrogen bonds : angle 4.57892 ( 3177) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 321 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 PHE cc_start: 0.8264 (t80) cc_final: 0.7698 (m-80) REVERT: A 853 MET cc_start: 0.9239 (mmm) cc_final: 0.8895 (mmp) REVERT: B 193 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7566 (mm) REVERT: B 210 ARG cc_start: 0.7079 (ttp80) cc_final: 0.6545 (ttp80) REVERT: B 229 MET cc_start: 0.7106 (tpp) cc_final: 0.6715 (tpp) REVERT: D 54 PHE cc_start: 0.6057 (OUTLIER) cc_final: 0.5680 (t80) REVERT: D 255 LYS cc_start: 0.8125 (tptt) cc_final: 0.7737 (mmtm) REVERT: E 21 GLU cc_start: 0.8016 (pt0) cc_final: 0.7616 (pm20) REVERT: E 105 ARG cc_start: 0.7715 (ptp-170) cc_final: 0.7443 (ptp-170) REVERT: E 119 GLN cc_start: 0.6733 (OUTLIER) cc_final: 0.5906 (pm20) REVERT: E 343 TYR cc_start: 0.8006 (t80) cc_final: 0.7391 (t80) REVERT: F 5 ARG cc_start: 0.7501 (ptm-80) cc_final: 0.7288 (ptm160) REVERT: F 14 LYS cc_start: 0.9071 (mmtt) cc_final: 0.8773 (ptpp) REVERT: F 53 ARG cc_start: 0.8845 (ptp-110) cc_final: 0.8542 (mtm110) REVERT: F 61 ARG cc_start: 0.8668 (ptp90) cc_final: 0.8118 (ptm-80) REVERT: F 91 ARG cc_start: 0.7188 (ptm-80) cc_final: 0.6327 (ptm-80) REVERT: F 139 MET cc_start: 0.2462 (OUTLIER) cc_final: 0.2023 (ppp) REVERT: F 144 PHE cc_start: 0.8767 (t80) cc_final: 0.7969 (t80) REVERT: F 148 CYS cc_start: 0.8844 (m) cc_final: 0.8334 (m) REVERT: G 13 LYS cc_start: 0.8178 (ttmm) cc_final: 0.7704 (mttp) REVERT: G 87 ILE cc_start: 0.7464 (OUTLIER) cc_final: 0.6947 (pp) REVERT: G 199 MET cc_start: 0.2756 (ptt) cc_final: 0.2342 (ptt) REVERT: H 27 CYS cc_start: 0.8217 (t) cc_final: 0.7818 (p) REVERT: H 131 GLN cc_start: 0.6796 (tm130) cc_final: 0.6156 (tm-30) outliers start: 73 outliers final: 65 residues processed: 366 average time/residue: 0.1639 time to fit residues: 90.9116 Evaluate side-chains 377 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 307 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 177 CYS Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 246 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 14 optimal weight: 10.0000 chunk 112 optimal weight: 0.0470 chunk 25 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 236 optimal weight: 9.9990 chunk 251 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 overall best weight: 1.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 HIS F 38 GLN ** H 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 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 = 0.4602 r_free = 0.4602 target = 0.189709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.155197 restraints weight = 34286.440| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 2.61 r_work: 0.3992 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21027 Z= 0.147 Angle : 0.690 11.152 28454 Z= 0.343 Chirality : 0.044 0.289 3317 Planarity : 0.005 0.075 3643 Dihedral : 6.801 127.744 2906 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.27 % Allowed : 21.99 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.17), residues: 2601 helix: 0.69 (0.15), residues: 1232 sheet: -0.35 (0.23), residues: 489 loop : -0.70 (0.23), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 51 TYR 0.020 0.001 TYR B 213 PHE 0.041 0.002 PHE E 339 TRP 0.013 0.001 TRP H 28 HIS 0.006 0.001 HIS F 153 Details of bonding type rmsd covalent geometry : bond 0.00343 (21027) covalent geometry : angle 0.68993 (28454) hydrogen bonds : bond 0.03505 ( 1103) hydrogen bonds : angle 4.58988 ( 3177) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5308.40 seconds wall clock time: 92 minutes 2.86 seconds (5522.86 seconds total)