Starting phenix.real_space_refine on Tue May 20 23:05:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8umt_42383/05_2025/8umt_42383.cif Found real_map, /net/cci-nas-00/data/ceres_data/8umt_42383/05_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_42383/05_2025/8umt_42383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8umt_42383/05_2025/8umt_42383.map" model { file = "/net/cci-nas-00/data/ceres_data/8umt_42383/05_2025/8umt_42383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8umt_42383/05_2025/8umt_42383.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 11.84, per 1000 atoms: 0.57 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: 5.24 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 2.61 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: 7.94 Time building geometry restraints manager: 6.13 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: 0.000 Normalize map: mean=0, sd=1: 1.360 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: 0.750 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 47.390 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.330 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.001 TRP H 28 HIS 0.005 0.001 HIS C 55 PHE 0.015 0.002 PHE F 169 TYR 0.012 0.001 TYR D 77 ARG 0.003 0.000 ARG C 311 Details of bonding type rmsd hydrogen bonds : bond 0.13946 ( 1103) hydrogen bonds : angle 6.43190 ( 3177) covalent geometry : bond 0.00372 (21027) covalent geometry : angle 0.74968 (28454) *********************** 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 : 2.142 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: symmetry clash REVERT: A 531 MET cc_start: 0.5988 (tpp) cc_final: 0.5637 (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: 0.6970 (m-10) REVERT: B 245 PHE cc_start: 0.7011 (t80) cc_final: 0.6803 (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: 0.5368 (m-80) REVERT: F 1 MET cc_start: 0.4277 (ppp) cc_final: 0.3349 (ppp) REVERT: F 14 LYS cc_start: 0.8759 (mmtt) cc_final: 0.8114 (ttpp) REVERT: G 87 ILE cc_start: 0.7059 (OUTLIER) cc_final: 0.6517 (pp) REVERT: G 154 ILE cc_start: 0.5604 (OUTLIER) cc_final: 0.5279 (tp) outliers start: 95 outliers final: 21 residues processed: 545 average time/residue: 0.3484 time to fit residues: 280.7941 Evaluate side-chains 341 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 317 time to evaluate : 1.970 ------------------------------------------------------------------------------- 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 158 VAL 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 154 ILE Chi-restraints excluded: chain H residue 224 THR 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 218 optimal weight: 0.9980 chunk 196 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 203 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 123 optimal weight: 8.9990 chunk 151 optimal weight: 5.9990 chunk 235 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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 655 ASN ** 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 55 GLN ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 GLN E 194 HIS E 213 HIS F 177 ASN G 65 ASN G 246 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.185908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.150378 restraints weight = 34394.418| |-----------------------------------------------------------------------------| r_work (start): 0.4177 rms_B_bonded: 2.96 r_work: 0.3884 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 21027 Z= 0.310 Angle : 0.798 10.694 28454 Z= 0.408 Chirality : 0.048 0.187 3317 Planarity : 0.007 0.083 3643 Dihedral : 8.536 138.716 2936 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.71 % Allowed : 15.92 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.16), residues: 2601 helix: -0.58 (0.14), residues: 1226 sheet: -0.66 (0.23), residues: 516 loop : -1.17 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 28 HIS 0.014 0.002 HIS F 153 PHE 0.031 0.003 PHE H 207 TYR 0.028 0.003 TYR F 133 ARG 0.012 0.001 ARG D 102 Details of bonding type rmsd hydrogen bonds : bond 0.04880 ( 1103) hydrogen bonds : angle 5.31233 ( 3177) covalent geometry : bond 0.00723 (21027) covalent geometry : angle 0.79761 (28454) *********************** 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 460 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 352 time to evaluate : 2.160 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 175 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6737 (pm20) REVERT: A 843 LEU cc_start: 0.9296 (tp) cc_final: 0.9061 (tp) REVERT: D 117 GLN cc_start: 0.7769 (tp40) cc_final: 0.6882 (tp-100) REVERT: D 193 ARG cc_start: 0.7402 (mmm160) cc_final: 0.7179 (mmm-85) REVERT: E 119 GLN cc_start: 0.6592 (OUTLIER) cc_final: 0.5795 (pm20) REVERT: F 1 MET cc_start: 0.6205 (ppp) cc_final: 0.4983 (ppp) REVERT: F 14 LYS cc_start: 0.9277 (mmtt) cc_final: 0.8728 (mtpp) REVERT: F 60 TYR cc_start: 0.4129 (t80) cc_final: 0.3799 (t80) REVERT: F 99 LEU cc_start: 0.8334 (pp) cc_final: 0.7977 (tp) REVERT: F 148 CYS cc_start: 0.8955 (m) cc_final: 0.8715 (m) REVERT: G 87 ILE cc_start: 0.7563 (OUTLIER) cc_final: 0.7258 (pp) REVERT: G 125 GLN cc_start: 0.7109 (tm-30) cc_final: 0.6785 (tm-30) REVERT: G 146 ARG cc_start: 0.8416 (ttp-110) cc_final: 0.7860 (ptp90) REVERT: H 184 GLN cc_start: 0.6590 (tm-30) cc_final: 0.6348 (tm-30) outliers start: 108 outliers final: 72 residues processed: 429 average time/residue: 0.3481 time to fit residues: 222.0307 Evaluate side-chains 380 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 305 time to evaluate : 2.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 GLU 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 369 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 525 VAL 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 163 LYS Chi-restraints excluded: chain B residue 181 ILE 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 23 VAL Chi-restraints excluded: chain C residue 35 ILE 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 154 ILE Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 206 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 C residue 314 VAL Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 222 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 55 ILE Chi-restraints excluded: chain E residue 93 LEU 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 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 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 209 LEU Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 8 GLN 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 123 VAL Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 224 THR 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 218 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 3 optimal weight: 0.1980 chunk 128 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 chunk 236 optimal weight: 9.9990 chunk 195 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 243 optimal weight: 10.0000 chunk 217 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 ASN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 GLN B 234 ASN ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 HIS F 184 GLN G 36 ASN H 44 HIS H 177 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.189460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.154024 restraints weight = 33957.155| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 2.70 r_work: 0.3978 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21027 Z= 0.141 Angle : 0.637 9.148 28454 Z= 0.322 Chirality : 0.043 0.237 3317 Planarity : 0.005 0.079 3643 Dihedral : 7.880 128.784 2918 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.88 % Allowed : 18.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.16), residues: 2601 helix: 0.14 (0.14), residues: 1220 sheet: -0.67 (0.23), residues: 520 loop : -1.01 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 307 HIS 0.013 0.001 HIS F 153 PHE 0.019 0.002 PHE H 207 TYR 0.018 0.002 TYR B 279 ARG 0.012 0.001 ARG E 149 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 1103) hydrogen bonds : angle 4.92922 ( 3177) covalent geometry : bond 0.00321 (21027) covalent geometry : angle 0.63651 (28454) *********************** 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 439 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 350 time to evaluate : 2.390 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 531 MET cc_start: 0.7142 (tpp) cc_final: 0.6735 (tpp) REVERT: A 843 LEU cc_start: 0.9308 (tp) cc_final: 0.9091 (tp) REVERT: B 199 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7813 (mm) REVERT: D 117 GLN cc_start: 0.7945 (tp40) cc_final: 0.7686 (tp-100) REVERT: E 105 ARG cc_start: 0.7547 (ptp-170) cc_final: 0.6978 (ptp-170) REVERT: E 150 ARG cc_start: 0.8521 (mtm-85) cc_final: 0.8237 (mtm110) REVERT: F 1 MET cc_start: 0.6245 (ppp) cc_final: 0.5095 (ppp) REVERT: F 14 LYS cc_start: 0.9240 (mmtt) cc_final: 0.8707 (mtpp) REVERT: F 53 ARG cc_start: 0.8699 (ptp-110) cc_final: 0.8449 (mtm110) REVERT: F 60 TYR cc_start: 0.3879 (t80) cc_final: 0.3598 (t80) REVERT: F 99 LEU cc_start: 0.8315 (pp) cc_final: 0.8045 (tp) REVERT: F 144 PHE cc_start: 0.8673 (t80) cc_final: 0.7952 (t80) REVERT: F 148 CYS cc_start: 0.8977 (m) cc_final: 0.8643 (m) REVERT: G 13 LYS cc_start: 0.8259 (ttmm) cc_final: 0.7761 (mttp) REVERT: G 87 ILE cc_start: 0.7384 (OUTLIER) cc_final: 0.6992 (pp) REVERT: G 146 ARG cc_start: 0.8367 (ttp-110) cc_final: 0.7836 (ptp90) REVERT: H 116 MET cc_start: 0.7236 (ttm) cc_final: 0.6997 (ttt) REVERT: H 119 MET cc_start: 0.6197 (mtp) cc_final: 0.5950 (mtp) outliers start: 89 outliers final: 58 residues processed: 406 average time/residue: 0.3484 time to fit residues: 211.4691 Evaluate side-chains 369 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 309 time to evaluate : 2.487 ------------------------------------------------------------------------------- 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 369 VAL Chi-restraints excluded: chain A residue 414 GLU 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 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 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 100 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 205 LEU 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 E residue 86 THR Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 137 VAL 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 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 196 THR Chi-restraints excluded: chain F residue 203 VAL 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 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 111 VAL Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 182 LEU 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 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 10 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 211 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 179 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 0.0270 chunk 9 optimal weight: 9.9990 overall best weight: 2.2046 ------------------------------------------------------------------------------- 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** ** B 152 GLN ** 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 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 HIS E 194 HIS E 213 HIS E 244 GLN G 8 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 = 0.4601 r_free = 0.4601 target = 0.189009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.155018 restraints weight = 34493.719| |-----------------------------------------------------------------------------| r_work (start): 0.4222 rms_B_bonded: 2.83 r_work: 0.3943 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21027 Z= 0.185 Angle : 0.653 10.176 28454 Z= 0.332 Chirality : 0.044 0.171 3317 Planarity : 0.005 0.076 3643 Dihedral : 7.662 127.923 2914 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.45 % Allowed : 18.59 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.16), residues: 2601 helix: 0.25 (0.14), residues: 1233 sheet: -0.69 (0.22), residues: 529 loop : -0.99 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 307 HIS 0.010 0.001 HIS F 153 PHE 0.027 0.002 PHE E 339 TYR 0.018 0.002 TYR B 213 ARG 0.007 0.001 ARG E 51 Details of bonding type rmsd hydrogen bonds : bond 0.03885 ( 1103) hydrogen bonds : angle 4.89114 ( 3177) covalent geometry : bond 0.00434 (21027) covalent geometry : angle 0.65307 (28454) *********************** 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 437 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 335 time to evaluate : 2.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 PHE cc_start: 0.8184 (OUTLIER) cc_final: 0.7653 (m-80) REVERT: A 843 LEU cc_start: 0.9321 (tp) cc_final: 0.9120 (tp) REVERT: A 853 MET cc_start: 0.9235 (mmm) cc_final: 0.8907 (mmp) REVERT: B 199 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8065 (mm) REVERT: D 117 GLN cc_start: 0.7876 (tp40) cc_final: 0.7529 (tp-100) REVERT: E 105 ARG cc_start: 0.7530 (ptp-170) cc_final: 0.6984 (ptp-170) REVERT: E 119 GLN cc_start: 0.6713 (OUTLIER) cc_final: 0.5896 (pm20) REVERT: F 1 MET cc_start: 0.6226 (ppp) cc_final: 0.5111 (ppp) REVERT: F 14 LYS cc_start: 0.9193 (mmtt) cc_final: 0.8772 (mtpp) REVERT: F 40 MET cc_start: 0.5738 (tpt) cc_final: 0.5479 (tpt) REVERT: F 53 ARG cc_start: 0.8723 (ptp-110) cc_final: 0.8468 (mtm110) REVERT: F 60 TYR cc_start: 0.3915 (t80) cc_final: 0.3507 (t80) REVERT: F 99 LEU cc_start: 0.8309 (pp) cc_final: 0.8068 (tp) REVERT: F 144 PHE cc_start: 0.8776 (t80) cc_final: 0.8143 (t80) REVERT: F 148 CYS cc_start: 0.8930 (m) cc_final: 0.8596 (m) REVERT: G 13 LYS cc_start: 0.8248 (ttmm) cc_final: 0.7766 (mttp) REVERT: G 87 ILE cc_start: 0.7510 (OUTLIER) cc_final: 0.6968 (pp) REVERT: G 125 GLN cc_start: 0.6966 (tm-30) cc_final: 0.6668 (tm-30) outliers start: 102 outliers final: 76 residues processed: 403 average time/residue: 0.3342 time to fit residues: 202.9661 Evaluate side-chains 386 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 306 time to evaluate : 2.177 ------------------------------------------------------------------------------- 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 369 VAL Chi-restraints excluded: chain A residue 409 PHE Chi-restraints excluded: chain A residue 448 LEU 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 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 156 ARG 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 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 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 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 118 VAL Chi-restraints excluded: chain D residue 157 SER 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 261 VAL Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 86 THR 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 137 VAL Chi-restraints excluded: chain E residue 246 ILE 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 68 MET Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 209 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 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 111 VAL Chi-restraints excluded: chain G residue 119 MET 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 G residue 182 LEU Chi-restraints excluded: chain H residue 45 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 235 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 212 optimal weight: 0.3980 chunk 111 optimal weight: 0.0770 chunk 137 optimal weight: 3.9990 chunk 252 optimal weight: 10.0000 chunk 194 optimal weight: 0.4980 chunk 114 optimal weight: 1.9990 chunk 233 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- 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** B 126 GLN B 182 GLN ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN D 301 HIS E 22 GLN E 37 HIS E 213 HIS ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.188743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.153381 restraints weight = 34470.786| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 2.91 r_work: 0.3923 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21027 Z= 0.121 Angle : 0.609 9.859 28454 Z= 0.306 Chirality : 0.042 0.174 3317 Planarity : 0.005 0.077 3643 Dihedral : 7.184 128.165 2911 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.93 % Allowed : 20.07 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.17), residues: 2601 helix: 0.60 (0.15), residues: 1229 sheet: -0.58 (0.22), residues: 527 loop : -0.83 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 307 HIS 0.008 0.001 HIS F 153 PHE 0.026 0.001 PHE E 339 TYR 0.013 0.001 TYR F 249 ARG 0.008 0.000 ARG B 210 Details of bonding type rmsd hydrogen bonds : bond 0.03422 ( 1103) hydrogen bonds : angle 4.66276 ( 3177) covalent geometry : bond 0.00272 (21027) covalent geometry : angle 0.60883 (28454) *********************** 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 425 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 335 time to evaluate : 3.265 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: 0.8169 (t80) cc_final: 0.7577 (m-80) REVERT: A 531 MET cc_start: 0.6747 (tpp) cc_final: 0.6455 (tpp) REVERT: A 853 MET cc_start: 0.9222 (mmm) cc_final: 0.8884 (mmp) REVERT: B 102 MET cc_start: 0.7655 (tpp) cc_final: 0.6971 (tpt) REVERT: B 176 LYS cc_start: 0.7397 (mtmt) cc_final: 0.7162 (mtmm) REVERT: B 199 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7961 (mm) REVERT: B 210 ARG cc_start: 0.6959 (ttp80) cc_final: 0.6500 (ttp80) REVERT: D 117 GLN cc_start: 0.7937 (tp40) cc_final: 0.7578 (tp-100) REVERT: D 240 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8366 (mtpp) REVERT: D 255 LYS cc_start: 0.8252 (tptt) cc_final: 0.8031 (tptp) REVERT: E 21 GLU cc_start: 0.8088 (pt0) cc_final: 0.7667 (pm20) REVERT: E 105 ARG cc_start: 0.7521 (ptp-170) cc_final: 0.6964 (ptp-170) REVERT: E 119 GLN cc_start: 0.6701 (OUTLIER) cc_final: 0.5901 (pm20) REVERT: F 1 MET cc_start: 0.6306 (ppp) cc_final: 0.5203 (ppp) REVERT: F 14 LYS cc_start: 0.9157 (mmtt) cc_final: 0.8924 (mmtp) REVERT: F 53 ARG cc_start: 0.8740 (ptp-110) cc_final: 0.8086 (mtm110) REVERT: F 60 TYR cc_start: 0.3981 (t80) cc_final: 0.3488 (t80) REVERT: F 99 LEU cc_start: 0.8324 (pp) cc_final: 0.8027 (pt) REVERT: F 144 PHE cc_start: 0.8745 (t80) cc_final: 0.8034 (t80) REVERT: F 148 CYS cc_start: 0.8993 (m) cc_final: 0.8645 (m) REVERT: F 248 LYS cc_start: 0.9139 (mtpt) cc_final: 0.8677 (pttm) REVERT: G 13 LYS cc_start: 0.8195 (ttmm) cc_final: 0.7687 (mttp) REVERT: G 87 ILE cc_start: 0.7410 (OUTLIER) cc_final: 0.6879 (pp) REVERT: H 199 MET cc_start: 0.6195 (tpp) cc_final: 0.5868 (tpp) outliers start: 90 outliers final: 62 residues processed: 395 average time/residue: 0.3512 time to fit residues: 210.2786 Evaluate side-chains 377 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 311 time to evaluate : 2.180 ------------------------------------------------------------------------------- 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 448 LEU Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 560 TYR Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 588 SER 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 109 ASN Chi-restraints excluded: chain B residue 114 ASP 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 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 113 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 94 GLU 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 261 VAL Chi-restraints excluded: chain D residue 311 HIS 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 233 CYS 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 196 THR Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 219 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 81 CYS Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 111 VAL 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 G residue 182 LEU Chi-restraints excluded: chain G residue 233 VAL 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 125 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 156 optimal weight: 9.9990 chunk 229 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 181 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 overall best weight: 4.0786 ------------------------------------------------------------------------------- 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** B 182 GLN ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 HIS ** 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 ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 HIS 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.181505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.145611 restraints weight = 34949.680| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 3.45 r_work: 0.3768 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 21027 Z= 0.295 Angle : 0.768 10.343 28454 Z= 0.390 Chirality : 0.047 0.176 3317 Planarity : 0.006 0.078 3643 Dihedral : 7.734 129.888 2909 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 5.63 % Allowed : 19.11 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.16), residues: 2601 helix: 0.03 (0.14), residues: 1225 sheet: -0.83 (0.22), residues: 531 loop : -1.02 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 307 HIS 0.010 0.001 HIS C 289 PHE 0.034 0.003 PHE E 339 TYR 0.021 0.002 TYR E 318 ARG 0.008 0.001 ARG C 52 Details of bonding type rmsd hydrogen bonds : bond 0.04537 ( 1103) hydrogen bonds : angle 5.11616 ( 3177) covalent geometry : bond 0.00696 (21027) covalent geometry : angle 0.76782 (28454) *********************** 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 457 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 328 time to evaluate : 2.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6558 (pm20) REVERT: A 409 PHE cc_start: 0.8262 (OUTLIER) cc_final: 0.7702 (m-80) REVERT: A 853 MET cc_start: 0.9321 (mmm) cc_final: 0.9022 (mmp) REVERT: B 102 MET cc_start: 0.8055 (tpp) cc_final: 0.7169 (tpt) REVERT: B 155 ARG cc_start: 0.7251 (mtp85) cc_final: 0.6709 (mtp85) REVERT: B 176 LYS cc_start: 0.7548 (mtmt) cc_final: 0.7321 (mtmm) REVERT: C 309 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6773 (tt0) REVERT: D 117 GLN cc_start: 0.8135 (tp40) cc_final: 0.7823 (tp-100) REVERT: D 240 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8435 (mtpp) REVERT: D 246 GLN cc_start: 0.6960 (tp40) cc_final: 0.6556 (tp-100) REVERT: E 105 ARG cc_start: 0.7629 (ptp-170) cc_final: 0.7008 (ptp-170) REVERT: E 119 GLN cc_start: 0.6867 (OUTLIER) cc_final: 0.6086 (pm20) REVERT: E 194 HIS cc_start: 0.7298 (OUTLIER) cc_final: 0.7085 (t-90) REVERT: F 1 MET cc_start: 0.6489 (ppp) cc_final: 0.5366 (ppp) REVERT: F 53 ARG cc_start: 0.8821 (ptp-110) cc_final: 0.8557 (mtm110) REVERT: F 91 ARG cc_start: 0.7118 (ptm-80) cc_final: 0.6483 (ptm-80) REVERT: F 99 LEU cc_start: 0.8409 (pp) cc_final: 0.8187 (pt) REVERT: F 144 PHE cc_start: 0.8924 (t80) cc_final: 0.8548 (t80) REVERT: F 148 CYS cc_start: 0.9020 (m) cc_final: 0.8803 (m) REVERT: F 248 LYS cc_start: 0.9171 (mtpt) cc_final: 0.8622 (pttm) REVERT: G 13 LYS cc_start: 0.8344 (ttmm) cc_final: 0.7821 (mttp) REVERT: G 87 ILE cc_start: 0.7630 (OUTLIER) cc_final: 0.7119 (pp) REVERT: G 125 GLN cc_start: 0.7035 (tm-30) cc_final: 0.6747 (tm-30) REVERT: G 139 MET cc_start: 0.6497 (ppp) cc_final: 0.6086 (ttp) REVERT: H 27 CYS cc_start: 0.8481 (t) cc_final: 0.8194 (p) REVERT: H 49 GLN cc_start: 0.7115 (mp10) cc_final: 0.6775 (mm-40) outliers start: 129 outliers final: 98 residues processed: 423 average time/residue: 0.3323 time to fit residues: 211.9794 Evaluate side-chains 406 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 301 time to evaluate : 2.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 409 PHE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 560 TYR Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 753 THR 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 109 ASN Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 246 ILE 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 69 THR 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 148 ASN Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 157 SER 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 249 THR 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 5 VAL Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 93 LEU 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 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 303 CYS 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 68 MET Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 233 VAL 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 111 VAL Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 179 ASN Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 233 VAL 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 158 VAL Chi-restraints excluded: chain H residue 162 CYS 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 34 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 156 optimal weight: 8.9990 chunk 155 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 123 optimal weight: 20.0000 chunk 225 optimal weight: 7.9990 chunk 237 optimal weight: 3.9990 chunk 91 optimal weight: 0.0470 chunk 38 optimal weight: 0.9980 chunk 150 optimal weight: 0.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 ASN ** 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** D 125 ASN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 HIS E 213 HIS F 38 GLN F 65 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.185265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.149594 restraints weight = 34594.882| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 3.22 r_work: 0.3856 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21027 Z= 0.151 Angle : 0.667 11.855 28454 Z= 0.332 Chirality : 0.044 0.370 3317 Planarity : 0.005 0.081 3643 Dihedral : 7.444 130.874 2909 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.93 % Allowed : 21.25 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.17), residues: 2601 helix: 0.44 (0.15), residues: 1226 sheet: -0.65 (0.22), residues: 512 loop : -0.88 (0.22), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 307 HIS 0.021 0.001 HIS E 194 PHE 0.058 0.002 PHE F 215 TYR 0.022 0.002 TYR E 330 ARG 0.011 0.000 ARG B 210 Details of bonding type rmsd hydrogen bonds : bond 0.03671 ( 1103) hydrogen bonds : angle 4.78364 ( 3177) covalent geometry : bond 0.00352 (21027) covalent geometry : angle 0.66744 (28454) *********************** 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 414 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 324 time to evaluate : 2.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 PHE cc_start: 0.8244 (t80) cc_final: 0.7621 (m-80) REVERT: A 531 MET cc_start: 0.7108 (tpp) cc_final: 0.6702 (tpp) REVERT: A 853 MET cc_start: 0.9311 (mmm) cc_final: 0.9005 (mmp) REVERT: B 102 MET cc_start: 0.7963 (tpp) cc_final: 0.7208 (tpt) REVERT: B 176 LYS cc_start: 0.7472 (mtmt) cc_final: 0.7265 (mtmm) REVERT: B 229 MET cc_start: 0.7081 (tpp) cc_final: 0.6687 (tpp) REVERT: C 106 LEU cc_start: 0.6618 (OUTLIER) cc_final: 0.6283 (tp) REVERT: D 54 PHE cc_start: 0.6165 (OUTLIER) cc_final: 0.5801 (t80) REVERT: D 109 ASN cc_start: 0.7576 (t0) cc_final: 0.7232 (t0) REVERT: D 167 MET cc_start: 0.7023 (mmt) cc_final: 0.6595 (mmt) REVERT: D 240 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8436 (mtpp) REVERT: D 246 GLN cc_start: 0.6844 (tp40) cc_final: 0.6458 (tp-100) REVERT: E 105 ARG cc_start: 0.7491 (ptp-170) cc_final: 0.6956 (ptp-170) REVERT: E 119 GLN cc_start: 0.6795 (OUTLIER) cc_final: 0.5970 (pm20) REVERT: F 1 MET cc_start: 0.6470 (ppp) cc_final: 0.5292 (ppp) REVERT: F 14 LYS cc_start: 0.9129 (mmtt) cc_final: 0.8828 (mtmt) REVERT: F 53 ARG cc_start: 0.8784 (ptp-110) cc_final: 0.8532 (mtm110) REVERT: F 91 ARG cc_start: 0.7060 (ptm-80) cc_final: 0.6465 (ptm-80) REVERT: F 99 LEU cc_start: 0.8337 (pp) cc_final: 0.8132 (pt) REVERT: F 144 PHE cc_start: 0.8873 (t80) cc_final: 0.8171 (t80) REVERT: F 148 CYS cc_start: 0.9029 (m) cc_final: 0.8681 (m) REVERT: G 13 LYS cc_start: 0.8278 (ttmm) cc_final: 0.7770 (mttp) REVERT: G 87 ILE cc_start: 0.7540 (OUTLIER) cc_final: 0.7005 (pp) REVERT: G 125 GLN cc_start: 0.7082 (tm-30) cc_final: 0.6827 (tm-30) REVERT: H 27 CYS cc_start: 0.8335 (t) cc_final: 0.8039 (p) REVERT: H 131 GLN cc_start: 0.6657 (tm-30) cc_final: 0.6007 (tm-30) outliers start: 90 outliers final: 76 residues processed: 388 average time/residue: 0.3506 time to fit residues: 202.0906 Evaluate side-chains 376 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 295 time to evaluate : 2.360 ------------------------------------------------------------------------------- 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 369 VAL Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 483 MET 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 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 109 ASN Chi-restraints excluded: chain B residue 175 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 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 105 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 94 GLU 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 288 LYS Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 93 LEU 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 155 TYR 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 314 MET Chi-restraints excluded: chain F residue 11 ILE 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 158 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 209 LEU 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 111 VAL Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 179 ASN Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 233 VAL 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 235 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 56 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 220 optimal weight: 20.0000 chunk 252 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 165 optimal weight: 0.8980 chunk 150 optimal weight: 5.9990 chunk 203 optimal weight: 0.9980 chunk 256 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 overall best weight: 2.5784 ------------------------------------------------------------------------------- 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 55 HIS ** 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 44 HIS ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 GLN ** H 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.183414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.147796 restraints weight = 34984.417| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 3.32 r_work: 0.3822 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 21027 Z= 0.208 Angle : 0.707 12.474 28454 Z= 0.355 Chirality : 0.045 0.385 3317 Planarity : 0.005 0.077 3643 Dihedral : 7.502 130.510 2909 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 4.58 % Allowed : 21.07 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.17), residues: 2601 helix: 0.34 (0.15), residues: 1224 sheet: -0.67 (0.22), residues: 512 loop : -0.88 (0.22), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 307 HIS 0.009 0.001 HIS E 194 PHE 0.034 0.002 PHE E 339 TYR 0.023 0.002 TYR F 249 ARG 0.012 0.001 ARG B 210 Details of bonding type rmsd hydrogen bonds : bond 0.03919 ( 1103) hydrogen bonds : angle 4.89075 ( 3177) covalent geometry : bond 0.00492 (21027) covalent geometry : angle 0.70651 (28454) *********************** 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 421 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 316 time to evaluate : 2.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6453 (pm20) REVERT: A 409 PHE cc_start: 0.8283 (t80) cc_final: 0.7657 (m-80) REVERT: A 531 MET cc_start: 0.6987 (tpp) cc_final: 0.6597 (tpp) REVERT: A 853 MET cc_start: 0.9275 (mmm) cc_final: 0.8974 (mmp) REVERT: B 102 MET cc_start: 0.8085 (tpp) cc_final: 0.7356 (tpt) REVERT: B 176 LYS cc_start: 0.7536 (mtmt) cc_final: 0.7307 (mtmm) REVERT: C 106 LEU cc_start: 0.6645 (OUTLIER) cc_final: 0.6296 (tp) REVERT: D 109 ASN cc_start: 0.7635 (t0) cc_final: 0.7279 (t0) REVERT: D 246 GLN cc_start: 0.6936 (tp40) cc_final: 0.6503 (tp-100) REVERT: D 255 LYS cc_start: 0.8428 (tptt) cc_final: 0.8144 (tptt) REVERT: E 105 ARG cc_start: 0.7516 (ptp-170) cc_final: 0.6993 (ptp-170) REVERT: E 119 GLN cc_start: 0.6812 (OUTLIER) cc_final: 0.5957 (pm20) REVERT: F 1 MET cc_start: 0.6501 (ppp) cc_final: 0.5380 (ppp) REVERT: F 14 LYS cc_start: 0.9120 (mmtt) cc_final: 0.8846 (mtmt) REVERT: F 91 ARG cc_start: 0.7015 (ptm-80) cc_final: 0.6592 (ptm-80) REVERT: F 99 LEU cc_start: 0.8287 (pp) cc_final: 0.8068 (pt) REVERT: F 144 PHE cc_start: 0.8904 (t80) cc_final: 0.8560 (t80) REVERT: G 13 LYS cc_start: 0.8290 (ttmm) cc_final: 0.7780 (mttp) REVERT: G 87 ILE cc_start: 0.7622 (OUTLIER) cc_final: 0.7082 (pp) REVERT: G 125 GLN cc_start: 0.7156 (tm-30) cc_final: 0.6896 (tm-30) REVERT: G 139 MET cc_start: 0.6426 (ppp) cc_final: 0.5999 (ttp) REVERT: H 27 CYS cc_start: 0.8388 (t) cc_final: 0.8126 (p) REVERT: H 117 LYS cc_start: 0.7841 (ptmm) cc_final: 0.7351 (mttm) outliers start: 105 outliers final: 85 residues processed: 390 average time/residue: 0.3451 time to fit residues: 200.9414 Evaluate side-chains 390 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 301 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 313 LEU 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 483 MET 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 109 ASN Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 246 ILE 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 69 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 157 TYR 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 94 GLU 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 249 THR 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 86 THR Chi-restraints excluded: chain E residue 93 LEU 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 230 CYS 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 314 MET Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 28 TRP 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 139 MET Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 209 LEU 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 111 VAL Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 179 ASN Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 162 CYS 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 76 optimal weight: 0.8980 chunk 230 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 chunk 171 optimal weight: 0.9990 chunk 178 optimal weight: 1.9990 chunk 245 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 160 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 ASN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 213 HIS ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.188168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.153787 restraints weight = 34377.178| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 2.54 r_work: 0.3977 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21027 Z= 0.147 Angle : 0.671 12.692 28454 Z= 0.337 Chirality : 0.044 0.370 3317 Planarity : 0.005 0.079 3643 Dihedral : 7.332 129.910 2909 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.97 % Allowed : 21.82 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.17), residues: 2601 helix: 0.56 (0.15), residues: 1226 sheet: -0.65 (0.23), residues: 501 loop : -0.82 (0.22), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 307 HIS 0.007 0.001 HIS F 153 PHE 0.049 0.002 PHE F 215 TYR 0.017 0.001 TYR F 249 ARG 0.013 0.001 ARG B 210 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 1103) hydrogen bonds : angle 4.73355 ( 3177) covalent geometry : bond 0.00343 (21027) covalent geometry : angle 0.67087 (28454) *********************** 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 416 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 325 time to evaluate : 2.508 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 409 PHE cc_start: 0.8246 (t80) cc_final: 0.7613 (m-80) REVERT: A 531 MET cc_start: 0.6926 (tpp) cc_final: 0.6559 (tpp) REVERT: A 853 MET cc_start: 0.9269 (mmm) cc_final: 0.8977 (mmp) REVERT: B 102 MET cc_start: 0.7804 (tpp) cc_final: 0.7144 (tpt) REVERT: B 229 MET cc_start: 0.7069 (tpp) cc_final: 0.6834 (tpp) REVERT: C 106 LEU cc_start: 0.6541 (OUTLIER) cc_final: 0.6192 (tp) REVERT: D 54 PHE cc_start: 0.5996 (OUTLIER) cc_final: 0.5605 (t80) REVERT: D 109 ASN cc_start: 0.7838 (t0) cc_final: 0.7501 (t0) REVERT: D 246 GLN cc_start: 0.6703 (tp40) cc_final: 0.6365 (tp-100) REVERT: E 21 GLU cc_start: 0.8043 (pt0) cc_final: 0.7684 (pm20) REVERT: E 105 ARG cc_start: 0.7263 (ptp-170) cc_final: 0.6872 (ptp-170) REVERT: E 119 GLN cc_start: 0.6682 (OUTLIER) cc_final: 0.5797 (pm20) REVERT: F 1 MET cc_start: 0.6395 (ppp) cc_final: 0.5287 (ppp) REVERT: F 14 LYS cc_start: 0.9076 (mmtt) cc_final: 0.8837 (mtmt) REVERT: F 53 ARG cc_start: 0.8865 (ptp-110) cc_final: 0.8374 (mtm110) REVERT: F 91 ARG cc_start: 0.7038 (ptm-80) cc_final: 0.6638 (ptm-80) REVERT: F 99 LEU cc_start: 0.8163 (pp) cc_final: 0.7962 (pt) REVERT: F 116 MET cc_start: 0.6691 (tpt) cc_final: 0.6258 (tpt) REVERT: F 144 PHE cc_start: 0.8782 (t80) cc_final: 0.8218 (t80) REVERT: F 153 HIS cc_start: 0.6566 (m-70) cc_final: 0.6350 (m-70) REVERT: F 248 LYS cc_start: 0.9181 (mtpt) cc_final: 0.8794 (pttm) REVERT: G 13 LYS cc_start: 0.8170 (ttmm) cc_final: 0.7731 (mttp) REVERT: G 87 ILE cc_start: 0.7445 (OUTLIER) cc_final: 0.6898 (pp) REVERT: G 125 GLN cc_start: 0.7171 (tm-30) cc_final: 0.6931 (tm-30) REVERT: G 139 MET cc_start: 0.6300 (ppp) cc_final: 0.5914 (ttp) REVERT: H 27 CYS cc_start: 0.8295 (t) cc_final: 0.8074 (p) outliers start: 91 outliers final: 76 residues processed: 390 average time/residue: 0.3564 time to fit residues: 206.0956 Evaluate side-chains 384 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 304 time to evaluate : 2.318 ------------------------------------------------------------------------------- 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 417 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 483 MET 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 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 109 ASN Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 175 ASP 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 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 105 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 157 TYR 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 94 GLU 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 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 86 THR Chi-restraints excluded: chain E residue 93 LEU 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 134 LEU 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 246 ILE 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 68 MET Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 209 LEU 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 111 VAL Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 179 ASN Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain H residue 21 ASP 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 184 GLN Chi-restraints excluded: chain H residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 222 optimal weight: 8.9990 chunk 194 optimal weight: 20.0000 chunk 34 optimal weight: 0.9980 chunk 220 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 chunk 235 optimal weight: 6.9990 chunk 174 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 232 optimal weight: 8.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- 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** B 152 GLN ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 213 HIS ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 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 = 0.4576 r_free = 0.4576 target = 0.187600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.153258 restraints weight = 34330.435| |-----------------------------------------------------------------------------| r_work (start): 0.4211 rms_B_bonded: 2.59 r_work: 0.3966 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.250 21027 Z= 0.244 Angle : 0.828 59.200 28454 Z= 0.449 Chirality : 0.049 0.655 3317 Planarity : 0.005 0.077 3643 Dihedral : 7.315 129.945 2908 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.77 % Favored : 96.19 % Rotamer: Outliers : 4.06 % Allowed : 21.77 % Favored : 74.17 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.17), residues: 2601 helix: 0.54 (0.15), residues: 1226 sheet: -0.64 (0.23), residues: 505 loop : -0.83 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 307 HIS 0.007 0.001 HIS E 37 PHE 0.081 0.003 PHE F 215 TYR 0.037 0.002 TYR F 114 ARG 0.015 0.001 ARG B 210 Details of bonding type rmsd hydrogen bonds : bond 0.03629 ( 1103) hydrogen bonds : angle 4.74966 ( 3177) covalent geometry : bond 0.00592 (21027) covalent geometry : angle 0.82846 (28454) ********************** 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 400 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 307 time to evaluate : 2.138 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 409 PHE cc_start: 0.8256 (t80) cc_final: 0.7625 (m-80) REVERT: A 531 MET cc_start: 0.6929 (tpp) cc_final: 0.6572 (tpp) REVERT: A 853 MET cc_start: 0.9283 (mmm) cc_final: 0.8989 (mmp) REVERT: B 102 MET cc_start: 0.7830 (tpp) cc_final: 0.7154 (tpt) REVERT: B 229 MET cc_start: 0.7093 (tpp) cc_final: 0.6823 (tpp) REVERT: C 106 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.6200 (tp) REVERT: D 54 PHE cc_start: 0.6019 (OUTLIER) cc_final: 0.5622 (t80) REVERT: D 109 ASN cc_start: 0.7829 (t0) cc_final: 0.7487 (t0) REVERT: D 246 GLN cc_start: 0.6745 (tp40) cc_final: 0.6389 (tp-100) REVERT: D 255 LYS cc_start: 0.8330 (tptt) cc_final: 0.8118 (tptt) REVERT: E 21 GLU cc_start: 0.8059 (pt0) cc_final: 0.7691 (pm20) REVERT: E 105 ARG cc_start: 0.7277 (ptp-170) cc_final: 0.6860 (ptp-170) REVERT: E 119 GLN cc_start: 0.6682 (OUTLIER) cc_final: 0.5798 (pm20) REVERT: F 1 MET cc_start: 0.6439 (ppp) cc_final: 0.5330 (ppp) REVERT: F 14 LYS cc_start: 0.9090 (mmtt) cc_final: 0.8843 (mtmt) REVERT: F 53 ARG cc_start: 0.8874 (ptp-110) cc_final: 0.8374 (mtm110) REVERT: F 91 ARG cc_start: 0.7062 (ptm-80) cc_final: 0.6679 (ptm-80) REVERT: F 99 LEU cc_start: 0.8189 (pp) cc_final: 0.7983 (pt) REVERT: F 144 PHE cc_start: 0.8853 (t80) cc_final: 0.8272 (t80) REVERT: F 153 HIS cc_start: 0.6590 (m-70) cc_final: 0.6361 (m-70) REVERT: F 248 LYS cc_start: 0.9176 (mtpt) cc_final: 0.8837 (pttm) REVERT: G 13 LYS cc_start: 0.8165 (ttmm) cc_final: 0.7735 (mttp) REVERT: G 87 ILE cc_start: 0.7482 (OUTLIER) cc_final: 0.6923 (pp) REVERT: G 125 GLN cc_start: 0.7179 (tm-30) cc_final: 0.6931 (tm-30) REVERT: G 139 MET cc_start: 0.6322 (ppp) cc_final: 0.5939 (ttp) REVERT: H 27 CYS cc_start: 0.8301 (t) cc_final: 0.8073 (p) outliers start: 93 outliers final: 84 residues processed: 368 average time/residue: 0.3531 time to fit residues: 192.7082 Evaluate side-chains 391 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 303 time to evaluate : 2.205 ------------------------------------------------------------------------------- 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 417 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 483 MET 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 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 109 ASN Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 203 MET 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 B residue 310 GLU Chi-restraints excluded: chain B residue 325 MET 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 105 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 157 TYR 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 94 GLU 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 212 LEU 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 D residue 357 GLN Chi-restraints excluded: chain E residue 72 GLN Chi-restraints excluded: chain E residue 93 LEU 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 134 LEU 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 303 CYS 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 68 MET 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 158 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 209 LEU 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 111 VAL Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 179 ASN 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 71 ASN Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 162 CYS 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 29 optimal weight: 0.0070 chunk 99 optimal weight: 2.9990 chunk 231 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 51 optimal weight: 0.0980 chunk 132 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 198 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 199 optimal weight: 3.9990 chunk 165 optimal weight: 0.6980 overall best weight: 0.4798 ------------------------------------------------------------------------------- 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 213 HIS ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.187713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.153363 restraints weight = 34468.603| |-----------------------------------------------------------------------------| r_work (start): 0.4213 rms_B_bonded: 2.69 r_work: 0.3959 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.250 21027 Z= 0.244 Angle : 0.828 59.200 28454 Z= 0.449 Chirality : 0.049 0.655 3317 Planarity : 0.005 0.077 3643 Dihedral : 7.315 129.945 2908 Min Nonbonded Distance : 1.508 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.77 % Favored : 96.19 % Rotamer: Outliers : 3.84 % Allowed : 21.95 % Favored : 74.21 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.17), residues: 2601 helix: 0.54 (0.15), residues: 1226 sheet: -0.64 (0.23), residues: 505 loop : -0.83 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 307 HIS 0.007 0.001 HIS E 37 PHE 0.081 0.003 PHE F 215 TYR 0.037 0.002 TYR F 114 ARG 0.015 0.001 ARG B 210 Details of bonding type rmsd hydrogen bonds : bond 0.03629 ( 1103) hydrogen bonds : angle 4.74966 ( 3177) covalent geometry : bond 0.00592 (21027) covalent geometry : angle 0.82846 (28454) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10461.96 seconds wall clock time: 181 minutes 59.47 seconds (10919.47 seconds total)