Starting phenix.real_space_refine on Wed Jun 18 00:58:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8umt_42383/06_2025/8umt_42383.cif Found real_map, /net/cci-nas-00/data/ceres_data/8umt_42383/06_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_42383/06_2025/8umt_42383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8umt_42383/06_2025/8umt_42383.map" model { file = "/net/cci-nas-00/data/ceres_data/8umt_42383/06_2025/8umt_42383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8umt_42383/06_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 12.62, per 1000 atoms: 0.61 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: 4.90 Conformation dependent library (CDL) restraints added in 2.7 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: 2.72 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: 7.43 Time building geometry restraints manager: 5.80 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: 1.960 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: 0.010 Extract box with map and model: 0.850 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 48.260 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.010 ------------------------------------------------------------------------------- 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 : 2.404 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: 0.3554 time to fit residues: 286.2655 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 : 2.665 ------------------------------------------------------------------------------- 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 = 34394.423| |-----------------------------------------------------------------------------| r_work (start): 0.4177 rms_B_bonded: 2.96 r_work: 0.3883 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 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 : 2.571 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: 0.7221 (OUTLIER) cc_final: 0.6726 (pm20) REVERT: A 843 LEU cc_start: 0.9304 (tp) cc_final: 0.9070 (tp) REVERT: D 117 GLN cc_start: 0.7766 (tp40) cc_final: 0.6882 (tp-100) REVERT: D 193 ARG cc_start: 0.7405 (mmm160) cc_final: 0.7182 (mmm-85) REVERT: E 119 GLN cc_start: 0.6592 (OUTLIER) cc_final: 0.5795 (pm20) REVERT: F 1 MET cc_start: 0.6281 (ppp) cc_final: 0.5045 (ppp) REVERT: F 14 LYS cc_start: 0.9283 (mmtt) cc_final: 0.8734 (mtpp) REVERT: F 60 TYR cc_start: 0.4201 (t80) cc_final: 0.3879 (t80) REVERT: F 99 LEU cc_start: 0.8383 (pp) cc_final: 0.8014 (tp) REVERT: F 148 CYS cc_start: 0.8983 (m) cc_final: 0.8740 (m) REVERT: G 87 ILE cc_start: 0.7565 (OUTLIER) cc_final: 0.7260 (pp) REVERT: G 125 GLN cc_start: 0.7108 (tm-30) cc_final: 0.6786 (tm-30) REVERT: G 146 ARG cc_start: 0.8432 (ttp-110) cc_final: 0.7867 (ptp90) REVERT: H 184 GLN cc_start: 0.6601 (tm-30) cc_final: 0.6358 (tm-30) outliers start: 108 outliers final: 72 residues processed: 429 average time/residue: 0.4048 time to fit residues: 262.0604 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 : 2.453 ------------------------------------------------------------------------------- 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: 0.9980 chunk 3 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 165 optimal weight: 0.7980 chunk 236 optimal weight: 6.9990 chunk 195 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 243 optimal weight: 10.0000 chunk 217 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 ASN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 GLN 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 Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.190317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.154618 restraints weight = 33952.437| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 2.61 r_work: 0.4001 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21027 Z= 0.130 Angle : 0.626 9.187 28454 Z= 0.316 Chirality : 0.043 0.223 3317 Planarity : 0.005 0.079 3643 Dihedral : 7.773 126.195 2918 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.45 % Allowed : 18.32 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.64 (0.16), residues: 2601 helix: 0.20 (0.15), residues: 1222 sheet: -0.63 (0.23), residues: 521 loop : -0.98 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 307 HIS 0.013 0.001 HIS F 153 PHE 0.018 0.002 PHE A 506 TYR 0.017 0.001 TYR B 279 ARG 0.009 0.001 ARG E 149 Details of bonding type rmsd hydrogen bonds : bond 0.03761 ( 1103) hydrogen bonds : angle 4.86812 ( 3177) covalent geometry : bond 0.00290 (21027) covalent geometry : angle 0.62636 (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 431 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 352 time to evaluate : 2.564 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 531 MET cc_start: 0.7080 (tpp) cc_final: 0.6695 (tpp) REVERT: A 843 LEU cc_start: 0.9288 (tp) cc_final: 0.9069 (tp) REVERT: D 117 GLN cc_start: 0.7969 (tp40) cc_final: 0.7718 (tp-100) REVERT: E 16 LEU cc_start: 0.7640 (mt) cc_final: 0.7170 (mt) REVERT: E 105 ARG cc_start: 0.7509 (ptp-170) cc_final: 0.6946 (ptp-170) REVERT: F 1 MET cc_start: 0.6069 (ppp) cc_final: 0.4956 (ppp) REVERT: F 14 LYS cc_start: 0.9212 (mmtt) cc_final: 0.8549 (mtpp) REVERT: F 53 ARG cc_start: 0.8621 (ptp-110) cc_final: 0.8405 (mtm110) REVERT: F 60 TYR cc_start: 0.3752 (t80) cc_final: 0.3449 (t80) REVERT: F 99 LEU cc_start: 0.8224 (pp) cc_final: 0.7990 (tp) REVERT: F 144 PHE cc_start: 0.8637 (t80) cc_final: 0.7883 (t80) REVERT: F 148 CYS cc_start: 0.8897 (m) cc_final: 0.8473 (m) REVERT: G 13 LYS cc_start: 0.8224 (ttmm) cc_final: 0.7731 (mttp) REVERT: G 87 ILE cc_start: 0.7355 (OUTLIER) cc_final: 0.6927 (pp) REVERT: G 146 ARG cc_start: 0.8324 (ttp-110) cc_final: 0.7821 (ptp90) REVERT: H 116 MET cc_start: 0.7270 (ttm) cc_final: 0.7069 (ttt) REVERT: H 119 MET cc_start: 0.6144 (mtp) cc_final: 0.5912 (mtp) outliers start: 79 outliers final: 48 residues processed: 403 average time/residue: 0.3970 time to fit residues: 239.4452 Evaluate side-chains 360 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 311 time to evaluate : 3.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 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 233 LEU 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 208 LEU 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 102 ASN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 155 TYR Chi-restraints excluded: chain E residue 171 VAL 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 10 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 211 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 137 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 22 GLN ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 HIS E 194 HIS E 213 HIS E 244 GLN ** H 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.185548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.151108 restraints weight = 34547.067| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 3.06 r_work: 0.3895 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 21027 Z= 0.242 Angle : 0.701 9.513 28454 Z= 0.358 Chirality : 0.045 0.181 3317 Planarity : 0.006 0.076 3643 Dihedral : 7.810 128.492 2914 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.49 % Allowed : 18.59 % Favored : 76.92 % 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: -0.79 (0.16), residues: 2601 helix: 0.05 (0.14), residues: 1229 sheet: -0.71 (0.22), residues: 529 loop : -1.02 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 307 HIS 0.010 0.001 HIS F 153 PHE 0.029 0.002 PHE E 339 TYR 0.017 0.002 TYR B 213 ARG 0.008 0.001 ARG C 168 Details of bonding type rmsd hydrogen bonds : bond 0.04206 ( 1103) hydrogen bonds : angle 5.03624 ( 3177) covalent geometry : bond 0.00574 (21027) covalent geometry : angle 0.70050 (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 425 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 322 time to evaluate : 2.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.7672 (m-80) REVERT: A 679 ASP cc_start: 0.8425 (t0) cc_final: 0.7607 (m-30) REVERT: A 853 MET cc_start: 0.9242 (mmm) cc_final: 0.8908 (mmp) REVERT: D 117 GLN cc_start: 0.7932 (tp40) cc_final: 0.7596 (tp-100) REVERT: E 105 ARG cc_start: 0.7533 (ptp-170) cc_final: 0.6989 (ptp-170) REVERT: E 119 GLN cc_start: 0.6742 (OUTLIER) cc_final: 0.5896 (pm20) REVERT: F 1 MET cc_start: 0.6306 (ppp) cc_final: 0.5193 (ppp) REVERT: F 14 LYS cc_start: 0.9186 (mmtt) cc_final: 0.8578 (mtpp) REVERT: F 40 MET cc_start: 0.5833 (tpt) cc_final: 0.5533 (tpt) REVERT: F 53 ARG cc_start: 0.8711 (ptp-110) cc_final: 0.8452 (mtm110) REVERT: F 60 TYR cc_start: 0.4120 (t80) cc_final: 0.3672 (t80) REVERT: F 99 LEU cc_start: 0.8315 (pp) cc_final: 0.8062 (tp) REVERT: F 112 SER cc_start: 0.8354 (m) cc_final: 0.8096 (m) REVERT: F 144 PHE cc_start: 0.8809 (t80) cc_final: 0.8519 (t80) REVERT: F 148 CYS cc_start: 0.8918 (m) cc_final: 0.8703 (m) REVERT: G 13 LYS cc_start: 0.8297 (ttmm) cc_final: 0.7794 (mttp) REVERT: G 87 ILE cc_start: 0.7573 (OUTLIER) cc_final: 0.7030 (pp) REVERT: G 125 GLN cc_start: 0.7047 (tm-30) cc_final: 0.6750 (tm-30) REVERT: H 119 MET cc_start: 0.6400 (mtp) cc_final: 0.6182 (mtp) outliers start: 103 outliers final: 78 residues processed: 397 average time/residue: 0.3999 time to fit residues: 241.3459 Evaluate side-chains 372 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 291 time to evaluate : 2.671 ------------------------------------------------------------------------------- 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 409 PHE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 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 156 ARG Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 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 148 ASN 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 C residue 332 THR 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 249 THR Chi-restraints excluded: chain D residue 261 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 302 ASN Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 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 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 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: 3.9990 chunk 86 optimal weight: 5.9990 chunk 212 optimal weight: 0.0980 chunk 111 optimal weight: 0.3980 chunk 137 optimal weight: 4.9990 chunk 252 optimal weight: 6.9990 chunk 194 optimal weight: 30.0000 chunk 114 optimal weight: 0.8980 chunk 233 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 ASN A 655 ASN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 HIS G 177 ASN ** H 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 HIS ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.185372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.149418 restraints weight = 34564.970| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 2.99 r_work: 0.3869 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 21027 Z= 0.167 Angle : 0.640 9.952 28454 Z= 0.324 Chirality : 0.043 0.175 3317 Planarity : 0.005 0.079 3643 Dihedral : 7.551 129.698 2910 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.80 % Allowed : 19.37 % Favored : 75.83 % 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: -0.52 (0.16), residues: 2601 helix: 0.34 (0.15), residues: 1227 sheet: -0.64 (0.22), residues: 523 loop : -0.95 (0.22), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 307 HIS 0.008 0.001 HIS F 153 PHE 0.029 0.002 PHE E 339 TYR 0.017 0.002 TYR B 213 ARG 0.009 0.001 ARG E 51 Details of bonding type rmsd hydrogen bonds : bond 0.03733 ( 1103) hydrogen bonds : angle 4.84637 ( 3177) covalent geometry : bond 0.00391 (21027) covalent geometry : angle 0.64031 (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 431 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 321 time to evaluate : 2.903 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: 0.7064 (OUTLIER) cc_final: 0.6601 (pm20) REVERT: A 409 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.7658 (m-80) REVERT: A 853 MET cc_start: 0.9252 (mmm) cc_final: 0.8933 (mmp) REVERT: B 176 LYS cc_start: 0.7445 (mtmt) cc_final: 0.7232 (mtmm) REVERT: B 210 ARG cc_start: 0.6964 (ttp80) cc_final: 0.6472 (ttp80) REVERT: C 69 THR cc_start: 0.6247 (OUTLIER) cc_final: 0.5910 (m) REVERT: D 117 GLN cc_start: 0.7955 (tp40) cc_final: 0.7663 (tp-100) REVERT: D 167 MET cc_start: 0.7078 (mmt) cc_final: 0.6657 (mmt) REVERT: D 240 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8361 (mtpp) REVERT: E 105 ARG cc_start: 0.7541 (ptp-170) cc_final: 0.6980 (ptp-170) REVERT: E 119 GLN cc_start: 0.6777 (OUTLIER) cc_final: 0.5933 (pm20) REVERT: F 1 MET cc_start: 0.6371 (ppp) cc_final: 0.5245 (ppp) REVERT: F 14 LYS cc_start: 0.9167 (mmtt) cc_final: 0.8910 (mttm) REVERT: F 53 ARG cc_start: 0.8774 (ptp-110) cc_final: 0.8506 (mtm110) REVERT: F 60 TYR cc_start: 0.4254 (t80) cc_final: 0.3608 (t80) REVERT: F 99 LEU cc_start: 0.8401 (pp) cc_final: 0.8133 (pt) REVERT: F 144 PHE cc_start: 0.8747 (t80) cc_final: 0.7995 (t80) REVERT: F 148 CYS cc_start: 0.8996 (m) cc_final: 0.8645 (m) REVERT: F 248 LYS cc_start: 0.9131 (mtpt) cc_final: 0.8572 (pttm) REVERT: G 13 LYS cc_start: 0.8279 (ttmm) cc_final: 0.7753 (mttp) REVERT: G 87 ILE cc_start: 0.7479 (OUTLIER) cc_final: 0.6946 (pp) REVERT: G 125 GLN cc_start: 0.7057 (tm-30) cc_final: 0.6771 (tm-30) outliers start: 110 outliers final: 82 residues processed: 397 average time/residue: 0.4682 time to fit residues: 284.5015 Evaluate side-chains 388 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 300 time to evaluate : 4.087 ------------------------------------------------------------------------------- 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 409 PHE Chi-restraints excluded: chain A residue 430 ASN 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 560 TYR Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 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 181 ILE 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 69 THR 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 157 TYR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 55 ILE 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 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 302 ASN Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 196 THR 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 6 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 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 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 Chi-restraints excluded: chain H residue 246 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 125 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 156 optimal weight: 10.0000 chunk 229 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 181 optimal weight: 0.8980 chunk 135 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 ASN ** 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 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 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 HIS E 213 HIS ** H 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.182423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.146859 restraints weight = 34866.094| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 3.52 r_work: 0.3782 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 21027 Z= 0.265 Angle : 0.731 12.147 28454 Z= 0.369 Chirality : 0.046 0.240 3317 Planarity : 0.006 0.078 3643 Dihedral : 7.759 130.859 2910 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 5.58 % Allowed : 19.55 % Favored : 74.87 % 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: -0.78 (0.16), residues: 2601 helix: 0.08 (0.14), residues: 1226 sheet: -0.68 (0.23), residues: 514 loop : -1.06 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 307 HIS 0.007 0.001 HIS C 289 PHE 0.037 0.002 PHE F 215 TYR 0.019 0.002 TYR E 318 ARG 0.008 0.001 ARG F 91 Details of bonding type rmsd hydrogen bonds : bond 0.04239 ( 1103) hydrogen bonds : angle 5.06761 ( 3177) covalent geometry : bond 0.00627 (21027) covalent geometry : angle 0.73071 (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 446 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 318 time to evaluate : 7.452 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: 0.7013 (OUTLIER) cc_final: 0.6552 (pm20) REVERT: A 409 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7691 (m-80) REVERT: A 853 MET cc_start: 0.9305 (mmm) cc_final: 0.8991 (mmp) REVERT: B 102 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7166 (tpp) REVERT: B 176 LYS cc_start: 0.7509 (mtmt) cc_final: 0.7284 (mtmm) REVERT: B 210 ARG cc_start: 0.7091 (ttp80) cc_final: 0.6621 (ttp80) REVERT: C 106 LEU cc_start: 0.6682 (OUTLIER) cc_final: 0.6352 (tp) REVERT: C 309 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6826 (tt0) REVERT: D 117 GLN cc_start: 0.8112 (tp40) cc_final: 0.7794 (tp-100) REVERT: D 240 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8497 (mtpp) REVERT: E 105 ARG cc_start: 0.7611 (ptp-170) cc_final: 0.7062 (ptp-170) REVERT: E 119 GLN cc_start: 0.6831 (OUTLIER) cc_final: 0.6014 (pm20) REVERT: E 194 HIS cc_start: 0.7327 (OUTLIER) cc_final: 0.7124 (t-90) REVERT: F 1 MET cc_start: 0.6555 (ppp) cc_final: 0.5417 (ppp) REVERT: F 14 LYS cc_start: 0.9162 (mmtt) cc_final: 0.8843 (mtmt) REVERT: F 53 ARG cc_start: 0.8814 (ptp-110) cc_final: 0.8536 (mtm110) REVERT: F 99 LEU cc_start: 0.8429 (pp) cc_final: 0.8179 (pt) REVERT: F 144 PHE cc_start: 0.8885 (t80) cc_final: 0.8520 (t80) REVERT: F 148 CYS cc_start: 0.9035 (m) cc_final: 0.8830 (m) REVERT: G 13 LYS cc_start: 0.8341 (ttmm) cc_final: 0.7806 (mttp) REVERT: G 87 ILE cc_start: 0.7570 (OUTLIER) cc_final: 0.7048 (pp) REVERT: G 125 GLN cc_start: 0.7133 (tm-30) cc_final: 0.6848 (tm-30) REVERT: G 139 MET cc_start: 0.6441 (ppp) cc_final: 0.6055 (ttp) REVERT: H 27 CYS cc_start: 0.8529 (t) cc_final: 0.8136 (p) outliers start: 128 outliers final: 101 residues processed: 408 average time/residue: 0.4905 time to fit residues: 305.0853 Evaluate side-chains 403 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 293 time to evaluate : 3.080 ------------------------------------------------------------------------------- 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 409 PHE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 560 TYR Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 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 821 VAL Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 175 ASP 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 30 THR 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 148 ASN Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 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 D residue 54 PHE 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 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 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 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 124 GLU 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 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 81 CYS 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 150 ASP 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 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 224 THR 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: 0.8980 chunk 210 optimal weight: 2.9990 chunk 156 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 123 optimal weight: 20.0000 chunk 225 optimal weight: 6.9990 chunk 237 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 38 optimal weight: 0.5980 chunk 150 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 ASN A 655 ASN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 37 HIS E 194 HIS E 213 HIS F 38 GLN F 65 ASN ** H 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.184950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.149053 restraints weight = 34602.545| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 3.26 r_work: 0.3850 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 21027 Z= 0.156 Angle : 0.649 12.036 28454 Z= 0.327 Chirality : 0.044 0.200 3317 Planarity : 0.005 0.081 3643 Dihedral : 7.533 130.802 2910 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.71 % Allowed : 20.68 % Favored : 74.61 % 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: -0.44 (0.17), residues: 2601 helix: 0.41 (0.15), residues: 1228 sheet: -0.62 (0.23), residues: 512 loop : -0.92 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 307 HIS 0.021 0.001 HIS E 194 PHE 0.056 0.002 PHE F 215 TYR 0.019 0.001 TYR F 249 ARG 0.008 0.000 ARG D 93 Details of bonding type rmsd hydrogen bonds : bond 0.03663 ( 1103) hydrogen bonds : angle 4.79911 ( 3177) covalent geometry : bond 0.00366 (21027) covalent geometry : angle 0.64908 (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 429 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 321 time to evaluate : 2.470 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: 0.8304 (t80) cc_final: 0.7715 (m-80) REVERT: A 655 ASN cc_start: 0.7261 (OUTLIER) cc_final: 0.6920 (m110) REVERT: A 853 MET cc_start: 0.9309 (mmm) cc_final: 0.9000 (mmp) REVERT: B 102 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.6786 (tpt) REVERT: B 176 LYS cc_start: 0.7441 (mtmt) cc_final: 0.7219 (mtmm) REVERT: B 210 ARG cc_start: 0.7104 (ttp80) cc_final: 0.6694 (ttp80) REVERT: B 229 MET cc_start: 0.7084 (tpp) cc_final: 0.6706 (tpp) REVERT: C 69 THR cc_start: 0.6574 (OUTLIER) cc_final: 0.6253 (m) REVERT: D 54 PHE cc_start: 0.6198 (OUTLIER) cc_final: 0.5819 (t80) REVERT: D 109 ASN cc_start: 0.7622 (t0) cc_final: 0.7285 (t0) REVERT: D 240 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8399 (mtpp) REVERT: D 246 GLN cc_start: 0.6921 (tp40) cc_final: 0.6574 (tp-100) REVERT: E 105 ARG cc_start: 0.7519 (ptp-170) cc_final: 0.6977 (ptp-170) REVERT: E 119 GLN cc_start: 0.6802 (OUTLIER) cc_final: 0.5985 (pm20) REVERT: F 1 MET cc_start: 0.6556 (ppp) cc_final: 0.5446 (ppp) REVERT: F 14 LYS cc_start: 0.9134 (mmtt) cc_final: 0.8830 (mtmt) REVERT: F 53 ARG cc_start: 0.8776 (ptp-110) cc_final: 0.8506 (mtm110) REVERT: F 99 LEU cc_start: 0.8404 (pp) cc_final: 0.8135 (pt) REVERT: F 139 MET cc_start: 0.3061 (OUTLIER) cc_final: 0.2589 (ppp) REVERT: F 144 PHE cc_start: 0.8869 (t80) cc_final: 0.8077 (t80) REVERT: F 148 CYS cc_start: 0.9004 (m) cc_final: 0.8661 (m) REVERT: G 13 LYS cc_start: 0.8266 (ttmm) cc_final: 0.7765 (mttp) REVERT: G 87 ILE cc_start: 0.7496 (OUTLIER) cc_final: 0.6954 (pp) REVERT: G 125 GLN cc_start: 0.7147 (tm-30) cc_final: 0.6859 (tm-30) REVERT: H 27 CYS cc_start: 0.8357 (t) cc_final: 0.8026 (p) REVERT: H 117 LYS cc_start: 0.7787 (ptmm) cc_final: 0.7270 (mttt) REVERT: H 131 GLN cc_start: 0.6694 (tm130) cc_final: 0.6411 (tm-30) outliers start: 108 outliers final: 80 residues processed: 399 average time/residue: 0.4457 time to fit residues: 269.6286 Evaluate side-chains 384 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 296 time to evaluate : 3.084 ------------------------------------------------------------------------------- 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 448 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 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 801 LEU Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 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 113 THR 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 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 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 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 155 TYR 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 302 ASN Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 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 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 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 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 150 ASP 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 H residue 71 ASN Chi-restraints excluded: chain H residue 123 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: 0.0770 chunk 93 optimal weight: 5.9990 chunk 220 optimal weight: 20.0000 chunk 252 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 131 optimal weight: 0.4980 chunk 165 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 203 optimal weight: 4.9990 chunk 256 optimal weight: 0.0980 chunk 5 optimal weight: 10.0000 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN 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** D 117 GLN D 125 ASN E 194 HIS E 213 HIS H 36 ASN ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 184 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.188941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.154404 restraints weight = 34430.577| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 2.55 r_work: 0.3994 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21027 Z= 0.134 Angle : 0.654 12.303 28454 Z= 0.327 Chirality : 0.043 0.325 3317 Planarity : 0.005 0.078 3643 Dihedral : 7.256 129.545 2910 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.23 % Allowed : 21.34 % Favored : 74.43 % 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: -0.23 (0.17), residues: 2601 helix: 0.59 (0.15), residues: 1227 sheet: -0.56 (0.23), residues: 503 loop : -0.79 (0.22), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 307 HIS 0.012 0.001 HIS E 194 PHE 0.038 0.002 PHE E 339 TYR 0.018 0.001 TYR F 249 ARG 0.008 0.000 ARG C 52 Details of bonding type rmsd hydrogen bonds : bond 0.03463 ( 1103) hydrogen bonds : angle 4.69279 ( 3177) covalent geometry : bond 0.00314 (21027) covalent geometry : angle 0.65433 (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 423 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 326 time to evaluate : 2.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6440 (pm20) REVERT: A 409 PHE cc_start: 0.8240 (t80) cc_final: 0.7650 (m-80) REVERT: A 655 ASN cc_start: 0.7295 (OUTLIER) cc_final: 0.6880 (m110) REVERT: A 853 MET cc_start: 0.9290 (mmm) cc_final: 0.8989 (mmp) REVERT: B 102 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.6828 (tpt) REVERT: B 210 ARG cc_start: 0.7010 (ttp80) cc_final: 0.6686 (ttp80) REVERT: D 54 PHE cc_start: 0.6030 (OUTLIER) cc_final: 0.5683 (t80) REVERT: D 109 ASN cc_start: 0.7751 (t0) cc_final: 0.7424 (t0) REVERT: D 246 GLN cc_start: 0.6797 (tp40) cc_final: 0.6480 (tp-100) REVERT: E 105 ARG cc_start: 0.7320 (ptp-170) cc_final: 0.6854 (ptp-170) REVERT: E 119 GLN cc_start: 0.6689 (OUTLIER) cc_final: 0.5843 (pm20) REVERT: F 1 MET cc_start: 0.6412 (ppp) cc_final: 0.5228 (ppp) REVERT: F 14 LYS cc_start: 0.9120 (mmtt) cc_final: 0.8833 (mtmt) REVERT: F 99 LEU cc_start: 0.8292 (pp) cc_final: 0.8016 (pt) REVERT: F 144 PHE cc_start: 0.8855 (t80) cc_final: 0.8145 (t80) REVERT: F 148 CYS cc_start: 0.8974 (m) cc_final: 0.8624 (m) REVERT: G 13 LYS cc_start: 0.8188 (ttmm) cc_final: 0.7718 (mttp) REVERT: G 87 ILE cc_start: 0.7378 (OUTLIER) cc_final: 0.6822 (pp) REVERT: G 125 GLN cc_start: 0.7187 (tm-30) cc_final: 0.6908 (tm-30) REVERT: G 139 MET cc_start: 0.6354 (ppp) cc_final: 0.6009 (ttp) REVERT: H 27 CYS cc_start: 0.8153 (t) cc_final: 0.7837 (p) REVERT: H 117 LYS cc_start: 0.7743 (ptmm) cc_final: 0.7295 (mttt) REVERT: H 131 GLN cc_start: 0.6834 (tm130) cc_final: 0.6508 (tm-30) outliers start: 97 outliers final: 72 residues processed: 391 average time/residue: 0.3771 time to fit residues: 220.4610 Evaluate side-chains 377 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 299 time to evaluate : 2.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 114 ASP 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 246 ILE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 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 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 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 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 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 150 ASP 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 H residue 36 ASN Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 235 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 76 optimal weight: 0.9990 chunk 230 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 171 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 chunk 245 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 56 optimal weight: 0.0970 chunk 160 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 ASN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 213 HIS H 36 ASN ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.187441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.152634 restraints weight = 34346.760| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 2.56 r_work: 0.3961 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 21027 Z= 0.178 Angle : 0.681 10.927 28454 Z= 0.342 Chirality : 0.045 0.370 3317 Planarity : 0.005 0.074 3643 Dihedral : 7.287 128.948 2909 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.97 % Allowed : 22.21 % Favored : 73.82 % 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: -0.33 (0.17), residues: 2601 helix: 0.48 (0.15), residues: 1234 sheet: -0.56 (0.23), residues: 491 loop : -0.84 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 307 HIS 0.006 0.001 HIS F 153 PHE 0.050 0.002 PHE F 215 TYR 0.017 0.001 TYR F 249 ARG 0.008 0.000 ARG C 52 Details of bonding type rmsd hydrogen bonds : bond 0.03682 ( 1103) hydrogen bonds : angle 4.78925 ( 3177) covalent geometry : bond 0.00425 (21027) covalent geometry : angle 0.68076 (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 405 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 314 time to evaluate : 3.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6515 (pm20) REVERT: A 409 PHE cc_start: 0.8263 (t80) cc_final: 0.7700 (m-80) REVERT: A 655 ASN cc_start: 0.7387 (OUTLIER) cc_final: 0.7073 (m110) REVERT: A 853 MET cc_start: 0.9308 (mmm) cc_final: 0.9018 (mmp) REVERT: B 102 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.6772 (tpt) REVERT: B 193 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7566 (mm) REVERT: B 229 MET cc_start: 0.7198 (tpp) cc_final: 0.6879 (tpp) REVERT: C 69 THR cc_start: 0.6546 (OUTLIER) cc_final: 0.6195 (m) REVERT: D 54 PHE cc_start: 0.6054 (OUTLIER) cc_final: 0.5658 (t80) REVERT: D 109 ASN cc_start: 0.7850 (t0) cc_final: 0.7516 (t0) REVERT: D 246 GLN cc_start: 0.6734 (tp40) cc_final: 0.6442 (tp-100) REVERT: D 255 LYS cc_start: 0.8348 (tptt) cc_final: 0.8140 (tptt) REVERT: E 105 ARG cc_start: 0.7274 (ptp-170) cc_final: 0.6848 (ptp-170) REVERT: E 119 GLN cc_start: 0.6657 (OUTLIER) cc_final: 0.5777 (pm20) REVERT: E 121 LEU cc_start: 0.5524 (OUTLIER) cc_final: 0.5123 (tt) REVERT: F 1 MET cc_start: 0.6345 (ppp) cc_final: 0.5249 (ppp) REVERT: F 14 LYS cc_start: 0.9109 (mmtt) cc_final: 0.8855 (mtmt) REVERT: F 91 ARG cc_start: 0.6926 (ptm-80) cc_final: 0.6544 (ptm-80) REVERT: F 139 MET cc_start: 0.2947 (OUTLIER) cc_final: 0.2508 (ppp) REVERT: F 144 PHE cc_start: 0.8859 (t80) cc_final: 0.8062 (t80) REVERT: F 148 CYS cc_start: 0.8883 (m) cc_final: 0.8544 (m) REVERT: F 248 LYS cc_start: 0.9151 (mtpt) cc_final: 0.8820 (pttm) REVERT: G 13 LYS cc_start: 0.8177 (ttmm) cc_final: 0.7745 (mttp) REVERT: G 87 ILE cc_start: 0.7423 (OUTLIER) cc_final: 0.6868 (pp) REVERT: G 125 GLN cc_start: 0.7138 (tm-30) cc_final: 0.6879 (tm-30) REVERT: G 139 MET cc_start: 0.6276 (ppp) cc_final: 0.5905 (ttp) REVERT: H 27 CYS cc_start: 0.8229 (t) cc_final: 0.7973 (p) REVERT: H 117 LYS cc_start: 0.7823 (ptmm) cc_final: 0.7403 (mttt) outliers start: 91 outliers final: 75 residues processed: 376 average time/residue: 0.4996 time to fit residues: 282.6226 Evaluate side-chains 389 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 304 time to evaluate : 2.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 655 ASN 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 B residue 48 ASN Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 114 ASP 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 246 ILE 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 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 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 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 121 LEU Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 137 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 271 LEU 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 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 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 150 ASP 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 36 ASN Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 162 CYS 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: 0.5980 chunk 34 optimal weight: 0.8980 chunk 220 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 235 optimal weight: 6.9990 chunk 174 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 161 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 232 optimal weight: 9.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 ASN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 213 HIS F 38 GLN H 36 ASN ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.186649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.150646 restraints weight = 34227.561| |-----------------------------------------------------------------------------| r_work (start): 0.4177 rms_B_bonded: 2.80 r_work: 0.3926 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 21027 Z= 0.194 Angle : 0.701 10.282 28454 Z= 0.354 Chirality : 0.045 0.373 3317 Planarity : 0.005 0.077 3643 Dihedral : 7.386 129.437 2908 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.10 % Allowed : 22.08 % Favored : 73.82 % 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: -0.44 (0.17), residues: 2601 helix: 0.41 (0.15), residues: 1230 sheet: -0.65 (0.23), residues: 503 loop : -0.88 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 28 HIS 0.006 0.001 HIS F 153 PHE 0.043 0.002 PHE F 215 TYR 0.015 0.002 TYR F 249 ARG 0.017 0.001 ARG B 210 Details of bonding type rmsd hydrogen bonds : bond 0.03796 ( 1103) hydrogen bonds : angle 4.83964 ( 3177) covalent geometry : bond 0.00462 (21027) covalent geometry : angle 0.70144 (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 405 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 311 time to evaluate : 2.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6459 (pm20) REVERT: A 409 PHE cc_start: 0.8301 (t80) cc_final: 0.7702 (m-80) REVERT: A 655 ASN cc_start: 0.7314 (OUTLIER) cc_final: 0.6966 (m110) REVERT: A 853 MET cc_start: 0.9316 (mmm) cc_final: 0.9022 (mmp) REVERT: B 102 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.6874 (tpt) REVERT: B 193 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7573 (mm) REVERT: B 229 MET cc_start: 0.7172 (tpp) cc_final: 0.6801 (tpp) REVERT: C 309 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6760 (tt0) REVERT: D 54 PHE cc_start: 0.6116 (OUTLIER) cc_final: 0.5727 (t80) REVERT: D 109 ASN cc_start: 0.7822 (t0) cc_final: 0.7470 (t0) REVERT: D 246 GLN cc_start: 0.6874 (tp40) cc_final: 0.6498 (tp-100) REVERT: D 255 LYS cc_start: 0.8399 (tptt) cc_final: 0.8162 (tptt) REVERT: E 105 ARG cc_start: 0.7373 (ptp-170) cc_final: 0.6923 (ptp-170) REVERT: E 119 GLN cc_start: 0.6730 (OUTLIER) cc_final: 0.5855 (pm20) REVERT: E 121 LEU cc_start: 0.5664 (OUTLIER) cc_final: 0.5183 (tt) REVERT: F 1 MET cc_start: 0.6576 (ppp) cc_final: 0.5426 (ppp) REVERT: F 14 LYS cc_start: 0.9126 (mmtt) cc_final: 0.8862 (mtmt) REVERT: F 53 ARG cc_start: 0.8958 (ptp-110) cc_final: 0.8620 (mtm110) REVERT: F 139 MET cc_start: 0.2912 (OUTLIER) cc_final: 0.2482 (ppp) REVERT: F 144 PHE cc_start: 0.8921 (t80) cc_final: 0.8480 (t80) REVERT: F 148 CYS cc_start: 0.8988 (m) cc_final: 0.8779 (m) REVERT: G 13 LYS cc_start: 0.8189 (ttmm) cc_final: 0.7736 (mttp) REVERT: G 87 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.6924 (pp) REVERT: G 125 GLN cc_start: 0.7156 (tm-30) cc_final: 0.6884 (tm-30) REVERT: G 139 MET cc_start: 0.6416 (ppp) cc_final: 0.6075 (ttp) REVERT: H 27 CYS cc_start: 0.8325 (t) cc_final: 0.8050 (p) REVERT: H 117 LYS cc_start: 0.8024 (ptmm) cc_final: 0.7474 (mttt) outliers start: 94 outliers final: 80 residues processed: 376 average time/residue: 0.3535 time to fit residues: 198.8952 Evaluate side-chains 390 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 300 time to evaluate : 2.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 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 B residue 48 ASN Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 114 ASP 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 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 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 C residue 309 GLU Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 177 CYS Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 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 121 LEU Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 137 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 271 LEU 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 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 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 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 128 ILE Chi-restraints excluded: chain G residue 150 ASP 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 36 ASN Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 162 CYS 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 29 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 231 optimal weight: 0.4980 chunk 100 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 198 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 199 optimal weight: 10.0000 chunk 165 optimal weight: 2.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 ASN ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 213 HIS F 38 GLN ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.187485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.152458 restraints weight = 34361.129| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 2.72 r_work: 0.3947 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 21027 Z= 0.164 Angle : 0.689 12.807 28454 Z= 0.344 Chirality : 0.044 0.370 3317 Planarity : 0.005 0.075 3643 Dihedral : 7.373 129.436 2908 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.14 % Allowed : 22.16 % Favored : 73.69 % 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: -0.36 (0.17), residues: 2601 helix: 0.48 (0.15), residues: 1229 sheet: -0.69 (0.23), residues: 496 loop : -0.80 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 28 HIS 0.006 0.001 HIS F 153 PHE 0.042 0.002 PHE E 339 TYR 0.025 0.001 TYR F 249 ARG 0.016 0.001 ARG B 210 Details of bonding type rmsd hydrogen bonds : bond 0.03637 ( 1103) hydrogen bonds : angle 4.78421 ( 3177) covalent geometry : bond 0.00390 (21027) covalent geometry : angle 0.68913 (28454) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12120.52 seconds wall clock time: 221 minutes 12.74 seconds (13272.74 seconds total)