Starting phenix.real_space_refine on Sat Aug 23 23:49:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lsh_63355/08_2025/9lsh_63355.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lsh_63355/08_2025/9lsh_63355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lsh_63355/08_2025/9lsh_63355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lsh_63355/08_2025/9lsh_63355.map" model { file = "/net/cci-nas-00/data/ceres_data/9lsh_63355/08_2025/9lsh_63355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lsh_63355/08_2025/9lsh_63355.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 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: 4 Type Number sf(0) Gaussians S 74 5.16 5 C 9916 2.51 5 N 2503 2.21 5 O 2850 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15343 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3194 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 12, 'TRANS': 418} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 3201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3201 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 418} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 5308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5308 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 26, 'TRANS': 638} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "D" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1697 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain breaks: 1 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: "E" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1744 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'CIT': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 3.36, per 1000 atoms: 0.22 Number of scatterers: 15343 At special positions: 0 Unit cell: (107.8, 122.1, 189.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 74 16.00 O 2850 8.00 N 2503 7.00 C 9916 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 122 " distance=2.03 Simple disulfide: pdb=" SG CYS C 649 " - pdb=" SG CYS C 677 " distance=2.02 Simple disulfide: pdb=" SG CYS E 295 " - pdb=" SG CYS E 369 " distance=2.04 Simple disulfide: pdb=" SG CYS E 422 " - pdb=" SG CYS E 488 " distance=2.04 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 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " NAG G 3 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG C1001 " - " ASN C 52 " " NAG C1002 " - " ASN C 124 " " NAG C1003 " - " ASN C 275 " " NAG C1004 " - " ASN C 398 " " NAG C1005 " - " ASN C 507 " " NAG F 1 " - " ASN C 291 " " NAG G 1 " - " ASN C 413 " " NAG H 1 " - " ASN C 252 " Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 463.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3630 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 22 sheets defined 39.6% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 28 through 45 removed outlier: 3.720A pdb=" N ALA A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 70 removed outlier: 4.667A pdb=" N ALA A 56 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS A 70 " --> pdb=" O GLY A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 97 removed outlier: 3.529A pdb=" N VAL A 84 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE A 87 " --> pdb=" O PRO A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 112 removed outlier: 3.903A pdb=" N ILE A 104 " --> pdb=" O THR A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 130 Processing helix chain 'A' and resid 131 through 132 No H-bonds generated for 'chain 'A' and resid 131 through 132' Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 136 through 142 removed outlier: 4.024A pdb=" N SER A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 167 removed outlier: 3.974A pdb=" N THR A 147 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 177 Processing helix chain 'A' and resid 177 through 183 Processing helix chain 'A' and resid 190 through 202 Processing helix chain 'A' and resid 205 through 237 removed outlier: 3.990A pdb=" N ALA A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR A 217 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE A 222 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 289 removed outlier: 3.542A pdb=" N GLY A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 315 removed outlier: 3.863A pdb=" N TRP A 303 " --> pdb=" O HIS A 299 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET A 304 " --> pdb=" O TYR A 300 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A 305 " --> pdb=" O PHE A 301 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 335 removed outlier: 3.828A pdb=" N LYS A 322 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 348 removed outlier: 3.888A pdb=" N VAL A 342 " --> pdb=" O TRP A 338 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 357 removed outlier: 3.839A pdb=" N ILE A 354 " --> pdb=" O ASP A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 385 Processing helix chain 'A' and resid 387 through 394 Processing helix chain 'A' and resid 402 through 414 Processing helix chain 'A' and resid 419 through 446 removed outlier: 3.928A pdb=" N GLY A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 45 removed outlier: 3.526A pdb=" N THR B 37 " --> pdb=" O PHE B 33 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 71 removed outlier: 3.535A pdb=" N ILE B 57 " --> pdb=" O GLY B 53 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE B 61 " --> pdb=" O ILE B 57 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE B 68 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY B 69 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.672A pdb=" N TYR B 78 " --> pdb=" O ILE B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 97 removed outlier: 3.859A pdb=" N MET B 85 " --> pdb=" O GLY B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 113 removed outlier: 3.970A pdb=" N VAL B 110 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N MET B 111 " --> pdb=" O ILE B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 131 removed outlier: 3.696A pdb=" N LEU B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER B 131 " --> pdb=" O GLY B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 141 Processing helix chain 'B' and resid 143 through 166 removed outlier: 3.864A pdb=" N THR B 147 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE B 148 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B 158 " --> pdb=" O GLY B 154 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 177 Processing helix chain 'B' and resid 177 through 182 removed outlier: 3.844A pdb=" N ILE B 181 " --> pdb=" O TYR B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 201 Processing helix chain 'B' and resid 205 through 237 removed outlier: 3.984A pdb=" N ALA B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE B 215 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALA B 228 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 241 Processing helix chain 'B' and resid 264 through 288 removed outlier: 3.982A pdb=" N GLY B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU B 272 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 273 " --> pdb=" O ALA B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 315 removed outlier: 3.523A pdb=" N TRP B 303 " --> pdb=" O HIS B 299 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 333 removed outlier: 3.570A pdb=" N ALA B 323 " --> pdb=" O PRO B 319 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS B 326 " --> pdb=" O LYS B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 349 removed outlier: 3.613A pdb=" N VAL B 342 " --> pdb=" O TRP B 338 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY B 343 " --> pdb=" O VAL B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 357 removed outlier: 3.669A pdb=" N ILE B 354 " --> pdb=" O ASP B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 384 removed outlier: 4.106A pdb=" N ALA B 366 " --> pdb=" O ASN B 362 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 367 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 371 " --> pdb=" O ALA B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 394 Processing helix chain 'B' and resid 406 through 414 removed outlier: 3.539A pdb=" N LEU B 411 " --> pdb=" O ASP B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 446 removed outlier: 4.337A pdb=" N GLY B 432 " --> pdb=" O ARG B 428 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU B 435 " --> pdb=" O GLY B 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 73 removed outlier: 3.633A pdb=" N PHE C 71 " --> pdb=" O PRO C 67 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 98 removed outlier: 4.027A pdb=" N GLN C 96 " --> pdb=" O PRO C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 removed outlier: 3.886A pdb=" N ASP C 192 " --> pdb=" O GLU C 189 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE C 193 " --> pdb=" O GLU C 190 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE C 194 " --> pdb=" O LEU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 219 removed outlier: 3.807A pdb=" N ALA C 219 " --> pdb=" O CYS C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 245 removed outlier: 3.955A pdb=" N LEU C 237 " --> pdb=" O LEU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 274 removed outlier: 5.409A pdb=" N GLY C 270 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU C 271 " --> pdb=" O PHE C 268 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TRP C 273 " --> pdb=" O GLY C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 319 removed outlier: 4.120A pdb=" N LEU C 318 " --> pdb=" O SER C 315 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS C 319 " --> pdb=" O HIS C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 405 Processing helix chain 'C' and resid 449 through 453 removed outlier: 3.541A pdb=" N TRP C 452 " --> pdb=" O GLY C 449 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG C 453 " --> pdb=" O GLN C 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 449 through 453' Processing helix chain 'C' and resid 522 through 526 removed outlier: 4.135A pdb=" N MET C 525 " --> pdb=" O ASN C 522 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 526 " --> pdb=" O ASP C 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 522 through 526' Processing helix chain 'C' and resid 543 through 547 removed outlier: 3.643A pdb=" N TRP C 546 " --> pdb=" O ALA C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 664 removed outlier: 4.303A pdb=" N PHE C 657 " --> pdb=" O SER C 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 56 removed outlier: 3.919A pdb=" N SER D 56 " --> pdb=" O TYR D 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 53 through 56' Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'E' and resid 428 through 432 removed outlier: 3.961A pdb=" N ASN E 431 " --> pdb=" O VAL E 428 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 23 Processing sheet with id=AA2, first strand: chain 'A' and resid 292 through 293 Processing sheet with id=AA3, first strand: chain 'B' and resid 22 through 23 Processing sheet with id=AA4, first strand: chain 'C' and resid 55 through 57 removed outlier: 6.713A pdb=" N LEU C 80 " --> pdb=" O ASN C 105 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N GLN C 107 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL C 82 " --> pdb=" O GLN C 107 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU C 104 " --> pdb=" O HIS C 129 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N MET C 131 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU C 106 " --> pdb=" O MET C 131 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU C 128 " --> pdb=" O ASP C 153 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N SER C 155 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU C 130 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU C 176 " --> pdb=" O GLU C 203 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C 202 " --> pdb=" O GLY C 225 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE C 227 " --> pdb=" O LEU C 202 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER C 254 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 185 through 186 Processing sheet with id=AA6, first strand: chain 'C' and resid 262 through 263 Processing sheet with id=AA7, first strand: chain 'C' and resid 278 through 280 removed outlier: 7.128A pdb=" N LEU C 279 " --> pdb=" O PHE C 304 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN C 328 " --> pdb=" O PHE C 303 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 412 " --> pdb=" O VAL C 435 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP C 437 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE C 461 " --> pdb=" O MET C 486 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 485 " --> pdb=" O ILE C 510 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP C 512 " --> pdb=" O LEU C 485 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 312 through 313 removed outlier: 3.543A pdb=" N LEU C 313 " --> pdb=" O LYS C 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 395 through 396 Processing sheet with id=AB1, first strand: chain 'C' and resid 444 through 446 removed outlier: 7.039A pdb=" N GLN C 445 " --> pdb=" O GLN C 470 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU C 469 " --> pdb=" O LYS C 493 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 614 through 616 Processing sheet with id=AB3, first strand: chain 'C' and resid 676 through 677 Processing sheet with id=AB4, first strand: chain 'D' and resid 3 through 4 Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.017A pdb=" N GLY D 10 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ALA D 33 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET D 34 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 128 through 129 removed outlier: 3.977A pdb=" N VAL D 143 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE D 199 " --> pdb=" O VAL D 143 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE D 195 " --> pdb=" O CYS D 147 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 171 through 173 removed outlier: 5.917A pdb=" N LEU D 171 " --> pdb=" O GLN D 161 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N GLN D 161 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR D 173 " --> pdb=" O TRP D 159 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 276 through 278 removed outlier: 3.659A pdb=" N THR E 351 " --> pdb=" O ASP E 346 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 283 through 285 removed outlier: 3.522A pdb=" N LYS E 285 " --> pdb=" O THR E 391 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL E 390 " --> pdb=" O ALA E 365 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL E 307 " --> pdb=" O PHE E 323 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE E 323 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TRP E 309 " --> pdb=" O MET E 321 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 283 through 285 removed outlier: 3.522A pdb=" N LYS E 285 " --> pdb=" O THR E 391 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL E 390 " --> pdb=" O ALA E 365 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER E 383 " --> pdb=" O ARG E 371 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 403 through 404 removed outlier: 3.501A pdb=" N THR E 472 " --> pdb=" O SER E 465 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER E 465 " --> pdb=" O THR E 472 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 409 through 411 removed outlier: 6.099A pdb=" N LEU E 410 " --> pdb=" O GLU E 505 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL E 485 " --> pdb=" O GLN E 438 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N TRP E 435 " --> pdb=" O LEU E 447 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 489 through 490 removed outlier: 3.746A pdb=" N THR E 497 " --> pdb=" O GLN E 490 " (cutoff:3.500A) 608 hydrogen bonds defined for protein. 1716 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: 2.75 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4396 1.33 - 1.46: 2734 1.46 - 1.58: 8408 1.58 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 15658 Sorted by residual: bond pdb=" N VAL B 254 " pdb=" CA VAL B 254 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 9.85e+00 bond pdb=" N ILE B 389 " pdb=" CA ILE B 389 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.17e-02 7.31e+03 9.31e+00 bond pdb=" N ILE A 263 " pdb=" CA ILE A 263 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.08e-02 8.57e+03 9.24e+00 bond pdb=" N VAL B 296 " pdb=" CA VAL B 296 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.17e-02 7.31e+03 9.22e+00 bond pdb=" N PHE C 686 " pdb=" CA PHE C 686 " ideal model delta sigma weight residual 1.453 1.488 -0.036 1.18e-02 7.18e+03 9.20e+00 ... (remaining 15653 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 20856 2.69 - 5.39: 390 5.39 - 8.08: 10 8.08 - 10.77: 2 10.77 - 13.46: 1 Bond angle restraints: 21259 Sorted by residual: angle pdb=" C LYS E 285 " pdb=" N LYS E 286 " pdb=" CA LYS E 286 " ideal model delta sigma weight residual 120.69 134.15 -13.46 2.95e+00 1.15e-01 2.08e+01 angle pdb=" C TYR B 144 " pdb=" N ILE B 145 " pdb=" CA ILE B 145 " ideal model delta sigma weight residual 120.33 123.91 -3.58 8.00e-01 1.56e+00 2.00e+01 angle pdb=" N ASN C 678 " pdb=" CA ASN C 678 " pdb=" C ASN C 678 " ideal model delta sigma weight residual 114.31 108.74 5.57 1.29e+00 6.01e-01 1.87e+01 angle pdb=" CA GLN D 224 " pdb=" C GLN D 224 " pdb=" O GLN D 224 " ideal model delta sigma weight residual 122.01 118.15 3.86 1.05e+00 9.07e-01 1.35e+01 angle pdb=" N THR B 238 " pdb=" CA THR B 238 " pdb=" C THR B 238 " ideal model delta sigma weight residual 111.82 107.56 4.26 1.16e+00 7.43e-01 1.35e+01 ... (remaining 21254 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.09: 8987 24.09 - 48.18: 354 48.18 - 72.27: 30 72.27 - 96.36: 8 96.36 - 120.45: 1 Dihedral angle restraints: 9380 sinusoidal: 3708 harmonic: 5672 Sorted by residual: dihedral pdb=" CA GLU C 363 " pdb=" C GLU C 363 " pdb=" N ASP C 364 " pdb=" CA ASP C 364 " ideal model delta harmonic sigma weight residual 180.00 158.62 21.38 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" C2 NAG C1003 " pdb=" C1 NAG C1003 " pdb=" O5 NAG C1003 " pdb=" C5 NAG C1003 " ideal model delta sinusoidal sigma weight residual -62.96 57.49 -120.45 1 3.00e+01 1.11e-03 1.61e+01 dihedral pdb=" CA ASP C 523 " pdb=" C ASP C 523 " pdb=" N ASP C 524 " pdb=" CA ASP C 524 " ideal model delta harmonic sigma weight residual -180.00 -160.15 -19.85 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 9377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 2426 0.131 - 0.263: 92 0.263 - 0.394: 3 0.394 - 0.525: 0 0.525 - 0.657: 2 Chirality restraints: 2523 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.21e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.06e+01 chirality pdb=" C1 NAG G 3 " pdb=" O4 NAG G 2 " pdb=" C2 NAG G 3 " pdb=" O5 NAG G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.50e+01 ... (remaining 2520 not shown) Planarity restraints: 2658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " 0.074 2.00e-02 2.50e+03 6.07e-02 4.60e+01 pdb=" C7 NAG G 1 " -0.021 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " 0.056 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " -0.096 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " -0.038 2.00e-02 2.50e+03 3.15e-02 1.24e+01 pdb=" C7 NAG H 1 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " -0.030 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " 0.049 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.021 2.00e-02 2.50e+03 1.73e-02 3.74e+00 pdb=" C7 NAG F 2 " 0.005 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " -0.016 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.028 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " 0.004 2.00e-02 2.50e+03 ... (remaining 2655 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2684 2.77 - 3.30: 15783 3.30 - 3.83: 25054 3.83 - 4.37: 29052 4.37 - 4.90: 48266 Nonbonded interactions: 120839 Sorted by model distance: nonbonded pdb=" O TYR B 144 " pdb=" OG1 THR B 147 " model vdw 2.234 3.040 nonbonded pdb=" OG SER E 301 " pdb=" OG1 THR E 303 " model vdw 2.241 3.040 nonbonded pdb=" O GLN C 609 " pdb=" NH2 ARG C 635 " model vdw 2.250 3.120 nonbonded pdb=" N THR A 100 " pdb=" OE2 GLU A 103 " model vdw 2.258 3.120 nonbonded pdb=" O LEU C 178 " pdb=" ND2 ASN C 207 " model vdw 2.275 3.120 ... (remaining 120834 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 16 through 250 or (resid 251 through 259 and (name N or na \ me CA or name C or name O or name CB )) or resid 260 through 446)) selection = (chain 'B' and (resid 16 through 248 or (resid 249 through 259 and (name N or na \ me CA or name C or name O or name CB )) or resid 260 through 446)) } ncs_group { reference = chain 'F' selection = chain 'H' } 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 group one per residue 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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.560 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 15674 Z= 0.419 Angle : 0.892 14.447 21303 Z= 0.574 Chirality : 0.061 0.657 2523 Planarity : 0.003 0.061 2650 Dihedral : 12.573 120.455 5738 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.91 % Allowed : 1.34 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.19), residues: 1967 helix: 0.93 (0.21), residues: 674 sheet: -0.87 (0.33), residues: 244 loop : -1.27 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 266 TYR 0.018 0.001 TYR A 300 PHE 0.017 0.001 PHE A 386 TRP 0.016 0.001 TRP C 656 HIS 0.008 0.001 HIS E 489 Details of bonding type rmsd covalent geometry : bond 0.00600 (15658) covalent geometry : angle 0.85585 (21259) SS BOND : bond 0.00597 ( 4) SS BOND : angle 1.36310 ( 8) hydrogen bonds : bond 0.23359 ( 603) hydrogen bonds : angle 7.48419 ( 1716) link_BETA1-4 : bond 0.04585 ( 4) link_BETA1-4 : angle 7.40219 ( 12) link_NAG-ASN : bond 0.01139 ( 8) link_NAG-ASN : angle 5.38191 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.485 Fit side-chains REVERT: A 226 PHE cc_start: 0.8896 (m-10) cc_final: 0.8556 (m-80) REVERT: B 174 MET cc_start: 0.9246 (tpt) cc_final: 0.8986 (tpp) REVERT: B 304 MET cc_start: 0.9337 (ttp) cc_final: 0.9046 (ttp) REVERT: B 384 MET cc_start: 0.9301 (tpp) cc_final: 0.9076 (mmp) REVERT: B 399 MET cc_start: 0.8715 (tpt) cc_final: 0.8442 (tpt) REVERT: C 131 MET cc_start: 0.9694 (mmp) cc_final: 0.9470 (mmm) REVERT: C 362 MET cc_start: 0.9437 (mmp) cc_final: 0.9120 (mmm) REVERT: D 4 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9274 (pt) REVERT: D 34 MET cc_start: 0.9405 (mmp) cc_final: 0.9106 (mmp) REVERT: D 83 MET cc_start: 0.8288 (ttm) cc_final: 0.7776 (tmm) REVERT: D 214 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8076 (pp30) outliers start: 15 outliers final: 0 residues processed: 87 average time/residue: 0.0944 time to fit residues: 13.0408 Evaluate side-chains 58 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 214 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 HIS ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN C 678 ASN D 130 GLN D 151 GLN D 161 GLN E 279 GLN E 355 GLN ** E 405 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 = 0.3292 r_free = 0.3292 target = 0.036637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.025159 restraints weight = 170057.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.025937 restraints weight = 90290.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.026457 restraints weight = 60762.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.026784 restraints weight = 46894.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.027019 restraints weight = 39779.945| |-----------------------------------------------------------------------------| r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15674 Z= 0.164 Angle : 0.656 11.621 21303 Z= 0.338 Chirality : 0.043 0.162 2523 Planarity : 0.004 0.036 2650 Dihedral : 6.410 103.942 2372 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.37 % Allowed : 5.72 % Favored : 93.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.19), residues: 1967 helix: 1.24 (0.20), residues: 699 sheet: -0.68 (0.30), residues: 278 loop : -1.24 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 203 TYR 0.013 0.001 TYR A 95 PHE 0.016 0.001 PHE B 226 TRP 0.017 0.001 TRP C 656 HIS 0.006 0.001 HIS E 489 Details of bonding type rmsd covalent geometry : bond 0.00343 (15658) covalent geometry : angle 0.64602 (21259) SS BOND : bond 0.00385 ( 4) SS BOND : angle 1.01876 ( 8) hydrogen bonds : bond 0.06532 ( 603) hydrogen bonds : angle 5.74297 ( 1716) link_BETA1-4 : bond 0.00410 ( 4) link_BETA1-4 : angle 2.08957 ( 12) link_NAG-ASN : bond 0.00284 ( 8) link_NAG-ASN : angle 3.20769 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.477 Fit side-chains REVERT: A 85 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8546 (tmm) REVERT: A 174 MET cc_start: 0.9707 (mmm) cc_final: 0.9352 (mmm) REVERT: A 226 PHE cc_start: 0.9026 (m-10) cc_final: 0.8615 (m-80) REVERT: B 174 MET cc_start: 0.9173 (tpt) cc_final: 0.8969 (tpp) REVERT: B 304 MET cc_start: 0.9307 (ttp) cc_final: 0.8821 (ttp) REVERT: C 362 MET cc_start: 0.9704 (mmp) cc_final: 0.9352 (mmm) REVERT: C 642 MET cc_start: 0.9578 (mpp) cc_final: 0.9305 (mpp) REVERT: D 34 MET cc_start: 0.9453 (mmp) cc_final: 0.9229 (mmp) REVERT: D 128 MET cc_start: 0.8515 (mmm) cc_final: 0.7813 (tpt) REVERT: E 313 MET cc_start: 0.8617 (mmm) cc_final: 0.8399 (tpt) outliers start: 6 outliers final: 1 residues processed: 64 average time/residue: 0.0918 time to fit residues: 9.8385 Evaluate side-chains 56 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 398 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 145 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 183 optimal weight: 8.9990 chunk 143 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 6 optimal weight: 0.0470 chunk 138 optimal weight: 20.0000 chunk 56 optimal weight: 4.9990 chunk 59 optimal weight: 0.0770 chunk 92 optimal weight: 2.9990 chunk 112 optimal weight: 30.0000 overall best weight: 2.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.036693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.025239 restraints weight = 170979.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.026036 restraints weight = 90732.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.026557 restraints weight = 60462.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.026873 restraints weight = 46504.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.027123 restraints weight = 39567.382| |-----------------------------------------------------------------------------| r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15674 Z= 0.146 Angle : 0.609 11.426 21303 Z= 0.310 Chirality : 0.042 0.205 2523 Planarity : 0.003 0.040 2650 Dihedral : 6.047 99.564 2367 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.49 % Allowed : 8.10 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.19), residues: 1967 helix: 1.54 (0.21), residues: 694 sheet: -0.54 (0.31), residues: 264 loop : -1.23 (0.19), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 73 TYR 0.014 0.001 TYR E 368 PHE 0.017 0.001 PHE C 303 TRP 0.013 0.001 TRP C 656 HIS 0.006 0.001 HIS E 489 Details of bonding type rmsd covalent geometry : bond 0.00312 (15658) covalent geometry : angle 0.60034 (21259) SS BOND : bond 0.00272 ( 4) SS BOND : angle 0.77171 ( 8) hydrogen bonds : bond 0.05377 ( 603) hydrogen bonds : angle 5.26175 ( 1716) link_BETA1-4 : bond 0.00265 ( 4) link_BETA1-4 : angle 1.69157 ( 12) link_NAG-ASN : bond 0.00305 ( 8) link_NAG-ASN : angle 2.80481 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.429 Fit side-chains REVERT: A 85 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8626 (tmm) REVERT: A 174 MET cc_start: 0.9724 (mmm) cc_final: 0.9411 (mmm) REVERT: A 226 PHE cc_start: 0.9026 (m-10) cc_final: 0.8618 (m-80) REVERT: B 175 MET cc_start: 0.8710 (mtm) cc_final: 0.8463 (ptp) REVERT: B 304 MET cc_start: 0.9307 (ttp) cc_final: 0.8775 (ttp) REVERT: B 399 MET cc_start: 0.8696 (tpp) cc_final: 0.8421 (tpp) REVERT: C 362 MET cc_start: 0.9700 (mmp) cc_final: 0.9370 (mmp) REVERT: C 525 MET cc_start: 0.8869 (tpp) cc_final: 0.8542 (tpp) REVERT: D 128 MET cc_start: 0.8552 (mmm) cc_final: 0.7877 (tpt) outliers start: 8 outliers final: 1 residues processed: 67 average time/residue: 0.1045 time to fit residues: 11.5737 Evaluate side-chains 58 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 398 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 109 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 165 optimal weight: 20.0000 chunk 162 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 30 optimal weight: 0.2980 chunk 190 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 355 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.037097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.025722 restraints weight = 168101.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.026518 restraints weight = 89885.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.027048 restraints weight = 60255.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.027406 restraints weight = 46221.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.027637 restraints weight = 38718.464| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15674 Z= 0.112 Angle : 0.572 9.002 21303 Z= 0.288 Chirality : 0.042 0.252 2523 Planarity : 0.003 0.044 2650 Dihedral : 5.733 93.809 2367 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.61 % Allowed : 10.35 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.19), residues: 1967 helix: 1.82 (0.21), residues: 687 sheet: -0.41 (0.32), residues: 253 loop : -1.25 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 73 TYR 0.013 0.001 TYR E 368 PHE 0.017 0.001 PHE A 386 TRP 0.013 0.001 TRP E 320 HIS 0.007 0.001 HIS C 129 Details of bonding type rmsd covalent geometry : bond 0.00233 (15658) covalent geometry : angle 0.56446 (21259) SS BOND : bond 0.00250 ( 4) SS BOND : angle 0.71700 ( 8) hydrogen bonds : bond 0.04560 ( 603) hydrogen bonds : angle 4.88847 ( 1716) link_BETA1-4 : bond 0.00264 ( 4) link_BETA1-4 : angle 1.54968 ( 12) link_NAG-ASN : bond 0.00297 ( 8) link_NAG-ASN : angle 2.65668 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.598 Fit side-chains REVERT: A 85 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8627 (tmm) REVERT: A 174 MET cc_start: 0.9703 (mmm) cc_final: 0.9305 (mmm) REVERT: A 179 LEU cc_start: 0.9741 (mm) cc_final: 0.9442 (pp) REVERT: A 226 PHE cc_start: 0.9010 (m-10) cc_final: 0.8594 (m-80) REVERT: B 175 MET cc_start: 0.8727 (mtm) cc_final: 0.8465 (mtm) REVERT: B 304 MET cc_start: 0.9309 (ttp) cc_final: 0.8762 (ttp) REVERT: C 362 MET cc_start: 0.9705 (mmp) cc_final: 0.9400 (mmm) REVERT: C 525 MET cc_start: 0.8974 (tpp) cc_final: 0.8732 (tpp) REVERT: D 34 MET cc_start: 0.9483 (OUTLIER) cc_final: 0.9171 (mmp) REVERT: D 128 MET cc_start: 0.8530 (mmm) cc_final: 0.7836 (tpt) outliers start: 10 outliers final: 4 residues processed: 67 average time/residue: 0.0865 time to fit residues: 10.0120 Evaluate side-chains 66 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 398 CYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain E residue 364 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 180 optimal weight: 0.0000 chunk 121 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 127 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 73 optimal weight: 0.0870 chunk 192 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 165 optimal weight: 7.9990 chunk 133 optimal weight: 3.9990 overall best weight: 1.6168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 108 HIS ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.037008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.025607 restraints weight = 166907.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.026402 restraints weight = 89442.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.026921 restraints weight = 59859.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.027278 restraints weight = 46067.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.027483 restraints weight = 38787.743| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15674 Z= 0.111 Angle : 0.560 8.708 21303 Z= 0.283 Chirality : 0.041 0.233 2523 Planarity : 0.003 0.045 2650 Dihedral : 5.519 89.259 2367 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.73 % Allowed : 11.14 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.20), residues: 1967 helix: 1.95 (0.21), residues: 686 sheet: -0.47 (0.30), residues: 274 loop : -1.16 (0.19), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 73 TYR 0.012 0.001 TYR D 95 PHE 0.013 0.001 PHE A 442 TRP 0.012 0.001 TRP E 320 HIS 0.005 0.001 HIS E 489 Details of bonding type rmsd covalent geometry : bond 0.00234 (15658) covalent geometry : angle 0.55267 (21259) SS BOND : bond 0.00225 ( 4) SS BOND : angle 0.62923 ( 8) hydrogen bonds : bond 0.04359 ( 603) hydrogen bonds : angle 4.77466 ( 1716) link_BETA1-4 : bond 0.00353 ( 4) link_BETA1-4 : angle 1.50054 ( 12) link_NAG-ASN : bond 0.00272 ( 8) link_NAG-ASN : angle 2.56673 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.613 Fit side-chains REVERT: A 85 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8675 (tmm) REVERT: A 174 MET cc_start: 0.9689 (mmm) cc_final: 0.9349 (mmm) REVERT: A 226 PHE cc_start: 0.9013 (m-10) cc_final: 0.8588 (m-80) REVERT: A 304 MET cc_start: 0.9595 (tpt) cc_final: 0.9375 (tpt) REVERT: A 445 MET cc_start: 0.8448 (mmm) cc_final: 0.8134 (mmm) REVERT: B 304 MET cc_start: 0.9293 (ttp) cc_final: 0.8753 (ttp) REVERT: C 131 MET cc_start: 0.9517 (ppp) cc_final: 0.9253 (pmm) REVERT: C 362 MET cc_start: 0.9700 (mmp) cc_final: 0.9363 (mmm) REVERT: C 525 MET cc_start: 0.8926 (tpp) cc_final: 0.8707 (tpp) REVERT: D 34 MET cc_start: 0.9441 (OUTLIER) cc_final: 0.9224 (mmm) REVERT: D 128 MET cc_start: 0.8549 (mmm) cc_final: 0.7862 (tpt) outliers start: 12 outliers final: 6 residues processed: 69 average time/residue: 0.0900 time to fit residues: 10.5685 Evaluate side-chains 66 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 398 CYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain E residue 364 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 162 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 195 optimal weight: 20.0000 chunk 134 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 ASN D 216 ASN E 489 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.036641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.025170 restraints weight = 170503.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.025945 restraints weight = 90450.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.026464 restraints weight = 60669.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.026812 restraints weight = 46758.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.027043 restraints weight = 39293.245| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15674 Z= 0.140 Angle : 0.580 9.112 21303 Z= 0.291 Chirality : 0.041 0.195 2523 Planarity : 0.003 0.045 2650 Dihedral : 5.407 83.836 2367 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.04 % Allowed : 12.24 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.20), residues: 1967 helix: 2.00 (0.21), residues: 686 sheet: -0.41 (0.31), residues: 272 loop : -1.14 (0.20), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 402 TYR 0.010 0.001 TYR D 95 PHE 0.013 0.001 PHE B 87 TRP 0.011 0.001 TRP E 320 HIS 0.005 0.001 HIS E 489 Details of bonding type rmsd covalent geometry : bond 0.00299 (15658) covalent geometry : angle 0.57370 (21259) SS BOND : bond 0.00215 ( 4) SS BOND : angle 0.65620 ( 8) hydrogen bonds : bond 0.04465 ( 603) hydrogen bonds : angle 4.77664 ( 1716) link_BETA1-4 : bond 0.00308 ( 4) link_BETA1-4 : angle 1.47039 ( 12) link_NAG-ASN : bond 0.00247 ( 8) link_NAG-ASN : angle 2.51793 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: A 85 MET cc_start: 0.9154 (ttp) cc_final: 0.8722 (tmm) REVERT: A 174 MET cc_start: 0.9711 (mmm) cc_final: 0.9422 (mmm) REVERT: A 226 PHE cc_start: 0.9046 (m-10) cc_final: 0.8616 (m-80) REVERT: A 445 MET cc_start: 0.8476 (mmm) cc_final: 0.8265 (mmm) REVERT: B 304 MET cc_start: 0.9305 (ttp) cc_final: 0.8765 (ttp) REVERT: B 332 PHE cc_start: 0.9481 (OUTLIER) cc_final: 0.8917 (t80) REVERT: C 131 MET cc_start: 0.9572 (ppp) cc_final: 0.9302 (pmm) REVERT: C 362 MET cc_start: 0.9715 (mmp) cc_final: 0.9366 (mmm) REVERT: D 34 MET cc_start: 0.9440 (OUTLIER) cc_final: 0.9152 (mmp) REVERT: D 83 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.7684 (tmm) REVERT: D 86 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.8996 (pp) REVERT: D 128 MET cc_start: 0.8512 (mmm) cc_final: 0.7809 (tpt) outliers start: 17 outliers final: 7 residues processed: 71 average time/residue: 0.0955 time to fit residues: 11.5271 Evaluate side-chains 68 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 CYS Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 364 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 192 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 178 optimal weight: 0.0770 chunk 127 optimal weight: 10.0000 chunk 165 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 65 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 overall best weight: 1.5142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.036895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.025657 restraints weight = 163756.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.026443 restraints weight = 88825.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.026963 restraints weight = 59629.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.027317 restraints weight = 45883.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.027489 restraints weight = 38491.147| |-----------------------------------------------------------------------------| r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15674 Z= 0.107 Angle : 0.578 14.284 21303 Z= 0.285 Chirality : 0.041 0.184 2523 Planarity : 0.003 0.045 2650 Dihedral : 5.177 75.647 2367 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.97 % Allowed : 12.91 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.20), residues: 1967 helix: 2.02 (0.21), residues: 693 sheet: -0.27 (0.31), residues: 270 loop : -1.17 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 73 TYR 0.012 0.001 TYR E 368 PHE 0.013 0.001 PHE B 87 TRP 0.012 0.001 TRP E 320 HIS 0.003 0.000 HIS B 237 Details of bonding type rmsd covalent geometry : bond 0.00224 (15658) covalent geometry : angle 0.57104 (21259) SS BOND : bond 0.00188 ( 4) SS BOND : angle 0.58833 ( 8) hydrogen bonds : bond 0.04112 ( 603) hydrogen bonds : angle 4.61061 ( 1716) link_BETA1-4 : bond 0.00273 ( 4) link_BETA1-4 : angle 1.35495 ( 12) link_NAG-ASN : bond 0.00252 ( 8) link_NAG-ASN : angle 2.51433 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.575 Fit side-chains REVERT: A 85 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8689 (tmm) REVERT: A 174 MET cc_start: 0.9644 (mmm) cc_final: 0.9318 (mmm) REVERT: A 226 PHE cc_start: 0.9005 (m-10) cc_final: 0.8572 (m-80) REVERT: A 304 MET cc_start: 0.9587 (tpt) cc_final: 0.9384 (tpt) REVERT: A 445 MET cc_start: 0.8541 (mmm) cc_final: 0.8256 (mmm) REVERT: B 304 MET cc_start: 0.9264 (ttp) cc_final: 0.8765 (ttp) REVERT: B 332 PHE cc_start: 0.9467 (OUTLIER) cc_final: 0.8864 (t80) REVERT: B 344 VAL cc_start: 0.9552 (t) cc_final: 0.9340 (t) REVERT: C 131 MET cc_start: 0.9565 (ppp) cc_final: 0.9314 (pmm) REVERT: C 362 MET cc_start: 0.9668 (mmp) cc_final: 0.9333 (mmm) REVERT: D 86 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.8945 (pp) REVERT: D 128 MET cc_start: 0.8475 (mmm) cc_final: 0.7783 (tpt) outliers start: 16 outliers final: 7 residues processed: 73 average time/residue: 0.0884 time to fit residues: 11.2062 Evaluate side-chains 67 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain E residue 364 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 46 optimal weight: 0.0030 chunk 57 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 chunk 71 optimal weight: 0.1980 chunk 53 optimal weight: 0.7980 chunk 162 optimal weight: 0.0570 chunk 138 optimal weight: 10.0000 chunk 111 optimal weight: 7.9990 chunk 181 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 106 optimal weight: 30.0000 overall best weight: 0.4108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.037505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.026192 restraints weight = 167631.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.027005 restraints weight = 89599.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.027560 restraints weight = 59486.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.027916 restraints weight = 45505.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.028160 restraints weight = 38188.045| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15674 Z= 0.097 Angle : 0.583 11.373 21303 Z= 0.282 Chirality : 0.041 0.169 2523 Planarity : 0.003 0.045 2650 Dihedral : 4.795 61.977 2367 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.85 % Allowed : 13.22 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.20), residues: 1967 helix: 2.09 (0.21), residues: 692 sheet: -0.13 (0.32), residues: 268 loop : -1.14 (0.19), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 416 TYR 0.013 0.001 TYR E 368 PHE 0.013 0.001 PHE B 226 TRP 0.014 0.001 TRP E 320 HIS 0.003 0.000 HIS B 237 Details of bonding type rmsd covalent geometry : bond 0.00198 (15658) covalent geometry : angle 0.57534 (21259) SS BOND : bond 0.00261 ( 4) SS BOND : angle 1.01763 ( 8) hydrogen bonds : bond 0.03676 ( 603) hydrogen bonds : angle 4.45905 ( 1716) link_BETA1-4 : bond 0.00320 ( 4) link_BETA1-4 : angle 1.33535 ( 12) link_NAG-ASN : bond 0.00291 ( 8) link_NAG-ASN : angle 2.63617 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: A 85 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.8777 (ppp) REVERT: A 174 MET cc_start: 0.9588 (mmm) cc_final: 0.9277 (mmm) REVERT: A 226 PHE cc_start: 0.9005 (m-10) cc_final: 0.8583 (m-80) REVERT: A 445 MET cc_start: 0.8480 (mmm) cc_final: 0.8248 (mmm) REVERT: B 304 MET cc_start: 0.9216 (ttp) cc_final: 0.8698 (ttp) REVERT: B 332 PHE cc_start: 0.9427 (OUTLIER) cc_final: 0.8799 (t80) REVERT: C 131 MET cc_start: 0.9569 (ppp) cc_final: 0.9338 (pmm) REVERT: C 362 MET cc_start: 0.9664 (mmp) cc_final: 0.9321 (mmp) REVERT: C 442 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8726 (pm20) REVERT: D 83 MET cc_start: 0.8533 (mtt) cc_final: 0.7983 (tmm) REVERT: D 86 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9019 (pp) REVERT: D 128 MET cc_start: 0.8501 (mmm) cc_final: 0.7815 (tpt) outliers start: 14 outliers final: 9 residues processed: 75 average time/residue: 0.0873 time to fit residues: 11.3559 Evaluate side-chains 70 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 364 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 186 optimal weight: 20.0000 chunk 158 optimal weight: 10.0000 chunk 182 optimal weight: 8.9990 chunk 121 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 173 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 GLN C 522 ASN C 539 HIS C 565 HIS ** E 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.035849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.024441 restraints weight = 168337.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.025184 restraints weight = 91474.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.025681 restraints weight = 61951.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.026014 restraints weight = 48038.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.026237 restraints weight = 40653.022| |-----------------------------------------------------------------------------| r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 15674 Z= 0.213 Angle : 0.681 11.628 21303 Z= 0.338 Chirality : 0.042 0.195 2523 Planarity : 0.004 0.045 2650 Dihedral : 4.957 50.508 2367 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.85 % Allowed : 13.95 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.19), residues: 1967 helix: 1.92 (0.21), residues: 688 sheet: -0.40 (0.31), residues: 274 loop : -1.17 (0.20), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 327 TYR 0.014 0.002 TYR A 422 PHE 0.016 0.002 PHE B 87 TRP 0.047 0.002 TRP C 660 HIS 0.004 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00455 (15658) covalent geometry : angle 0.67411 (21259) SS BOND : bond 0.00261 ( 4) SS BOND : angle 1.43282 ( 8) hydrogen bonds : bond 0.04948 ( 603) hydrogen bonds : angle 4.93198 ( 1716) link_BETA1-4 : bond 0.00323 ( 4) link_BETA1-4 : angle 1.51899 ( 12) link_NAG-ASN : bond 0.00258 ( 8) link_NAG-ASN : angle 2.68441 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: A 85 MET cc_start: 0.9238 (OUTLIER) cc_final: 0.8808 (tmm) REVERT: A 174 MET cc_start: 0.9716 (mmm) cc_final: 0.9377 (mmm) REVERT: A 226 PHE cc_start: 0.9124 (m-10) cc_final: 0.8671 (m-80) REVERT: A 445 MET cc_start: 0.8510 (mmm) cc_final: 0.7773 (mmm) REVERT: B 304 MET cc_start: 0.9287 (ttp) cc_final: 0.8757 (ttp) REVERT: C 131 MET cc_start: 0.9616 (ppp) cc_final: 0.9377 (pmm) REVERT: C 362 MET cc_start: 0.9709 (mmp) cc_final: 0.9388 (mmp) REVERT: C 442 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.8845 (pm20) REVERT: D 83 MET cc_start: 0.8591 (mtt) cc_final: 0.7994 (tmm) REVERT: D 86 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9002 (pp) REVERT: D 128 MET cc_start: 0.8475 (mmm) cc_final: 0.7807 (tpt) outliers start: 14 outliers final: 9 residues processed: 70 average time/residue: 0.0929 time to fit residues: 10.8992 Evaluate side-chains 68 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 364 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 142 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 189 optimal weight: 8.9990 chunk 125 optimal weight: 0.9990 chunk 193 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 135 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.036530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.025004 restraints weight = 170782.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.025781 restraints weight = 91236.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.026296 restraints weight = 61316.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.026639 restraints weight = 47434.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.026857 restraints weight = 40136.649| |-----------------------------------------------------------------------------| r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15674 Z= 0.124 Angle : 0.626 13.051 21303 Z= 0.306 Chirality : 0.041 0.175 2523 Planarity : 0.003 0.044 2650 Dihedral : 4.766 52.364 2367 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.85 % Allowed : 13.82 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.20), residues: 1967 helix: 2.04 (0.21), residues: 695 sheet: -0.34 (0.31), residues: 273 loop : -1.12 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 402 TYR 0.011 0.001 TYR E 368 PHE 0.015 0.001 PHE B 87 TRP 0.050 0.001 TRP C 660 HIS 0.002 0.001 HIS B 237 Details of bonding type rmsd covalent geometry : bond 0.00267 (15658) covalent geometry : angle 0.61828 (21259) SS BOND : bond 0.00189 ( 4) SS BOND : angle 1.11589 ( 8) hydrogen bonds : bond 0.04321 ( 603) hydrogen bonds : angle 4.72468 ( 1716) link_BETA1-4 : bond 0.00265 ( 4) link_BETA1-4 : angle 1.29042 ( 12) link_NAG-ASN : bond 0.00187 ( 8) link_NAG-ASN : angle 2.73005 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: A 85 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8697 (tmm) REVERT: A 174 MET cc_start: 0.9668 (mmm) cc_final: 0.9330 (mmm) REVERT: A 226 PHE cc_start: 0.9100 (m-10) cc_final: 0.8657 (m-80) REVERT: B 304 MET cc_start: 0.9296 (ttp) cc_final: 0.8735 (ttp) REVERT: C 131 MET cc_start: 0.9608 (ppp) cc_final: 0.9371 (pmm) REVERT: C 362 MET cc_start: 0.9725 (mmp) cc_final: 0.9372 (mmp) REVERT: C 429 TRP cc_start: 0.9022 (OUTLIER) cc_final: 0.8587 (m-10) REVERT: C 442 GLU cc_start: 0.9152 (OUTLIER) cc_final: 0.8821 (pm20) REVERT: D 83 MET cc_start: 0.8563 (mtt) cc_final: 0.7944 (tmm) REVERT: D 86 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9013 (pp) REVERT: D 128 MET cc_start: 0.8461 (mmm) cc_final: 0.7749 (tpt) outliers start: 14 outliers final: 9 residues processed: 70 average time/residue: 0.0824 time to fit residues: 9.9257 Evaluate side-chains 70 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 429 TRP Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 364 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 119 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 35 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 166 optimal weight: 8.9990 chunk 148 optimal weight: 9.9990 chunk 164 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 357 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.035996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.024591 restraints weight = 167840.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.025352 restraints weight = 91279.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.025855 restraints weight = 61649.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.026190 restraints weight = 47619.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.026394 restraints weight = 40182.019| |-----------------------------------------------------------------------------| r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15674 Z= 0.165 Angle : 0.662 13.037 21303 Z= 0.324 Chirality : 0.042 0.192 2523 Planarity : 0.003 0.044 2650 Dihedral : 4.792 51.207 2367 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.85 % Allowed : 13.95 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.20), residues: 1967 helix: 1.93 (0.21), residues: 695 sheet: -0.44 (0.31), residues: 274 loop : -1.11 (0.20), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 402 TYR 0.013 0.001 TYR E 367 PHE 0.014 0.001 PHE B 87 TRP 0.045 0.001 TRP C 660 HIS 0.003 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00358 (15658) covalent geometry : angle 0.65492 (21259) SS BOND : bond 0.00196 ( 4) SS BOND : angle 1.07083 ( 8) hydrogen bonds : bond 0.04502 ( 603) hydrogen bonds : angle 4.85433 ( 1716) link_BETA1-4 : bond 0.00297 ( 4) link_BETA1-4 : angle 1.33749 ( 12) link_NAG-ASN : bond 0.00182 ( 8) link_NAG-ASN : angle 2.72305 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2464.87 seconds wall clock time: 43 minutes 21.49 seconds (2601.49 seconds total)