Starting phenix.real_space_refine on Fri Jun 13 22:45:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lsh_63355/06_2025/9lsh_63355.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lsh_63355/06_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_63355/06_2025/9lsh_63355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lsh_63355/06_2025/9lsh_63355.map" model { file = "/net/cci-nas-00/data/ceres_data/9lsh_63355/06_2025/9lsh_63355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lsh_63355/06_2025/9lsh_63355.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1, '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: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1, '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: {'PHE:plan': 2, 'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP: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: {'GLU:plan': 1, 'ARG: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: 9.10, per 1000 atoms: 0.59 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: 4.40 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.64 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: 4.60 Time building geometry restraints manager: 5.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 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: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.170 Process input model: 36.060 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.170 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (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 TRP 0.016 0.001 TRP C 656 HIS 0.008 0.001 HIS E 489 PHE 0.017 0.001 PHE A 386 TYR 0.018 0.001 TYR A 300 ARG 0.003 0.000 ARG A 266 Details of bonding type rmsd link_NAG-ASN : bond 0.01139 ( 8) link_NAG-ASN : angle 5.38191 ( 24) link_BETA1-4 : bond 0.04585 ( 4) link_BETA1-4 : angle 7.40219 ( 12) hydrogen bonds : bond 0.23359 ( 603) hydrogen bonds : angle 7.48419 ( 1716) SS BOND : bond 0.00597 ( 4) SS BOND : angle 1.36310 ( 8) covalent geometry : bond 0.00600 (15658) covalent geometry : angle 0.85585 (21259) *********************** 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 : 1.981 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: 0.8988 (tpp) REVERT: B 175 MET cc_start: 0.8800 (mtm) cc_final: 0.8567 (mtp) 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: 0.3058 time to fit residues: 42.6419 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 : 1.685 ------------------------------------------------------------------------------- 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 165 optimal weight: 20.0000 chunk 148 optimal weight: 20.0000 chunk 82 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 100 optimal weight: 30.0000 chunk 79 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 177 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 GLN E 355 GLN ** E 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.036609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.025138 restraints weight = 168583.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.025926 restraints weight = 89962.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.026428 restraints weight = 60372.083| |-----------------------------------------------------------------------------| r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15674 Z= 0.163 Angle : 0.654 11.678 21303 Z= 0.337 Chirality : 0.043 0.164 2523 Planarity : 0.003 0.035 2650 Dihedral : 6.409 103.788 2372 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.37 % Allowed : 5.54 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.19), residues: 1967 helix: 1.25 (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 TRP 0.016 0.001 TRP C 656 HIS 0.006 0.001 HIS E 489 PHE 0.017 0.001 PHE B 226 TYR 0.013 0.001 TYR A 95 ARG 0.003 0.000 ARG B 203 Details of bonding type rmsd link_NAG-ASN : bond 0.00297 ( 8) link_NAG-ASN : angle 3.19551 ( 24) link_BETA1-4 : bond 0.00347 ( 4) link_BETA1-4 : angle 2.06606 ( 12) hydrogen bonds : bond 0.06539 ( 603) hydrogen bonds : angle 5.73705 ( 1716) SS BOND : bond 0.00374 ( 4) SS BOND : angle 1.05496 ( 8) covalent geometry : bond 0.00344 (15658) covalent geometry : angle 0.64344 (21259) *********************** 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 : 1.664 Fit side-chains REVERT: A 85 MET cc_start: 0.9062 (OUTLIER) cc_final: 0.8559 (tmm) REVERT: A 174 MET cc_start: 0.9713 (mmm) cc_final: 0.9352 (mmm) REVERT: A 226 PHE cc_start: 0.9039 (m-10) cc_final: 0.8629 (m-80) REVERT: B 175 MET cc_start: 0.8668 (mtm) cc_final: 0.8439 (mtp) REVERT: B 304 MET cc_start: 0.9287 (ttp) cc_final: 0.8793 (ttp) REVERT: C 362 MET cc_start: 0.9707 (mmp) cc_final: 0.9361 (mmm) REVERT: C 642 MET cc_start: 0.9592 (mpp) cc_final: 0.9314 (mpp) REVERT: D 34 MET cc_start: 0.9454 (mmp) cc_final: 0.9231 (mmp) REVERT: D 128 MET cc_start: 0.8510 (mmm) cc_final: 0.7796 (tpt) REVERT: E 313 MET cc_start: 0.8726 (mmm) cc_final: 0.8524 (tpt) outliers start: 6 outliers final: 1 residues processed: 64 average time/residue: 0.2413 time to fit residues: 25.7625 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 : 1.662 ------------------------------------------------------------------------------- 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 159 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 187 optimal weight: 0.0170 chunk 170 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 174 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 175 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 overall best weight: 1.4022 ------------------------------------------------------------------------------- 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 ** E 405 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 = 0.3310 r_free = 0.3310 target = 0.037104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.025858 restraints weight = 163810.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.026659 restraints weight = 88784.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.027173 restraints weight = 59463.028| |-----------------------------------------------------------------------------| r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15674 Z= 0.115 Angle : 0.586 11.669 21303 Z= 0.297 Chirality : 0.042 0.210 2523 Planarity : 0.003 0.041 2650 Dihedral : 5.977 99.335 2367 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.37 % Allowed : 7.98 % Favored : 91.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.19), residues: 1967 helix: 1.55 (0.21), residues: 699 sheet: -0.60 (0.30), residues: 276 loop : -1.24 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 656 HIS 0.006 0.001 HIS E 489 PHE 0.018 0.001 PHE A 386 TYR 0.013 0.001 TYR E 368 ARG 0.002 0.000 ARG D 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00335 ( 8) link_NAG-ASN : angle 2.83186 ( 24) link_BETA1-4 : bond 0.00315 ( 4) link_BETA1-4 : angle 1.74758 ( 12) hydrogen bonds : bond 0.05180 ( 603) hydrogen bonds : angle 5.13668 ( 1716) SS BOND : bond 0.00254 ( 4) SS BOND : angle 0.75318 ( 8) covalent geometry : bond 0.00237 (15658) covalent geometry : angle 0.57676 (21259) *********************** 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 69 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 1.587 Fit side-chains REVERT: A 85 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8636 (tmm) REVERT: A 174 MET cc_start: 0.9713 (mmm) cc_final: 0.9383 (mmm) REVERT: A 226 PHE cc_start: 0.8989 (m-10) cc_final: 0.8576 (m-80) REVERT: B 26 MET cc_start: 0.9098 (ttt) cc_final: 0.8753 (tpp) REVERT: B 175 MET cc_start: 0.8639 (mtm) cc_final: 0.8289 (mtt) REVERT: B 304 MET cc_start: 0.9268 (ttp) cc_final: 0.8746 (ttp) REVERT: B 399 MET cc_start: 0.8595 (tpp) cc_final: 0.8374 (tpp) REVERT: C 362 MET cc_start: 0.9681 (mmp) cc_final: 0.9368 (mmm) REVERT: D 128 MET cc_start: 0.8523 (mmm) cc_final: 0.7827 (tpt) outliers start: 6 outliers final: 1 residues processed: 68 average time/residue: 0.2299 time to fit residues: 26.2286 Evaluate side-chains 59 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 1.813 ------------------------------------------------------------------------------- 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 76 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 129 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 chunk 86 optimal weight: 20.0000 chunk 138 optimal weight: 8.9990 chunk 15 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 92 optimal weight: 8.9990 chunk 147 optimal weight: 6.9990 overall best weight: 3.8786 ------------------------------------------------------------------------------- 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 C 180 ASN C 522 ASN D 161 GLN ** E 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.036219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.024724 restraints weight = 170142.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.025483 restraints weight = 91594.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.025981 restraints weight = 61835.518| |-----------------------------------------------------------------------------| r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15674 Z= 0.194 Angle : 0.637 8.641 21303 Z= 0.323 Chirality : 0.042 0.197 2523 Planarity : 0.003 0.043 2650 Dihedral : 5.902 94.622 2367 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.73 % Allowed : 10.11 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.19), residues: 1967 helix: 1.58 (0.21), residues: 693 sheet: -0.68 (0.30), residues: 292 loop : -1.23 (0.20), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 656 HIS 0.008 0.001 HIS C 129 PHE 0.015 0.001 PHE A 386 TYR 0.012 0.001 TYR A 422 ARG 0.003 0.000 ARG A 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 8) link_NAG-ASN : angle 2.68398 ( 24) link_BETA1-4 : bond 0.00375 ( 4) link_BETA1-4 : angle 1.66158 ( 12) hydrogen bonds : bond 0.05309 ( 603) hydrogen bonds : angle 5.20467 ( 1716) SS BOND : bond 0.00302 ( 4) SS BOND : angle 0.79205 ( 8) covalent geometry : bond 0.00414 (15658) covalent geometry : angle 0.62955 (21259) *********************** 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: 12 poor density : 58 time to evaluate : 1.695 Fit side-chains REVERT: A 85 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8726 (tmm) REVERT: A 174 MET cc_start: 0.9715 (mmm) cc_final: 0.9374 (mmm) REVERT: A 182 MET cc_start: 0.9439 (mmm) cc_final: 0.9109 (mmm) REVERT: A 226 PHE cc_start: 0.9095 (m-10) cc_final: 0.8661 (m-80) REVERT: B 26 MET cc_start: 0.9152 (ttt) cc_final: 0.8806 (tpp) REVERT: B 175 MET cc_start: 0.8700 (mtm) cc_final: 0.8340 (mtt) REVERT: B 304 MET cc_start: 0.9321 (ttp) cc_final: 0.8775 (ttp) REVERT: B 399 MET cc_start: 0.9059 (tpp) cc_final: 0.8719 (tpp) REVERT: C 362 MET cc_start: 0.9720 (mmp) cc_final: 0.9399 (mmm) REVERT: D 128 MET cc_start: 0.8483 (mmm) cc_final: 0.7794 (tpt) outliers start: 12 outliers final: 5 residues processed: 68 average time/residue: 0.2216 time to fit residues: 26.1071 Evaluate side-chains 61 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 398 CYS Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain C residue 30 VAL 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 5 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 75 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 94 optimal weight: 0.1980 chunk 156 optimal weight: 8.9990 chunk 134 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 = 0.3284 r_free = 0.3284 target = 0.036494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.025015 restraints weight = 172282.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.025788 restraints weight = 92140.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.026297 restraints weight = 61850.089| |-----------------------------------------------------------------------------| r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15674 Z= 0.138 Angle : 0.579 8.770 21303 Z= 0.295 Chirality : 0.042 0.212 2523 Planarity : 0.003 0.045 2650 Dihedral : 5.736 90.266 2367 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.85 % Allowed : 11.57 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.19), residues: 1967 helix: 1.80 (0.21), residues: 687 sheet: -0.51 (0.31), residues: 263 loop : -1.22 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 656 HIS 0.005 0.001 HIS E 489 PHE 0.013 0.001 PHE B 87 TYR 0.013 0.001 TYR D 95 ARG 0.002 0.000 ARG B 402 Details of bonding type rmsd link_NAG-ASN : bond 0.00266 ( 8) link_NAG-ASN : angle 2.60540 ( 24) link_BETA1-4 : bond 0.00245 ( 4) link_BETA1-4 : angle 1.45360 ( 12) hydrogen bonds : bond 0.04785 ( 603) hydrogen bonds : angle 4.97628 ( 1716) SS BOND : bond 0.00256 ( 4) SS BOND : angle 0.69834 ( 8) covalent geometry : bond 0.00295 (15658) covalent geometry : angle 0.57173 (21259) *********************** 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 71 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 1.876 Fit side-chains REVERT: A 85 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8688 (tmm) REVERT: A 174 MET cc_start: 0.9722 (mmm) cc_final: 0.9417 (mmm) REVERT: A 182 MET cc_start: 0.9415 (mmm) cc_final: 0.9124 (mmm) REVERT: A 226 PHE cc_start: 0.9080 (m-10) cc_final: 0.8682 (m-80) REVERT: B 26 MET cc_start: 0.9141 (ttt) cc_final: 0.8774 (tpp) REVERT: B 175 MET cc_start: 0.8693 (mtm) cc_final: 0.8472 (mtp) REVERT: B 304 MET cc_start: 0.9313 (ttp) cc_final: 0.8777 (ttp) REVERT: C 131 MET cc_start: 0.9534 (ppp) cc_final: 0.9294 (pmm) REVERT: C 362 MET cc_start: 0.9718 (mmp) cc_final: 0.9362 (mmm) REVERT: D 128 MET cc_start: 0.8475 (mmm) cc_final: 0.7759 (tpt) outliers start: 14 outliers final: 7 residues processed: 69 average time/residue: 0.2356 time to fit residues: 27.6651 Evaluate side-chains 64 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 398 CYS Chi-restraints excluded: chain B residue 182 MET 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 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 189 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 76 optimal weight: 0.0010 chunk 193 optimal weight: 10.0000 chunk 147 optimal weight: 9.9990 chunk 135 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 overall best weight: 2.9994 ------------------------------------------------------------------------------- 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** D 216 ASN ** E 405 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 = 0.3278 r_free = 0.3278 target = 0.036285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.024814 restraints weight = 171244.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.025574 restraints weight = 92200.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.026059 restraints weight = 62182.682| |-----------------------------------------------------------------------------| r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15674 Z= 0.154 Angle : 0.593 9.714 21303 Z= 0.299 Chirality : 0.041 0.240 2523 Planarity : 0.003 0.045 2650 Dihedral : 5.645 86.296 2367 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.10 % Allowed : 12.36 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.19), residues: 1967 helix: 1.85 (0.21), residues: 687 sheet: -0.61 (0.30), residues: 266 loop : -1.18 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 656 HIS 0.005 0.001 HIS E 489 PHE 0.012 0.001 PHE B 87 TYR 0.011 0.001 TYR E 377 ARG 0.002 0.000 ARG B 402 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 8) link_NAG-ASN : angle 2.57148 ( 24) link_BETA1-4 : bond 0.00294 ( 4) link_BETA1-4 : angle 1.46580 ( 12) hydrogen bonds : bond 0.04712 ( 603) hydrogen bonds : angle 4.93978 ( 1716) SS BOND : bond 0.00244 ( 4) SS BOND : angle 0.65779 ( 8) covalent geometry : bond 0.00331 (15658) covalent geometry : angle 0.58568 (21259) *********************** 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: 18 poor density : 56 time to evaluate : 1.795 Fit side-chains revert: symmetry clash REVERT: A 85 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.8710 (tmm) REVERT: A 174 MET cc_start: 0.9692 (mmm) cc_final: 0.9392 (mmm) REVERT: A 182 MET cc_start: 0.9448 (mmm) cc_final: 0.9042 (mmm) REVERT: A 226 PHE cc_start: 0.9092 (m-10) cc_final: 0.8680 (m-80) REVERT: B 26 MET cc_start: 0.9149 (ttt) cc_final: 0.8774 (tpp) REVERT: B 175 MET cc_start: 0.8693 (mtm) cc_final: 0.8335 (mtt) REVERT: B 304 MET cc_start: 0.9330 (ttp) cc_final: 0.8777 (ttp) REVERT: B 332 PHE cc_start: 0.9511 (OUTLIER) cc_final: 0.8905 (t80) REVERT: B 399 MET cc_start: 0.9235 (tpp) cc_final: 0.8875 (tpp) REVERT: C 131 MET cc_start: 0.9573 (ppp) cc_final: 0.9327 (pmm) REVERT: C 362 MET cc_start: 0.9717 (mmp) cc_final: 0.9379 (mmm) REVERT: D 128 MET cc_start: 0.8498 (mmm) cc_final: 0.7791 (tpt) outliers start: 18 outliers final: 9 residues processed: 71 average time/residue: 0.2286 time to fit residues: 27.7042 Evaluate side-chains 67 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 MET 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 31 ASN Chi-restraints excluded: chain D residue 83 MET 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 70 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 chunk 133 optimal weight: 0.0770 chunk 104 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 152 optimal weight: 0.6980 chunk 122 optimal weight: 10.0000 overall best weight: 0.9342 ------------------------------------------------------------------------------- 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 180 ASN C 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.036990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.025583 restraints weight = 168321.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.026386 restraints weight = 90049.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.026913 restraints weight = 59989.609| |-----------------------------------------------------------------------------| r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15674 Z= 0.097 Angle : 0.558 10.695 21303 Z= 0.277 Chirality : 0.041 0.228 2523 Planarity : 0.003 0.045 2650 Dihedral : 5.260 77.265 2367 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.04 % Allowed : 12.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.20), residues: 1967 helix: 2.05 (0.21), residues: 688 sheet: -0.34 (0.31), residues: 271 loop : -1.20 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 320 HIS 0.005 0.001 HIS E 489 PHE 0.013 0.001 PHE B 226 TYR 0.012 0.001 TYR E 368 ARG 0.002 0.000 ARG B 416 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 8) link_NAG-ASN : angle 2.54401 ( 24) link_BETA1-4 : bond 0.00333 ( 4) link_BETA1-4 : angle 1.33876 ( 12) hydrogen bonds : bond 0.03988 ( 603) hydrogen bonds : angle 4.58524 ( 1716) SS BOND : bond 0.00195 ( 4) SS BOND : angle 0.59815 ( 8) covalent geometry : bond 0.00198 (15658) covalent geometry : angle 0.55066 (21259) *********************** 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 77 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 1.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8741 (ppp) REVERT: A 174 MET cc_start: 0.9664 (mmm) cc_final: 0.9334 (mmm) REVERT: A 182 MET cc_start: 0.9340 (mmm) cc_final: 0.9007 (mmm) REVERT: B 26 MET cc_start: 0.9062 (ttt) cc_final: 0.8714 (tpp) REVERT: B 175 MET cc_start: 0.8641 (mtm) cc_final: 0.8421 (mtp) REVERT: B 304 MET cc_start: 0.9272 (ttp) cc_final: 0.8741 (ttp) REVERT: B 332 PHE cc_start: 0.9469 (OUTLIER) cc_final: 0.8796 (t80) REVERT: C 95 CYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8242 (p) REVERT: C 131 MET cc_start: 0.9580 (ppp) cc_final: 0.9347 (pmm) REVERT: C 362 MET cc_start: 0.9710 (mmp) cc_final: 0.9338 (mmm) REVERT: D 86 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8919 (pp) REVERT: D 128 MET cc_start: 0.8483 (mmm) cc_final: 0.7735 (tpt) outliers start: 17 outliers final: 8 residues processed: 75 average time/residue: 0.2263 time to fit residues: 28.7861 Evaluate side-chains 70 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 398 CYS 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 95 CYS 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 285 LYS 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 22 optimal weight: 0.0770 chunk 54 optimal weight: 9.9990 chunk 135 optimal weight: 7.9990 chunk 119 optimal weight: 20.0000 chunk 132 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 109 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 131 optimal weight: 0.0020 overall best weight: 2.6152 ------------------------------------------------------------------------------- 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** E 489 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.036457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.024938 restraints weight = 169150.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.025700 restraints weight = 91152.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.026214 restraints weight = 61616.701| |-----------------------------------------------------------------------------| r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15674 Z= 0.141 Angle : 0.605 12.627 21303 Z= 0.298 Chirality : 0.041 0.272 2523 Planarity : 0.003 0.045 2650 Dihedral : 5.157 69.256 2367 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.91 % Allowed : 13.64 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.20), residues: 1967 helix: 2.04 (0.21), residues: 687 sheet: -0.40 (0.31), residues: 272 loop : -1.18 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 320 HIS 0.004 0.001 HIS E 489 PHE 0.012 0.001 PHE B 87 TYR 0.010 0.001 TYR E 368 ARG 0.002 0.000 ARG A 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 8) link_NAG-ASN : angle 2.55941 ( 24) link_BETA1-4 : bond 0.00197 ( 4) link_BETA1-4 : angle 1.42536 ( 12) hydrogen bonds : bond 0.04318 ( 603) hydrogen bonds : angle 4.68855 ( 1716) SS BOND : bond 0.00194 ( 4) SS BOND : angle 0.59709 ( 8) covalent geometry : bond 0.00303 (15658) covalent geometry : angle 0.59804 (21259) *********************** 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 71 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 1.820 Fit side-chains revert: symmetry clash REVERT: A 85 MET cc_start: 0.9226 (ttp) cc_final: 0.8745 (tmm) REVERT: A 174 MET cc_start: 0.9650 (mmm) cc_final: 0.9375 (mmm) REVERT: A 182 MET cc_start: 0.9396 (mmm) cc_final: 0.9144 (mmm) REVERT: A 226 PHE cc_start: 0.9075 (m-10) cc_final: 0.8671 (m-80) REVERT: A 445 MET cc_start: 0.8611 (mmm) cc_final: 0.8196 (mmm) REVERT: B 26 MET cc_start: 0.9109 (ttt) cc_final: 0.8702 (tpp) REVERT: B 175 MET cc_start: 0.8700 (mtm) cc_final: 0.8461 (mtp) REVERT: B 304 MET cc_start: 0.9300 (ttp) cc_final: 0.8755 (ttp) REVERT: B 332 PHE cc_start: 0.9506 (OUTLIER) cc_final: 0.8899 (t80) REVERT: B 399 MET cc_start: 0.9211 (tpp) cc_final: 0.8606 (tmm) REVERT: C 95 CYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8391 (p) REVERT: C 131 MET cc_start: 0.9601 (ppp) cc_final: 0.9384 (pmm) REVERT: C 362 MET cc_start: 0.9726 (mmp) cc_final: 0.9381 (mmm) REVERT: C 442 GLU cc_start: 0.9151 (OUTLIER) cc_final: 0.8793 (pm20) REVERT: D 83 MET cc_start: 0.8594 (mtt) cc_final: 0.8003 (tmm) REVERT: D 86 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8977 (pp) REVERT: D 128 MET cc_start: 0.8497 (mmm) cc_final: 0.7775 (tpt) REVERT: E 378 MET cc_start: 0.8042 (mmt) cc_final: 0.7816 (tpp) outliers start: 15 outliers final: 10 residues processed: 71 average time/residue: 0.2332 time to fit residues: 28.1856 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 : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 CYS 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 95 CYS 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 C residue 490 VAL 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 94 optimal weight: 20.0000 chunk 72 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 chunk 60 optimal weight: 0.0050 chunk 158 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 195 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 overall best weight: 3.1200 ------------------------------------------------------------------------------- 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 539 HIS C 565 HIS ** E 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.036000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.024518 restraints weight = 169131.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.025271 restraints weight = 91006.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.025792 restraints weight = 61498.525| |-----------------------------------------------------------------------------| r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15674 Z= 0.158 Angle : 0.619 12.742 21303 Z= 0.306 Chirality : 0.041 0.215 2523 Planarity : 0.003 0.044 2650 Dihedral : 5.079 54.756 2367 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.10 % Allowed : 13.76 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.20), residues: 1967 helix: 1.97 (0.21), residues: 687 sheet: -0.49 (0.31), residues: 268 loop : -1.17 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 660 HIS 0.003 0.001 HIS C 665 PHE 0.014 0.001 PHE B 87 TYR 0.012 0.001 TYR A 197 ARG 0.002 0.000 ARG A 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00209 ( 8) link_NAG-ASN : angle 2.67286 ( 24) link_BETA1-4 : bond 0.00282 ( 4) link_BETA1-4 : angle 1.36307 ( 12) hydrogen bonds : bond 0.04550 ( 603) hydrogen bonds : angle 4.77928 ( 1716) SS BOND : bond 0.00206 ( 4) SS BOND : angle 0.67683 ( 8) covalent geometry : bond 0.00340 (15658) covalent geometry : angle 0.61256 (21259) *********************** 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 74 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.9118 (ttp) cc_final: 0.8715 (tmm) REVERT: A 174 MET cc_start: 0.9730 (mmm) cc_final: 0.9455 (mmm) REVERT: A 182 MET cc_start: 0.9523 (mmm) cc_final: 0.9183 (mmm) REVERT: A 445 MET cc_start: 0.8558 (mmm) cc_final: 0.8206 (mmm) REVERT: B 26 MET cc_start: 0.9270 (ttt) cc_final: 0.8805 (tpp) REVERT: B 175 MET cc_start: 0.8787 (mtm) cc_final: 0.8505 (mtp) REVERT: B 304 MET cc_start: 0.9322 (ttp) cc_final: 0.8747 (ttp) REVERT: B 332 PHE cc_start: 0.9492 (OUTLIER) cc_final: 0.8831 (t80) REVERT: B 341 MET cc_start: 0.9599 (mmm) cc_final: 0.9374 (mmm) REVERT: C 95 CYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8085 (p) REVERT: C 131 MET cc_start: 0.9626 (ppp) cc_final: 0.9412 (pmm) REVERT: C 362 MET cc_start: 0.9746 (mmp) cc_final: 0.9394 (mmm) REVERT: C 442 GLU cc_start: 0.9273 (OUTLIER) cc_final: 0.8890 (pm20) REVERT: D 83 MET cc_start: 0.8610 (mtt) cc_final: 0.7974 (tmm) REVERT: D 86 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8960 (pp) REVERT: D 128 MET cc_start: 0.8460 (mmm) cc_final: 0.7724 (tpt) outliers start: 18 outliers final: 11 residues processed: 73 average time/residue: 0.2249 time to fit residues: 27.9206 Evaluate side-chains 70 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 CYS Chi-restraints excluded: chain B residue 182 MET 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 95 CYS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain D residue 31 ASN 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 182 optimal weight: 8.9990 chunk 109 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 160 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 161 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 86 optimal weight: 20.0000 overall best weight: 2.2984 ------------------------------------------------------------------------------- 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 = 0.3274 r_free = 0.3274 target = 0.036272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.024752 restraints weight = 171641.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.025531 restraints weight = 91174.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.026049 restraints weight = 60975.369| |-----------------------------------------------------------------------------| r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15674 Z= 0.128 Angle : 0.606 13.280 21303 Z= 0.296 Chirality : 0.041 0.239 2523 Planarity : 0.003 0.046 2650 Dihedral : 4.884 52.732 2367 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.97 % Allowed : 13.89 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.20), residues: 1967 helix: 2.06 (0.21), residues: 688 sheet: -0.46 (0.31), residues: 268 loop : -1.17 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 320 HIS 0.002 0.001 HIS B 237 PHE 0.013 0.001 PHE B 87 TYR 0.010 0.001 TYR E 368 ARG 0.001 0.000 ARG B 402 Details of bonding type rmsd link_NAG-ASN : bond 0.00201 ( 8) link_NAG-ASN : angle 2.78314 ( 24) link_BETA1-4 : bond 0.00251 ( 4) link_BETA1-4 : angle 1.28547 ( 12) hydrogen bonds : bond 0.04270 ( 603) hydrogen bonds : angle 4.67141 ( 1716) SS BOND : bond 0.00180 ( 4) SS BOND : angle 0.52766 ( 8) covalent geometry : bond 0.00277 (15658) covalent geometry : angle 0.59824 (21259) ********************** 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 73 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.9173 (ttp) cc_final: 0.8741 (tmm) REVERT: A 174 MET cc_start: 0.9640 (mmm) cc_final: 0.9379 (mmm) REVERT: A 182 MET cc_start: 0.9489 (mmm) cc_final: 0.9154 (mmm) REVERT: A 444 MET cc_start: 0.8886 (ptp) cc_final: 0.8207 (mtt) REVERT: B 26 MET cc_start: 0.9219 (ttt) cc_final: 0.8789 (tpp) REVERT: B 175 MET cc_start: 0.8749 (mtm) cc_final: 0.8447 (mtp) REVERT: B 304 MET cc_start: 0.9312 (ttp) cc_final: 0.8751 (ttp) REVERT: B 332 PHE cc_start: 0.9484 (OUTLIER) cc_final: 0.8803 (t80) REVERT: B 341 MET cc_start: 0.9558 (mmm) cc_final: 0.9352 (mmm) REVERT: C 95 CYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8272 (p) REVERT: C 131 MET cc_start: 0.9630 (ppp) cc_final: 0.9399 (pmm) REVERT: C 362 MET cc_start: 0.9739 (mmp) cc_final: 0.9387 (mmm) REVERT: C 442 GLU cc_start: 0.9276 (OUTLIER) cc_final: 0.8886 (pm20) REVERT: D 83 MET cc_start: 0.8550 (mtt) cc_final: 0.7907 (tmm) REVERT: D 86 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8889 (pp) REVERT: D 128 MET cc_start: 0.8487 (mmm) cc_final: 0.7744 (tpt) outliers start: 16 outliers final: 12 residues processed: 72 average time/residue: 0.2402 time to fit residues: 29.1658 Evaluate side-chains 72 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 CYS Chi-restraints excluded: chain B residue 182 MET 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 95 CYS 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 C residue 490 VAL Chi-restraints excluded: chain D residue 31 ASN 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 25 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 112 optimal weight: 6.9990 chunk 144 optimal weight: 0.6980 chunk 6 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.036638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.025332 restraints weight = 165445.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.026129 restraints weight = 88882.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.026661 restraints weight = 59293.264| |-----------------------------------------------------------------------------| r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15674 Z= 0.100 Angle : 0.599 13.521 21303 Z= 0.289 Chirality : 0.041 0.233 2523 Planarity : 0.003 0.046 2650 Dihedral : 4.635 52.954 2367 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.97 % Allowed : 13.89 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.20), residues: 1967 helix: 2.12 (0.21), residues: 695 sheet: -0.33 (0.32), residues: 268 loop : -1.17 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 320 HIS 0.002 0.000 HIS B 237 PHE 0.012 0.001 PHE B 87 TYR 0.015 0.001 TYR E 368 ARG 0.002 0.000 ARG C 331 Details of bonding type rmsd link_NAG-ASN : bond 0.00187 ( 8) link_NAG-ASN : angle 2.80598 ( 24) link_BETA1-4 : bond 0.00328 ( 4) link_BETA1-4 : angle 1.25079 ( 12) hydrogen bonds : bond 0.03877 ( 603) hydrogen bonds : angle 4.53989 ( 1716) SS BOND : bond 0.00155 ( 4) SS BOND : angle 0.57432 ( 8) covalent geometry : bond 0.00213 (15658) covalent geometry : angle 0.59097 (21259) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4818.77 seconds wall clock time: 85 minutes 45.79 seconds (5145.79 seconds total)