Starting phenix.real_space_refine on Sun Jul 27 07:35:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xss_38627/07_2025/8xss_38627.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xss_38627/07_2025/8xss_38627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xss_38627/07_2025/8xss_38627.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xss_38627/07_2025/8xss_38627.map" model { file = "/net/cci-nas-00/data/ceres_data/8xss_38627/07_2025/8xss_38627.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xss_38627/07_2025/8xss_38627.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 33 5.16 5 C 5781 2.51 5 N 1612 2.21 5 O 1690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9119 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4348 Classifications: {'peptide': 574} Link IDs: {'PTRANS': 19, 'TRANS': 554} Chain: "B" Number of atoms: 4743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4743 Classifications: {'peptide': 619} Link IDs: {'PTRANS': 18, 'TRANS': 600} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.79, per 1000 atoms: 0.63 Number of scatterers: 9119 At special positions: 0 Unit cell: (69.888, 91.52, 148.928, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 33 16.00 P 2 15.00 Mg 1 11.99 O 1690 8.00 N 1612 7.00 C 5781 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.18 Conformation dependent library (CDL) restraints added in 1.1 seconds 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2194 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 4 sheets defined 64.7% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid -1 through 10 removed outlier: 4.271A pdb=" N TRP A 3 " --> pdb=" O SER A -1 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TYR A 9 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL A 10 " --> pdb=" O LEU A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 30 removed outlier: 3.645A pdb=" N ILE A 26 " --> pdb=" O VAL A 22 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 45 removed outlier: 3.861A pdb=" N THR A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A 40 " --> pdb=" O THR A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 71 removed outlier: 3.963A pdb=" N ILE A 54 " --> pdb=" O ASP A 50 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A 55 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ALA A 59 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A 69 " --> pdb=" O THR A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 99 removed outlier: 3.673A pdb=" N ARG A 81 " --> pdb=" O PHE A 77 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 82 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N THR A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLY A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS A 88 " --> pdb=" O THR A 84 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N LEU A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 110 removed outlier: 3.563A pdb=" N ARG A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 130 removed outlier: 3.513A pdb=" N HIS A 124 " --> pdb=" O ASN A 120 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE A 125 " --> pdb=" O ASP A 121 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN A 130 " --> pdb=" O GLN A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 153 Processing helix chain 'A' and resid 154 through 156 No H-bonds generated for 'chain 'A' and resid 154 through 156' Processing helix chain 'A' and resid 157 through 203 removed outlier: 4.385A pdb=" N LEU A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Proline residue: A 166 - end of helix removed outlier: 3.780A pdb=" N ASN A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE A 175 " --> pdb=" O ALA A 171 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 176 " --> pdb=" O ASN A 172 " (cutoff:3.500A) Proline residue: A 181 - end of helix removed outlier: 3.567A pdb=" N GLN A 187 " --> pdb=" O PHE A 183 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN A 194 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 196 " --> pdb=" O GLY A 192 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY A 203 " --> pdb=" O ASP A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 210 Processing helix chain 'A' and resid 220 through 233 removed outlier: 3.514A pdb=" N GLN A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.675A pdb=" N TRP A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 265 removed outlier: 3.619A pdb=" N VAL A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR A 245 " --> pdb=" O MET A 241 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TRP A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG A 263 " --> pdb=" O PHE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 293 removed outlier: 4.050A pdb=" N LEU A 274 " --> pdb=" O GLN A 270 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 313 removed outlier: 3.861A pdb=" N VAL A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N CYS A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 382 removed outlier: 3.678A pdb=" N LEU A 377 " --> pdb=" O GLY A 373 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE A 378 " --> pdb=" O LYS A 374 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 402 Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.701A pdb=" N ALA A 410 " --> pdb=" O GLN A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 430 through 433 Processing helix chain 'A' and resid 437 through 448 removed outlier: 3.570A pdb=" N TRP A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 445 " --> pdb=" O MET A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 455 removed outlier: 3.779A pdb=" N VAL A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 503 through 518 Processing helix chain 'A' and resid 552 through 558 removed outlier: 4.225A pdb=" N ALA A 558 " --> pdb=" O ASP A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 569 removed outlier: 3.742A pdb=" N SER A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 27 Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 31 through 45 removed outlier: 3.626A pdb=" N VAL B 38 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU B 41 " --> pdb=" O ALA B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 68 removed outlier: 3.968A pdb=" N ARG B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 88 Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 109 through 158 removed outlier: 3.672A pdb=" N VAL B 113 " --> pdb=" O ASP B 109 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL B 131 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL B 133 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR B 145 " --> pdb=" O THR B 141 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA B 148 " --> pdb=" O ARG B 144 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN B 154 " --> pdb=" O ARG B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 167 removed outlier: 3.840A pdb=" N PHE B 165 " --> pdb=" O PRO B 161 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 177 removed outlier: 3.632A pdb=" N ARG B 176 " --> pdb=" O VAL B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 190 Processing helix chain 'B' and resid 195 through 213 removed outlier: 3.949A pdb=" N VAL B 202 " --> pdb=" O SER B 198 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N VAL B 205 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 206 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR B 211 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE B 212 " --> pdb=" O MET B 208 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER B 213 " --> pdb=" O MET B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 222 removed outlier: 3.689A pdb=" N LEU B 218 " --> pdb=" O PRO B 214 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR B 220 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 238 removed outlier: 3.766A pdb=" N VAL B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR B 235 " --> pdb=" O THR B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 262 removed outlier: 3.664A pdb=" N TRP B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY B 262 " --> pdb=" O GLU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 268 Processing helix chain 'B' and resid 271 through 299 removed outlier: 4.637A pdb=" N GLU B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN B 288 " --> pdb=" O SER B 284 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER B 289 " --> pdb=" O GLU B 285 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLY B 292 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA B 293 " --> pdb=" O SER B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 309 through 325 removed outlier: 3.663A pdb=" N ALA B 314 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 345 removed outlier: 3.554A pdb=" N ALA B 335 " --> pdb=" O GLY B 331 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN B 338 " --> pdb=" O GLN B 334 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN B 345 " --> pdb=" O ARG B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 363 removed outlier: 3.912A pdb=" N THR B 356 " --> pdb=" O GLY B 352 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER B 359 " --> pdb=" O ASN B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 372 removed outlier: 3.900A pdb=" N PHE B 368 " --> pdb=" O ALA B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 438 Processing helix chain 'B' and resid 459 through 468 removed outlier: 4.033A pdb=" N GLY B 468 " --> pdb=" O ARG B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 487 Processing helix chain 'B' and resid 493 through 503 removed outlier: 3.574A pdb=" N GLU B 499 " --> pdb=" O ASP B 495 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA B 503 " --> pdb=" O GLU B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 511 Processing helix chain 'B' and resid 529 through 545 removed outlier: 3.830A pdb=" N THR B 537 " --> pdb=" O LYS B 533 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 544 " --> pdb=" O ARG B 540 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 570 Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 608 through 614 Processing helix chain 'B' and resid 617 through 627 Processing sheet with id=AA1, first strand: chain 'A' and resid 335 through 341 removed outlier: 5.123A pdb=" N HIS A 337 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N PHE A 356 " --> pdb=" O HIS A 337 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N PHE A 341 " --> pdb=" O GLN A 352 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N GLN A 352 " --> pdb=" O PHE A 341 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 411 through 414 removed outlier: 6.445A pdb=" N GLY A 412 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ASP A 496 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL A 414 " --> pdb=" O ASP A 496 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR A 363 " --> pdb=" O GLN A 538 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL A 540 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ALA A 365 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ILE A 542 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N VAL A 367 " --> pdb=" O ILE A 542 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A 549 " --> pdb=" O VAL A 541 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 423 through 424 removed outlier: 4.152A pdb=" N GLY A 423 " --> pdb=" O VAL A 465 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 469 through 470 removed outlier: 6.582A pdb=" N VAL B 470 " --> pdb=" O ASP B 552 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU B 605 " --> pdb=" O VAL B 597 " (cutoff:3.500A) 449 hydrogen bonds defined for protein. 1326 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.43 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3076 1.34 - 1.46: 1905 1.46 - 1.58: 4228 1.58 - 1.70: 4 1.70 - 1.81: 61 Bond restraints: 9274 Sorted by residual: bond pdb=" CB PRO B 416 " pdb=" CG PRO B 416 " ideal model delta sigma weight residual 1.492 1.607 -0.115 5.00e-02 4.00e+02 5.32e+00 bond pdb=" C VAL A 165 " pdb=" N PRO A 166 " ideal model delta sigma weight residual 1.336 1.362 -0.026 1.23e-02 6.61e+03 4.53e+00 bond pdb=" CA ASP B 522 " pdb=" CB ASP B 522 " ideal model delta sigma weight residual 1.530 1.558 -0.027 1.69e-02 3.50e+03 2.64e+00 bond pdb=" CB ASN B 355 " pdb=" CG ASN B 355 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.30e+00 bond pdb=" N ARG A 217 " pdb=" CA ARG A 217 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.12e+00 ... (remaining 9269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 12369 2.39 - 4.78: 212 4.78 - 7.17: 33 7.17 - 9.56: 12 9.56 - 11.95: 2 Bond angle restraints: 12628 Sorted by residual: angle pdb=" C VAL A 165 " pdb=" N PRO A 166 " pdb=" CA PRO A 166 " ideal model delta sigma weight residual 119.19 112.59 6.60 1.06e+00 8.90e-01 3.88e+01 angle pdb=" N VAL A 19 " pdb=" CA VAL A 19 " pdb=" C VAL A 19 " ideal model delta sigma weight residual 113.43 106.83 6.60 1.09e+00 8.42e-01 3.67e+01 angle pdb=" N ILE B 48 " pdb=" CA ILE B 48 " pdb=" C ILE B 48 " ideal model delta sigma weight residual 112.96 107.36 5.60 1.00e+00 1.00e+00 3.14e+01 angle pdb=" N ILE B 192 " pdb=" CA ILE B 192 " pdb=" C ILE B 192 " ideal model delta sigma weight residual 113.71 108.44 5.27 9.50e-01 1.11e+00 3.08e+01 angle pdb=" CA PRO B 416 " pdb=" N PRO B 416 " pdb=" CD PRO B 416 " ideal model delta sigma weight residual 112.00 105.04 6.96 1.40e+00 5.10e-01 2.47e+01 ... (remaining 12623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.29: 5366 34.29 - 68.58: 129 68.58 - 102.88: 13 102.88 - 137.17: 2 137.17 - 171.46: 1 Dihedral angle restraints: 5511 sinusoidal: 2102 harmonic: 3409 Sorted by residual: dihedral pdb=" O2A ADP B 701 " pdb=" O3A ADP B 701 " pdb=" PA ADP B 701 " pdb=" PB ADP B 701 " ideal model delta sinusoidal sigma weight residual -60.00 111.46 -171.46 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" O1B ADP B 701 " pdb=" O3A ADP B 701 " pdb=" PB ADP B 701 " pdb=" PA ADP B 701 " ideal model delta sinusoidal sigma weight residual -60.00 71.34 -131.35 1 2.00e+01 2.50e-03 3.99e+01 dihedral pdb=" C5' ADP B 701 " pdb=" O5' ADP B 701 " pdb=" PA ADP B 701 " pdb=" O2A ADP B 701 " ideal model delta sinusoidal sigma weight residual -60.00 43.74 -103.73 1 2.00e+01 2.50e-03 2.97e+01 ... (remaining 5508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1118 0.046 - 0.091: 331 0.091 - 0.136: 65 0.136 - 0.182: 4 0.182 - 0.227: 2 Chirality restraints: 1520 Sorted by residual: chirality pdb=" CB ILE B 448 " pdb=" CA ILE B 448 " pdb=" CG1 ILE B 448 " pdb=" CG2 ILE B 448 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB ILE A 487 " pdb=" CA ILE A 487 " pdb=" CG1 ILE A 487 " pdb=" CG2 ILE A 487 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.53e-01 chirality pdb=" CA ASP A 154 " pdb=" N ASP A 154 " pdb=" C ASP A 154 " pdb=" CB ASP A 154 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.49e-01 ... (remaining 1517 not shown) Planarity restraints: 1617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 415 " -0.072 5.00e-02 4.00e+02 1.05e-01 1.78e+01 pdb=" N PRO B 416 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO B 416 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO B 416 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 213 " 0.044 5.00e-02 4.00e+02 6.76e-02 7.32e+00 pdb=" N PRO A 214 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 214 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 214 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 594 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.92e+00 pdb=" C LEU B 594 " -0.045 2.00e-02 2.50e+03 pdb=" O LEU B 594 " 0.017 2.00e-02 2.50e+03 pdb=" N ILE B 595 " 0.015 2.00e-02 2.50e+03 ... (remaining 1614 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 106 2.62 - 3.19: 8270 3.19 - 3.76: 14240 3.76 - 4.33: 19567 4.33 - 4.90: 32276 Nonbonded interactions: 74459 Sorted by model distance: nonbonded pdb=" O3B ADP B 701 " pdb="MG MG B 702 " model vdw 2.048 2.170 nonbonded pdb=" OG1 THR B 431 " pdb="MG MG B 702 " model vdw 2.141 2.170 nonbonded pdb=" OG1 THR A 36 " pdb=" OH TYR A 280 " model vdw 2.214 3.040 nonbonded pdb=" OD2 ASP B 166 " pdb=" OH TYR B 441 " model vdw 2.227 3.040 nonbonded pdb=" O LEU B 321 " pdb=" OG1 THR B 325 " model vdw 2.238 3.040 ... (remaining 74454 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 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: 0.460 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.760 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 : 0.003 0.115 9274 Z= 0.161 Angle : 0.812 11.950 12628 Z= 0.463 Chirality : 0.044 0.227 1520 Planarity : 0.005 0.105 1617 Dihedral : 15.457 171.460 3317 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.23 % Favored : 92.60 % Rotamer: Outliers : 1.04 % Allowed : 18.60 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.22), residues: 1189 helix: -1.78 (0.18), residues: 734 sheet: -1.90 (0.63), residues: 47 loop : -2.42 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 229 HIS 0.010 0.001 HIS A 337 PHE 0.024 0.001 PHE A 453 TYR 0.012 0.001 TYR B 482 ARG 0.007 0.000 ARG B 561 Details of bonding type rmsd hydrogen bonds : bond 0.19950 ( 449) hydrogen bonds : angle 7.57104 ( 1326) covalent geometry : bond 0.00335 ( 9274) covalent geometry : angle 0.81164 (12628) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 155 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8051 (m-30) REVERT: A 214 PRO cc_start: 0.8020 (Cg_exo) cc_final: 0.7801 (Cg_endo) REVERT: A 478 GLN cc_start: 0.7778 (tp40) cc_final: 0.7163 (mt0) REVERT: B 31 GLN cc_start: 0.6599 (OUTLIER) cc_final: 0.6303 (mm-40) REVERT: B 180 ASP cc_start: 0.8416 (t0) cc_final: 0.8134 (t0) REVERT: B 281 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7244 (mt-10) REVERT: B 345 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.7055 (tt0) REVERT: B 353 MET cc_start: 0.7975 (ttm) cc_final: 0.7482 (mtm) REVERT: B 438 MET cc_start: 0.8898 (mmm) cc_final: 0.8606 (tpp) REVERT: B 472 GLN cc_start: 0.8196 (tt0) cc_final: 0.7976 (tt0) outliers start: 10 outliers final: 2 residues processed: 162 average time/residue: 0.1927 time to fit residues: 45.5300 Evaluate side-chains 148 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 143 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 345 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 0.3980 chunk 47 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.164503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.120598 restraints weight = 10807.051| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.26 r_work: 0.3274 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9274 Z= 0.135 Angle : 0.678 12.197 12628 Z= 0.337 Chirality : 0.043 0.201 1520 Planarity : 0.005 0.059 1617 Dihedral : 8.196 153.963 1330 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 4.18 % Allowed : 15.78 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.23), residues: 1189 helix: -1.22 (0.18), residues: 758 sheet: -2.46 (0.57), residues: 64 loop : -2.06 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 229 HIS 0.008 0.001 HIS A 337 PHE 0.016 0.001 PHE A 453 TYR 0.019 0.001 TYR B 482 ARG 0.004 0.000 ARG A 326 Details of bonding type rmsd hydrogen bonds : bond 0.03510 ( 449) hydrogen bonds : angle 4.50708 ( 1326) covalent geometry : bond 0.00311 ( 9274) covalent geometry : angle 0.67840 (12628) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 160 time to evaluate : 0.876 Fit side-chains revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.8057 (m-30) REVERT: A 121 ASP cc_start: 0.8823 (OUTLIER) cc_final: 0.8542 (m-30) REVERT: A 195 ARG cc_start: 0.7762 (ttp80) cc_final: 0.7077 (tpt170) REVERT: A 300 ARG cc_start: 0.7224 (OUTLIER) cc_final: 0.6873 (ttp80) REVERT: B 180 ASP cc_start: 0.8380 (t0) cc_final: 0.8044 (t0) REVERT: B 213 SER cc_start: 0.8699 (t) cc_final: 0.7981 (p) REVERT: B 257 GLU cc_start: 0.8564 (tp30) cc_final: 0.8319 (tp30) REVERT: B 345 GLN cc_start: 0.7806 (tt0) cc_final: 0.7583 (tt0) REVERT: B 353 MET cc_start: 0.7946 (ttm) cc_final: 0.7342 (mtm) REVERT: B 392 GLU cc_start: 0.7797 (tt0) cc_final: 0.7580 (pt0) REVERT: B 472 GLN cc_start: 0.8336 (tt0) cc_final: 0.8091 (tt0) REVERT: B 613 LEU cc_start: 0.8892 (tp) cc_final: 0.8660 (tp) REVERT: B 621 GLU cc_start: 0.8554 (tt0) cc_final: 0.7367 (tm-30) outliers start: 40 outliers final: 20 residues processed: 187 average time/residue: 0.1997 time to fit residues: 53.1541 Evaluate side-chains 161 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 604 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 32 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 45 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 93 optimal weight: 0.1980 chunk 99 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN B 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.162558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.121052 restraints weight = 10955.292| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.04 r_work: 0.3250 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9274 Z= 0.146 Angle : 0.677 12.941 12628 Z= 0.330 Chirality : 0.043 0.207 1520 Planarity : 0.004 0.059 1617 Dihedral : 7.065 129.919 1321 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 4.49 % Allowed : 16.41 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.24), residues: 1189 helix: -0.90 (0.19), residues: 762 sheet: -2.10 (0.60), residues: 64 loop : -1.97 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 229 HIS 0.009 0.001 HIS A 337 PHE 0.010 0.001 PHE B 295 TYR 0.012 0.001 TYR B 482 ARG 0.003 0.000 ARG A 91 Details of bonding type rmsd hydrogen bonds : bond 0.03561 ( 449) hydrogen bonds : angle 4.26291 ( 1326) covalent geometry : bond 0.00345 ( 9274) covalent geometry : angle 0.67696 (12628) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 142 time to evaluate : 1.046 Fit side-chains REVERT: A 8 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.7619 (tp40) REVERT: A 183 PHE cc_start: 0.9152 (OUTLIER) cc_final: 0.8650 (t80) REVERT: A 195 ARG cc_start: 0.7828 (ttp80) cc_final: 0.7097 (tpt170) REVERT: A 326 ARG cc_start: 0.7488 (mmt-90) cc_final: 0.7034 (mmt-90) REVERT: A 352 GLN cc_start: 0.7368 (tm-30) cc_final: 0.7089 (tm-30) REVERT: A 535 GLU cc_start: 0.8401 (tp30) cc_final: 0.7977 (tp30) REVERT: B 180 ASP cc_start: 0.8374 (t0) cc_final: 0.8030 (t0) REVERT: B 213 SER cc_start: 0.8709 (t) cc_final: 0.7903 (p) REVERT: B 281 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7838 (mt-10) REVERT: B 353 MET cc_start: 0.7953 (ttm) cc_final: 0.7325 (mtm) REVERT: B 472 GLN cc_start: 0.8382 (tt0) cc_final: 0.8112 (tt0) REVERT: B 613 LEU cc_start: 0.8915 (tp) cc_final: 0.8705 (tp) REVERT: B 621 GLU cc_start: 0.8549 (tt0) cc_final: 0.7421 (tm-30) outliers start: 43 outliers final: 31 residues processed: 171 average time/residue: 0.1926 time to fit residues: 48.9143 Evaluate side-chains 164 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLN Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 604 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 95 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 100 optimal weight: 8.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN B 139 ASN B 143 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.159527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.117425 restraints weight = 10937.421| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.32 r_work: 0.3162 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 9274 Z= 0.192 Angle : 0.705 14.981 12628 Z= 0.345 Chirality : 0.045 0.218 1520 Planarity : 0.005 0.061 1617 Dihedral : 6.751 116.470 1319 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 5.43 % Allowed : 15.78 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.24), residues: 1189 helix: -0.80 (0.19), residues: 756 sheet: -2.02 (0.62), residues: 64 loop : -1.83 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 229 HIS 0.008 0.001 HIS A 337 PHE 0.015 0.002 PHE A 453 TYR 0.012 0.001 TYR A 9 ARG 0.006 0.000 ARG A 488 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 449) hydrogen bonds : angle 4.33184 ( 1326) covalent geometry : bond 0.00464 ( 9274) covalent geometry : angle 0.70528 (12628) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 131 time to evaluate : 0.906 Fit side-chains REVERT: A 8 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7426 (tp40) REVERT: A 136 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7959 (mp) REVERT: A 183 PHE cc_start: 0.9152 (OUTLIER) cc_final: 0.8695 (t80) REVERT: A 195 ARG cc_start: 0.7845 (ttp80) cc_final: 0.7078 (tpt170) REVERT: A 217 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7760 (ptt180) REVERT: A 326 ARG cc_start: 0.7523 (mmt-90) cc_final: 0.7074 (mpt180) REVERT: A 535 GLU cc_start: 0.8466 (tp30) cc_final: 0.8059 (tp30) REVERT: B 31 GLN cc_start: 0.6835 (OUTLIER) cc_final: 0.6480 (mm-40) REVERT: B 190 MET cc_start: 0.8030 (tmm) cc_final: 0.7783 (tmm) REVERT: B 245 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.7139 (tt0) REVERT: B 281 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7803 (mt-10) REVERT: B 605 GLU cc_start: 0.8145 (pm20) cc_final: 0.7768 (pm20) REVERT: B 613 LEU cc_start: 0.8906 (tp) cc_final: 0.8703 (tp) REVERT: B 621 GLU cc_start: 0.8578 (tt0) cc_final: 0.7461 (tm-30) outliers start: 52 outliers final: 35 residues processed: 167 average time/residue: 0.2032 time to fit residues: 49.2146 Evaluate side-chains 174 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 133 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLN Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 604 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 104 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 64 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN B 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.161205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.119291 restraints weight = 10953.325| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.09 r_work: 0.3197 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9274 Z= 0.152 Angle : 0.678 15.048 12628 Z= 0.330 Chirality : 0.043 0.194 1520 Planarity : 0.004 0.060 1617 Dihedral : 6.471 108.286 1319 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 4.60 % Allowed : 17.55 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.24), residues: 1189 helix: -0.67 (0.19), residues: 761 sheet: -1.91 (0.63), residues: 64 loop : -1.82 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 229 HIS 0.007 0.001 HIS A 337 PHE 0.011 0.001 PHE B 295 TYR 0.014 0.001 TYR A 9 ARG 0.003 0.000 ARG A 488 Details of bonding type rmsd hydrogen bonds : bond 0.03467 ( 449) hydrogen bonds : angle 4.18409 ( 1326) covalent geometry : bond 0.00361 ( 9274) covalent geometry : angle 0.67847 (12628) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 137 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.7502 (tp40) REVERT: A 136 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7954 (mp) REVERT: A 183 PHE cc_start: 0.9161 (OUTLIER) cc_final: 0.8708 (t80) REVERT: A 195 ARG cc_start: 0.7813 (ttp80) cc_final: 0.7070 (tpt170) REVERT: A 217 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7563 (ptt180) REVERT: A 300 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6308 (ttp80) REVERT: A 326 ARG cc_start: 0.7479 (mmt-90) cc_final: 0.7003 (mpt180) REVERT: A 352 GLN cc_start: 0.7381 (tm-30) cc_final: 0.7077 (tm-30) REVERT: A 535 GLU cc_start: 0.8463 (tp30) cc_final: 0.8061 (tp30) REVERT: B 31 GLN cc_start: 0.6707 (OUTLIER) cc_final: 0.6377 (mm-40) REVERT: B 190 MET cc_start: 0.7990 (tmm) cc_final: 0.7705 (tmm) REVERT: B 245 GLN cc_start: 0.7367 (OUTLIER) cc_final: 0.7002 (tt0) REVERT: B 281 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7784 (mt-10) REVERT: B 605 GLU cc_start: 0.8260 (pm20) cc_final: 0.7647 (pm20) REVERT: B 613 LEU cc_start: 0.8916 (tp) cc_final: 0.8713 (tp) REVERT: B 621 GLU cc_start: 0.8600 (tt0) cc_final: 0.7491 (tm-30) outliers start: 44 outliers final: 32 residues processed: 169 average time/residue: 0.2973 time to fit residues: 73.7133 Evaluate side-chains 169 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 130 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLN Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 604 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 2 optimal weight: 1.9990 chunk 96 optimal weight: 0.0970 chunk 98 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 97 optimal weight: 0.2980 chunk 42 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN B 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.162039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.118063 restraints weight = 10844.686| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.25 r_work: 0.3271 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9274 Z= 0.125 Angle : 0.662 15.779 12628 Z= 0.319 Chirality : 0.042 0.179 1520 Planarity : 0.004 0.059 1617 Dihedral : 6.155 98.968 1319 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 4.81 % Allowed : 18.18 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.25), residues: 1189 helix: -0.47 (0.19), residues: 762 sheet: -1.81 (0.64), residues: 64 loop : -1.81 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 229 HIS 0.007 0.001 HIS A 337 PHE 0.010 0.001 PHE A 453 TYR 0.012 0.001 TYR A 9 ARG 0.003 0.000 ARG B 561 Details of bonding type rmsd hydrogen bonds : bond 0.03182 ( 449) hydrogen bonds : angle 4.05520 ( 1326) covalent geometry : bond 0.00289 ( 9274) covalent geometry : angle 0.66166 (12628) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 143 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: A 8 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.7528 (tp40) REVERT: A 136 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7962 (mp) REVERT: A 183 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.8684 (t80) REVERT: A 195 ARG cc_start: 0.7853 (ttp80) cc_final: 0.7120 (tpt170) REVERT: A 217 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7566 (ptt-90) REVERT: A 300 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.6318 (ttp80) REVERT: A 326 ARG cc_start: 0.7523 (mmt-90) cc_final: 0.7029 (mpt180) REVERT: A 535 GLU cc_start: 0.8441 (tp30) cc_final: 0.8042 (tp30) REVERT: B 31 GLN cc_start: 0.6607 (OUTLIER) cc_final: 0.6195 (mm-40) REVERT: B 180 ASP cc_start: 0.8324 (t0) cc_final: 0.7882 (t0) REVERT: B 190 MET cc_start: 0.8010 (tmm) cc_final: 0.7740 (tmm) REVERT: B 257 GLU cc_start: 0.8575 (tp30) cc_final: 0.8330 (tp30) REVERT: B 605 GLU cc_start: 0.8259 (pm20) cc_final: 0.7637 (pm20) REVERT: B 621 GLU cc_start: 0.8598 (tt0) cc_final: 0.7488 (tm-30) outliers start: 46 outliers final: 31 residues processed: 177 average time/residue: 0.1936 time to fit residues: 49.5751 Evaluate side-chains 167 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLN Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 604 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 39 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN B 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.162621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.120054 restraints weight = 10897.130| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.25 r_work: 0.3252 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9274 Z= 0.140 Angle : 0.681 17.392 12628 Z= 0.326 Chirality : 0.043 0.182 1520 Planarity : 0.004 0.060 1617 Dihedral : 6.043 92.687 1319 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 4.81 % Allowed : 18.60 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.25), residues: 1189 helix: -0.43 (0.19), residues: 761 sheet: -1.93 (0.61), residues: 63 loop : -1.80 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 15 HIS 0.007 0.001 HIS A 337 PHE 0.010 0.001 PHE A 453 TYR 0.012 0.001 TYR A 9 ARG 0.003 0.000 ARG A 91 Details of bonding type rmsd hydrogen bonds : bond 0.03281 ( 449) hydrogen bonds : angle 4.06139 ( 1326) covalent geometry : bond 0.00331 ( 9274) covalent geometry : angle 0.68127 (12628) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 142 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 8 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.7553 (tp40) REVERT: A 43 ASP cc_start: 0.8238 (t0) cc_final: 0.7911 (m-30) REVERT: A 136 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7917 (mp) REVERT: A 183 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8745 (t80) REVERT: A 195 ARG cc_start: 0.7860 (ttp80) cc_final: 0.7098 (tpt170) REVERT: A 217 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7585 (ptt180) REVERT: A 326 ARG cc_start: 0.7481 (mmt-90) cc_final: 0.7050 (mmt-90) REVERT: B 31 GLN cc_start: 0.6463 (OUTLIER) cc_final: 0.5954 (mm-40) REVERT: B 180 ASP cc_start: 0.8364 (t0) cc_final: 0.7890 (t0) REVERT: B 190 MET cc_start: 0.7946 (tmm) cc_final: 0.7645 (tmm) REVERT: B 257 GLU cc_start: 0.8632 (tp30) cc_final: 0.8384 (tp30) REVERT: B 281 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7751 (mt-10) REVERT: B 605 GLU cc_start: 0.8276 (pm20) cc_final: 0.7655 (pm20) REVERT: B 621 GLU cc_start: 0.8613 (tt0) cc_final: 0.7520 (tm-30) outliers start: 46 outliers final: 35 residues processed: 176 average time/residue: 0.1758 time to fit residues: 45.2501 Evaluate side-chains 175 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 135 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLN Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 604 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 81 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 91 optimal weight: 0.3980 chunk 7 optimal weight: 0.0770 chunk 19 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 96 optimal weight: 0.0030 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 overall best weight: 0.4348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN B 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.165116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.121237 restraints weight = 11110.865| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.31 r_work: 0.3295 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9274 Z= 0.113 Angle : 0.660 16.844 12628 Z= 0.314 Chirality : 0.041 0.167 1520 Planarity : 0.004 0.059 1617 Dihedral : 5.742 79.424 1319 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 4.18 % Allowed : 19.44 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.25), residues: 1189 helix: -0.26 (0.19), residues: 759 sheet: -1.79 (0.62), residues: 63 loop : -1.84 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 15 HIS 0.006 0.001 HIS A 337 PHE 0.011 0.001 PHE A 453 TYR 0.011 0.001 TYR A 9 ARG 0.003 0.000 ARG B 32 Details of bonding type rmsd hydrogen bonds : bond 0.02994 ( 449) hydrogen bonds : angle 3.92926 ( 1326) covalent geometry : bond 0.00254 ( 9274) covalent geometry : angle 0.65969 (12628) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 150 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: A 8 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.7532 (tp40) REVERT: A 29 MET cc_start: 0.8324 (mmt) cc_final: 0.7640 (mmp) REVERT: A 43 ASP cc_start: 0.8157 (t0) cc_final: 0.7897 (m-30) REVERT: A 183 PHE cc_start: 0.9146 (OUTLIER) cc_final: 0.8676 (t80) REVERT: A 217 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7581 (ptt-90) REVERT: A 300 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.6398 (ttp80) REVERT: A 326 ARG cc_start: 0.7476 (mmt-90) cc_final: 0.7105 (mmt-90) REVERT: A 568 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8601 (mm-30) REVERT: B 31 GLN cc_start: 0.6438 (OUTLIER) cc_final: 0.5985 (mm-40) REVERT: B 180 ASP cc_start: 0.8344 (t0) cc_final: 0.7878 (t0) REVERT: B 257 GLU cc_start: 0.8620 (tp30) cc_final: 0.8376 (tp30) REVERT: B 281 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7836 (mt-10) REVERT: B 605 GLU cc_start: 0.8292 (pm20) cc_final: 0.7699 (pm20) REVERT: B 621 GLU cc_start: 0.8610 (tt0) cc_final: 0.7539 (tm-30) outliers start: 40 outliers final: 29 residues processed: 180 average time/residue: 0.1862 time to fit residues: 48.6605 Evaluate side-chains 173 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLN Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 578 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 15 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 56 optimal weight: 0.0870 chunk 73 optimal weight: 0.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN B 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.163596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.119140 restraints weight = 10914.105| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.35 r_work: 0.3207 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9274 Z= 0.131 Angle : 0.676 16.585 12628 Z= 0.321 Chirality : 0.042 0.180 1520 Planarity : 0.004 0.060 1617 Dihedral : 5.638 71.194 1319 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 4.18 % Allowed : 20.06 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.25), residues: 1189 helix: -0.26 (0.19), residues: 760 sheet: -1.73 (0.62), residues: 63 loop : -1.80 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 15 HIS 0.006 0.001 HIS A 337 PHE 0.011 0.001 PHE A 453 TYR 0.012 0.001 TYR A 9 ARG 0.005 0.000 ARG B 32 Details of bonding type rmsd hydrogen bonds : bond 0.03131 ( 449) hydrogen bonds : angle 3.94786 ( 1326) covalent geometry : bond 0.00306 ( 9274) covalent geometry : angle 0.67607 (12628) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: A 8 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7442 (tp40) REVERT: A 43 ASP cc_start: 0.8188 (t0) cc_final: 0.7896 (m-30) REVERT: A 148 PHE cc_start: 0.6918 (m-80) cc_final: 0.6351 (t80) REVERT: A 183 PHE cc_start: 0.9112 (OUTLIER) cc_final: 0.8643 (t80) REVERT: A 217 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7610 (ptt-90) REVERT: A 300 ARG cc_start: 0.6951 (OUTLIER) cc_final: 0.6353 (ttp80) REVERT: A 326 ARG cc_start: 0.7454 (mmt-90) cc_final: 0.7065 (mmt-90) REVERT: A 568 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8556 (mm-30) REVERT: B 106 GLN cc_start: 0.7998 (mt0) cc_final: 0.7769 (mt0) REVERT: B 180 ASP cc_start: 0.8366 (t0) cc_final: 0.7861 (t0) REVERT: B 190 MET cc_start: 0.7888 (tmm) cc_final: 0.7566 (tmm) REVERT: B 281 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7833 (mt-10) REVERT: B 605 GLU cc_start: 0.8297 (pm20) cc_final: 0.7645 (pm20) REVERT: B 621 GLU cc_start: 0.8637 (tt0) cc_final: 0.7559 (tm-30) outliers start: 40 outliers final: 33 residues processed: 171 average time/residue: 0.1747 time to fit residues: 44.0602 Evaluate side-chains 175 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLN Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 604 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 44 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 107 optimal weight: 0.1980 chunk 69 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 108 optimal weight: 0.5980 chunk 43 optimal weight: 0.0040 chunk 84 optimal weight: 1.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN B 31 GLN B 139 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.165787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.121484 restraints weight = 11020.272| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.36 r_work: 0.3255 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9274 Z= 0.114 Angle : 0.668 16.482 12628 Z= 0.315 Chirality : 0.042 0.166 1520 Planarity : 0.004 0.059 1617 Dihedral : 5.402 52.866 1319 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 4.18 % Allowed : 20.17 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.25), residues: 1189 helix: -0.14 (0.19), residues: 759 sheet: -1.60 (0.64), residues: 63 loop : -1.84 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 15 HIS 0.006 0.001 HIS A 337 PHE 0.012 0.001 PHE B 93 TYR 0.011 0.001 TYR A 9 ARG 0.002 0.000 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.02947 ( 449) hydrogen bonds : angle 3.88841 ( 1326) covalent geometry : bond 0.00257 ( 9274) covalent geometry : angle 0.66807 (12628) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7520 (tp40) REVERT: A 43 ASP cc_start: 0.8170 (t0) cc_final: 0.7918 (m-30) REVERT: A 148 PHE cc_start: 0.6863 (m-80) cc_final: 0.6357 (t80) REVERT: A 183 PHE cc_start: 0.9120 (OUTLIER) cc_final: 0.8655 (t80) REVERT: A 217 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7567 (ptt-90) REVERT: A 300 ARG cc_start: 0.6979 (OUTLIER) cc_final: 0.6381 (ttp80) REVERT: A 326 ARG cc_start: 0.7449 (mmt-90) cc_final: 0.7082 (mmt-90) REVERT: A 463 MET cc_start: 0.6646 (ptm) cc_final: 0.6402 (ptm) REVERT: A 568 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8558 (mm-30) REVERT: B 180 ASP cc_start: 0.8381 (t0) cc_final: 0.7841 (t0) REVERT: B 190 MET cc_start: 0.7897 (tmm) cc_final: 0.7597 (tmm) REVERT: B 257 GLU cc_start: 0.8625 (tp30) cc_final: 0.8373 (tp30) REVERT: B 281 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7861 (mt-10) REVERT: B 496 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7135 (mt-10) REVERT: B 605 GLU cc_start: 0.8259 (pm20) cc_final: 0.7635 (pm20) REVERT: B 621 GLU cc_start: 0.8658 (tt0) cc_final: 0.7580 (tm-30) outliers start: 40 outliers final: 35 residues processed: 170 average time/residue: 0.1649 time to fit residues: 41.6955 Evaluate side-chains 176 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 137 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLN Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 604 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 87 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 27 optimal weight: 0.0050 chunk 113 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN B 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.165372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.121087 restraints weight = 10904.440| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.36 r_work: 0.3245 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9274 Z= 0.120 Angle : 0.663 16.170 12628 Z= 0.314 Chirality : 0.042 0.170 1520 Planarity : 0.004 0.059 1617 Dihedral : 5.345 49.294 1319 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 4.18 % Allowed : 19.75 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.25), residues: 1189 helix: -0.08 (0.19), residues: 759 sheet: -1.57 (0.64), residues: 63 loop : -1.82 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 15 HIS 0.005 0.001 HIS A 337 PHE 0.009 0.001 PHE A 453 TYR 0.012 0.001 TYR A 9 ARG 0.003 0.000 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.02978 ( 449) hydrogen bonds : angle 3.86627 ( 1326) covalent geometry : bond 0.00276 ( 9274) covalent geometry : angle 0.66266 (12628) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5463.28 seconds wall clock time: 97 minutes 41.36 seconds (5861.36 seconds total)