Starting phenix.real_space_refine on Thu Jul 2 19:16:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mn6_23917/07_2026/7mn6_23917.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mn6_23917/07_2026/7mn6_23917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mn6_23917/07_2026/7mn6_23917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mn6_23917/07_2026/7mn6_23917.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7mn6_23917/07_2026/7mn6_23917.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mn6_23917/07_2026/7mn6_23917.cif" model { file = "/net/cci-nas-00/data/ceres_data/7mn6_23917/07_2026/7mn6_23917.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mn6_23917/07_2026/7mn6_23917.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 118 5.16 5 C 5981 2.51 5 N 1713 2.21 5 O 1837 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9649 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4614 Classifications: {'peptide': 599} Link IDs: {'PTRANS': 39, 'TRANS': 559} Chain breaks: 1 Chain: "B" Number of atoms: 4476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4476 Classifications: {'peptide': 579} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 540} Chain breaks: 3 Chain: "H" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain breaks: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.87, per 1000 atoms: 0.19 Number of scatterers: 9649 At special positions: 0 Unit cell: (78.49, 142.785, 131.095, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 118 16.00 O 1837 8.00 N 1713 7.00 C 5981 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=50, symmetry=0 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 56 " distance=2.03 Simple disulfide: pdb=" SG CYS A 156 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 186 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 202 " distance=2.03 Simple disulfide: pdb=" SG CYS A 210 " - pdb=" SG CYS A 218 " distance=2.02 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 226 " distance=2.02 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 235 " distance=2.03 Simple disulfide: pdb=" SG CYS A 231 " - pdb=" SG CYS A 243 " distance=2.03 Simple disulfide: pdb=" SG CYS A 246 " - pdb=" SG CYS A 255 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 286 " distance=2.03 Simple disulfide: pdb=" SG CYS A 290 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 305 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 354 " distance=2.04 Simple disulfide: pdb=" SG CYS A 463 " - pdb=" SG CYS A 493 " distance=2.03 Simple disulfide: pdb=" SG CYS A 500 " - pdb=" SG CYS A 509 " distance=2.02 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 517 " distance=2.02 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 529 " distance=2.04 Simple disulfide: pdb=" SG CYS A 533 " - pdb=" SG CYS A 549 " distance=2.02 Simple disulfide: pdb=" SG CYS A 552 " - pdb=" SG CYS A 565 " distance=2.04 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 573 " distance=2.02 Simple disulfide: pdb=" SG CYS A 576 " - pdb=" SG CYS A 585 " distance=2.03 Simple disulfide: pdb=" SG CYS A 589 " - pdb=" SG CYS A 610 " distance=2.05 Simple disulfide: pdb=" SG CYS A 613 " - pdb=" SG CYS A 621 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 629 " distance=2.05 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 53 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 192 " distance=2.02 Simple disulfide: pdb=" SG CYS B 195 " - pdb=" SG CYS B 204 " distance=2.02 Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 212 " distance=2.08 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS B 227 " distance=2.02 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 235 " distance=2.05 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 244 " distance=2.04 Simple disulfide: pdb=" SG CYS B 240 " - pdb=" SG CYS B 252 " distance=2.02 Simple disulfide: pdb=" SG CYS B 255 " - pdb=" SG CYS B 264 " distance=2.03 Simple disulfide: pdb=" SG CYS B 268 " - pdb=" SG CYS B 295 " distance=2.05 Simple disulfide: pdb=" SG CYS B 299 " - pdb=" SG CYS B 311 " distance=2.14 Simple disulfide: pdb=" SG CYS B 315 " - pdb=" SG CYS B 331 " distance=2.04 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 338 " distance=2.05 Simple disulfide: pdb=" SG CYS B 342 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 475 " - pdb=" SG CYS B 504 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 520 " distance=2.03 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 528 " distance=2.08 Simple disulfide: pdb=" SG CYS B 531 " - pdb=" SG CYS B 540 " distance=2.03 Simple disulfide: pdb=" SG CYS B 544 " - pdb=" SG CYS B 560 " distance=2.02 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 576 " distance=2.06 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 584 " distance=2.02 Simple disulfide: pdb=" SG CYS B 587 " - pdb=" SG CYS B 596 " distance=2.03 Simple disulfide: pdb=" SG CYS B 600 " - pdb=" SG CYS B 623 " distance=2.03 Simple disulfide: pdb=" SG CYS H 182 " - pdb=" SG CYS H 196 " distance=2.09 Simple disulfide: pdb=" SG CYS H 190 " - pdb=" SG CYS H 210 " distance=2.02 Simple disulfide: pdb=" SG CYS H 212 " - pdb=" SG CYS H 221 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG A1101 " - " ASN A 408 " " NAG A1102 " - " ASN A 353 " " NAG A1103 " - " ASN A 414 " " NAG B1501 " - " ASN B 530 " " NAG B1502 " - " ASN B 187 " " NAG C 1 " - " ASN A 469 " " NAG D 1 " - " ASN A 250 " " NAG E 1 " - " ASN B 259 " Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 223.6 milliseconds 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2250 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 29 sheets defined 15.1% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 41 through 54 Processing helix chain 'A' and resid 74 through 80 removed outlier: 4.214A pdb=" N TRP A 79 " --> pdb=" O PHE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 187 through 191 removed outlier: 3.796A pdb=" N LYS A 191 " --> pdb=" O GLU A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 202 removed outlier: 4.010A pdb=" N CYS A 202 " --> pdb=" O SER A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 352 removed outlier: 3.514A pdb=" N VAL A 352 " --> pdb=" O ASP A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.680A pdb=" N LEU A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 380 through 390 removed outlier: 4.234A pdb=" N THR A 389 " --> pdb=" O VAL A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'A' and resid 463 through 468 removed outlier: 3.557A pdb=" N HIS A 466 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER A 467 " --> pdb=" O TYR A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 473 Processing helix chain 'A' and resid 489 through 496 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'B' and resid 38 through 40 No H-bonds generated for 'chain 'B' and resid 38 through 40' Processing helix chain 'B' and resid 41 through 51 Processing helix chain 'B' and resid 71 through 77 removed outlier: 4.411A pdb=" N ASP B 76 " --> pdb=" O PHE B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 173 removed outlier: 3.963A pdb=" N ILE B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 212 removed outlier: 3.834A pdb=" N CYS B 212 " --> pdb=" O SER B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 removed outlier: 4.328A pdb=" N CYS B 235 " --> pdb=" O PRO B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 351 removed outlier: 3.762A pdb=" N ARG B 351 " --> pdb=" O GLU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 365 removed outlier: 3.620A pdb=" N PHE B 364 " --> pdb=" O ILE B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 removed outlier: 3.600A pdb=" N PHE B 381 " --> pdb=" O PRO B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 Processing helix chain 'B' and resid 422 through 426 Processing helix chain 'B' and resid 436 through 439 Processing helix chain 'B' and resid 481 through 485 Processing helix chain 'B' and resid 500 through 508 Processing helix chain 'H' and resid 185 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 7.391A pdb=" N CYS A 29 " --> pdb=" O MET A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 removed outlier: 7.077A pdb=" N VAL A 38 " --> pdb=" O CYS H 212 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 66 removed outlier: 5.409A pdb=" N GLY A 146 " --> pdb=" O PHE A 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 97 Processing sheet with id=AA5, first strand: chain 'A' and resid 231 through 235 removed outlier: 3.806A pdb=" N ALA A 245 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N GLY A 234 " --> pdb=" O CYS A 243 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N CYS A 243 " --> pdb=" O GLY A 234 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 249 through 251 Processing sheet with id=AA7, first strand: chain 'A' and resid 263 through 265 Processing sheet with id=AA8, first strand: chain 'A' and resid 280 through 282 Processing sheet with id=AA9, first strand: chain 'A' and resid 300 through 302 Processing sheet with id=AB1, first strand: chain 'A' and resid 356 through 357 Processing sheet with id=AB2, first strand: chain 'A' and resid 361 through 363 removed outlier: 6.515A pdb=" N LEU A 397 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N MET A 433 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE A 399 " --> pdb=" O MET A 433 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ARG A 453 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE A 454 " --> pdb=" O ASP A 483 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 523 through 525 removed outlier: 3.828A pdb=" N TYR A 523 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 528 " --> pdb=" O ARG A 525 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 542 through 545 Processing sheet with id=AB5, first strand: chain 'A' and resid 579 through 581 Processing sheet with id=AB6, first strand: chain 'A' and resid 593 through 595 Processing sheet with id=AB7, first strand: chain 'A' and resid 602 through 604 Processing sheet with id=AB8, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AB9, first strand: chain 'B' and resid 60 through 63 removed outlier: 5.330A pdb=" N GLY B 152 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL B 153 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 240 through 244 removed outlier: 7.202A pdb=" N GLY B 243 " --> pdb=" O CYS B 252 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N CYS B 252 " --> pdb=" O GLY B 243 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 258 through 260 Processing sheet with id=AC3, first strand: chain 'B' and resid 272 through 275 removed outlier: 3.627A pdb=" N GLU B 280 " --> pdb=" O ASN B 275 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 289 through 291 Processing sheet with id=AC5, first strand: chain 'B' and resid 319 through 322 Processing sheet with id=AC6, first strand: chain 'B' and resid 342 through 343 removed outlier: 6.786A pdb=" N CYS B 342 " --> pdb=" O PHE B 371 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 374 through 376 removed outlier: 6.553A pdb=" N LEU B 374 " --> pdb=" O TYR B 411 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N LEU B 465 " --> pdb=" O TYR B 441 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 443 " --> pdb=" O LEU B 465 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA B 466 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N THR B 496 " --> pdb=" O ALA B 466 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE B 468 " --> pdb=" O THR B 496 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 553 through 556 Processing sheet with id=AC9, first strand: chain 'B' and resid 590 through 592 Processing sheet with id=AD1, first strand: chain 'B' and resid 615 through 617 Processing sheet with id=AD2, first strand: chain 'H' and resid 216 through 217 195 hydrogen bonds defined for protein. 375 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: 1.78 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1612 1.28 - 1.42: 2482 1.42 - 1.55: 5630 1.55 - 1.69: 14 1.69 - 1.82: 134 Bond restraints: 9872 Sorted by residual: bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.536 -0.130 2.00e-02 2.50e+03 4.22e+01 bond pdb=" CA HIS B 589 " pdb=" C HIS B 589 " ideal model delta sigma weight residual 1.520 1.544 -0.024 4.80e-03 4.34e+04 2.52e+01 bond pdb=" CA MET B 347 " pdb=" C MET B 347 " ideal model delta sigma weight residual 1.522 1.580 -0.058 1.20e-02 6.94e+03 2.30e+01 bond pdb=" N GLU B 348 " pdb=" CA GLU B 348 " ideal model delta sigma weight residual 1.457 1.517 -0.059 1.29e-02 6.01e+03 2.11e+01 bond pdb=" N ARG B 351 " pdb=" CA ARG B 351 " ideal model delta sigma weight residual 1.459 1.509 -0.050 1.21e-02 6.83e+03 1.67e+01 ... (remaining 9867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 12254 2.69 - 5.37: 1087 5.37 - 8.06: 55 8.06 - 10.75: 1 10.75 - 13.44: 3 Bond angle restraints: 13400 Sorted by residual: angle pdb=" C GLU B 109 " pdb=" N ASP B 110 " pdb=" CA ASP B 110 " ideal model delta sigma weight residual 122.45 135.89 -13.44 1.78e+00 3.16e-01 5.70e+01 angle pdb=" C SER H 177 " pdb=" N HIS H 178 " pdb=" CA HIS H 178 " ideal model delta sigma weight residual 122.54 133.19 -10.65 1.65e+00 3.67e-01 4.16e+01 angle pdb=" N CYS A 214 " pdb=" CA CYS A 214 " pdb=" C CYS A 214 " ideal model delta sigma weight residual 113.23 121.19 -7.96 1.24e+00 6.50e-01 4.13e+01 angle pdb=" C HIS A 486 " pdb=" CA HIS A 486 " pdb=" CB HIS A 486 " ideal model delta sigma weight residual 116.63 109.72 6.91 1.16e+00 7.43e-01 3.55e+01 angle pdb=" N GLU A 54 " pdb=" CA GLU A 54 " pdb=" C GLU A 54 " ideal model delta sigma weight residual 111.33 118.09 -6.76 1.21e+00 6.83e-01 3.12e+01 ... (remaining 13395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 5681 17.74 - 35.48: 197 35.48 - 53.22: 59 53.22 - 70.96: 21 70.96 - 88.70: 14 Dihedral angle restraints: 5972 sinusoidal: 2469 harmonic: 3503 Sorted by residual: dihedral pdb=" CB CYS A 290 " pdb=" SG CYS A 290 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 178.45 -85.45 1 1.00e+01 1.00e-02 8.84e+01 dihedral pdb=" CB CYS B 299 " pdb=" SG CYS B 299 " pdb=" SG CYS B 311 " pdb=" CB CYS B 311 " ideal model delta sinusoidal sigma weight residual 93.00 173.79 -80.79 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS B 268 " pdb=" SG CYS B 268 " pdb=" SG CYS B 295 " pdb=" CB CYS B 295 " ideal model delta sinusoidal sigma weight residual 93.00 166.92 -73.92 1 1.00e+01 1.00e-02 6.94e+01 ... (remaining 5969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 1317 0.120 - 0.240: 159 0.240 - 0.359: 11 0.359 - 0.479: 3 0.479 - 0.599: 2 Chirality restraints: 1492 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.76 0.36 2.00e-02 2.50e+03 3.28e+02 chirality pdb=" C1 BMA E 3 " pdb=" O4 NAG E 2 " pdb=" C2 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.55e+02 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.03e+02 ... (remaining 1489 not shown) Planarity restraints: 1772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 353 " -0.080 2.00e-02 2.50e+03 8.94e-02 9.98e+01 pdb=" CG ASN A 353 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN A 353 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 353 " 0.145 2.00e-02 2.50e+03 pdb=" C1 NAG A1102 " -0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 50 " -0.119 2.00e-02 2.50e+03 6.76e-02 9.14e+01 pdb=" CG TYR A 50 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 50 " 0.063 2.00e-02 2.50e+03 pdb=" CD2 TYR A 50 " 0.052 2.00e-02 2.50e+03 pdb=" CE1 TYR A 50 " 0.037 2.00e-02 2.50e+03 pdb=" CE2 TYR A 50 " 0.046 2.00e-02 2.50e+03 pdb=" CZ TYR A 50 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 50 " -0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 530 " -0.070 2.00e-02 2.50e+03 7.26e-02 6.59e+01 pdb=" CG ASN B 530 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN B 530 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN B 530 " 0.111 2.00e-02 2.50e+03 pdb=" C1 NAG B1501 " -0.086 2.00e-02 2.50e+03 ... (remaining 1769 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 3473 2.89 - 3.40: 8353 3.40 - 3.90: 16368 3.90 - 4.40: 18467 4.40 - 4.90: 30392 Nonbonded interactions: 77053 Sorted by model distance: nonbonded pdb=" OD1 ASP A 313 " pdb=" NZ LYS A 318 " model vdw 2.392 3.120 nonbonded pdb=" OD1 ASP B 30 " pdb=" NZ LYS B 32 " model vdw 2.414 3.120 nonbonded pdb=" OH TYR B 411 " pdb=" OE1 GLN B 446 " model vdw 2.456 3.040 nonbonded pdb=" N ASP B 110 " pdb=" O ASP B 110 " model vdw 2.457 2.496 nonbonded pdb=" O5 NAG A1101 " pdb=" O6 NAG A1101 " model vdw 2.487 2.432 ... (remaining 77048 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } 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: 4.510 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.330 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 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 : 0.013 0.130 9935 Z= 0.798 Angle : 1.566 14.024 13539 Z= 1.040 Chirality : 0.079 0.599 1492 Planarity : 0.008 0.076 1764 Dihedral : 11.144 88.696 3572 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 0.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.47 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.23), residues: 1211 helix: -2.18 (0.51), residues: 68 sheet: -1.16 (0.41), residues: 154 loop : 0.33 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 164 TYR 0.119 0.005 TYR A 50 PHE 0.045 0.003 PHE B 400 TRP 0.076 0.004 TRP B 415 HIS 0.001 0.000 HIS B 349 Details of bonding type rmsd/Z covalent geometry : bond 0.01266 / 0.80 ( 9872) covalent geometry : angle 1.51118 / 1.03 (13400) SS BOND : bond 0.02224 / 2.29 ( 50) SS BOND : angle 3.71627 / 2.81 ( 100) hydrogen bonds : bond 0.21963 / 15.25 ( 195) hydrogen bonds : angle 8.29895 / 5.81 ( 375) link_ALPHA1-3 : bond 0.02699 / 1.42 ( 1) link_ALPHA1-3 : angle 2.11481 / 1.19 ( 3) link_BETA1-4 : bond 0.02653 / 1.21 ( 4) link_BETA1-4 : angle 6.01590 / 3.52 ( 12) link_NAG-ASN : bond 0.01046 / 0.57 ( 8) link_NAG-ASN : angle 5.66630 / 3.79 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 550 PHE cc_start: 0.8080 (m-80) cc_final: 0.7843 (m-80) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1173 time to fit residues: 17.8217 Evaluate side-chains 39 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN A 400 GLN A 545 HIS B 260 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.114820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.082037 restraints weight = 19457.671| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.98 r_work: 0.3312 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9935 Z= 0.146 Angle : 0.667 7.456 13539 Z= 0.345 Chirality : 0.048 0.230 1492 Planarity : 0.005 0.040 1764 Dihedral : 5.197 24.773 1318 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.47 % Allowed : 4.89 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.24), residues: 1211 helix: -1.26 (0.56), residues: 74 sheet: -0.43 (0.40), residues: 171 loop : 0.23 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 475 TYR 0.017 0.002 TYR B 554 PHE 0.013 0.002 PHE A 219 TRP 0.009 0.001 TRP B 415 HIS 0.011 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 9872) covalent geometry : angle 0.64636 / 0.34 (13400) SS BOND : bond 0.00354 / 0.24 ( 50) SS BOND : angle 1.29293 / 1.02 ( 100) hydrogen bonds : bond 0.04600 / 3.28 ( 195) hydrogen bonds : angle 6.31054 / 4.53 ( 375) link_ALPHA1-3 : bond 0.01160 / 0.61 ( 1) link_ALPHA1-3 : angle 1.32571 / 0.71 ( 3) link_BETA1-4 : bond 0.00374 / 0.18 ( 4) link_BETA1-4 : angle 2.21167 / 1.24 ( 12) link_NAG-ASN : bond 0.00407 / 0.20 ( 8) link_NAG-ASN : angle 2.83898 / 1.82 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 550 PHE cc_start: 0.7769 (m-80) cc_final: 0.7307 (m-80) REVERT: A 559 MET cc_start: 0.6872 (mmm) cc_final: 0.6317 (mmt) REVERT: H 187 LYS cc_start: 0.8411 (tptm) cc_final: 0.8190 (mttm) outliers start: 5 outliers final: 4 residues processed: 52 average time/residue: 0.0946 time to fit residues: 7.2327 Evaluate side-chains 37 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 509 CYS Chi-restraints excluded: chain B residue 35 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 116 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 114 optimal weight: 20.0000 chunk 68 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 27 optimal weight: 0.0670 overall best weight: 1.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 ASN A 133 GLN A 435 ASN B 193 HIS B 302 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.113449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.079520 restraints weight = 20521.562| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.02 r_work: 0.3190 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 9935 Z= 0.187 Angle : 0.633 10.639 13539 Z= 0.325 Chirality : 0.048 0.241 1492 Planarity : 0.005 0.051 1764 Dihedral : 5.135 28.487 1318 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.03 % Allowed : 5.64 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.24), residues: 1211 helix: -1.24 (0.58), residues: 75 sheet: -0.38 (0.40), residues: 172 loop : 0.10 (0.21), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 103 TYR 0.015 0.002 TYR A 424 PHE 0.022 0.002 PHE A 443 TRP 0.010 0.001 TRP B 482 HIS 0.009 0.001 HIS B 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.19 ( 9872) covalent geometry : angle 0.62048 / 0.32 (13400) SS BOND : bond 0.00451 / 0.32 ( 50) SS BOND : angle 1.19601 / 0.92 ( 100) hydrogen bonds : bond 0.03976 / 2.88 ( 195) hydrogen bonds : angle 6.02884 / 4.39 ( 375) link_ALPHA1-3 : bond 0.00733 / 0.39 ( 1) link_ALPHA1-3 : angle 1.21575 / 0.61 ( 3) link_BETA1-4 : bond 0.00389 / 0.19 ( 4) link_BETA1-4 : angle 1.45553 / 0.80 ( 12) link_NAG-ASN : bond 0.00203 / 0.09 ( 8) link_NAG-ASN : angle 1.97402 / 1.37 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.337 Fit side-chains REVERT: A 550 PHE cc_start: 0.7949 (m-80) cc_final: 0.7592 (m-80) outliers start: 11 outliers final: 7 residues processed: 45 average time/residue: 0.0656 time to fit residues: 4.9359 Evaluate side-chains 36 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 282 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 48 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 400 GLN B 302 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.107617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.072107 restraints weight = 20912.036| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.31 r_work: 0.3136 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9935 Z= 0.178 Angle : 0.589 8.495 13539 Z= 0.299 Chirality : 0.047 0.264 1492 Planarity : 0.005 0.050 1764 Dihedral : 5.029 25.223 1318 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.30 % Favored : 96.61 % Rotamer: Outliers : 1.03 % Allowed : 6.11 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.24), residues: 1211 helix: -1.36 (0.57), residues: 75 sheet: -0.38 (0.42), residues: 166 loop : 0.02 (0.21), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 103 TYR 0.015 0.001 TYR H 224 PHE 0.017 0.002 PHE A 443 TRP 0.012 0.001 TRP A 510 HIS 0.006 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 ( 9872) covalent geometry : angle 0.57987 / 0.30 (13400) SS BOND : bond 0.00400 / 0.29 ( 50) SS BOND : angle 0.85828 / 0.66 ( 100) hydrogen bonds : bond 0.03595 / 2.61 ( 195) hydrogen bonds : angle 5.96732 / 4.34 ( 375) link_ALPHA1-3 : bond 0.00522 / 0.27 ( 1) link_ALPHA1-3 : angle 1.24627 / 0.62 ( 3) link_BETA1-4 : bond 0.00324 / 0.16 ( 4) link_BETA1-4 : angle 1.18778 / 0.66 ( 12) link_NAG-ASN : bond 0.00271 / 0.11 ( 8) link_NAG-ASN : angle 1.96740 / 1.34 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.311 Fit side-chains REVERT: A 550 PHE cc_start: 0.7860 (m-80) cc_final: 0.7490 (m-80) outliers start: 11 outliers final: 6 residues processed: 40 average time/residue: 0.0698 time to fit residues: 4.7935 Evaluate side-chains 33 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 282 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 67 optimal weight: 0.0970 chunk 37 optimal weight: 0.3980 chunk 49 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 113 optimal weight: 0.0070 chunk 77 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 GLN B 302 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.108406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.075303 restraints weight = 19984.896| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.18 r_work: 0.3199 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9935 Z= 0.087 Angle : 0.521 7.154 13539 Z= 0.262 Chirality : 0.044 0.259 1492 Planarity : 0.004 0.046 1764 Dihedral : 4.555 22.302 1318 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.39 % Favored : 96.53 % Rotamer: Outliers : 0.47 % Allowed : 6.86 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.25), residues: 1211 helix: 0.10 (0.68), residues: 61 sheet: -0.39 (0.41), residues: 176 loop : 0.17 (0.21), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 135 TYR 0.009 0.001 TYR H 224 PHE 0.016 0.001 PHE B 534 TRP 0.010 0.001 TRP B 205 HIS 0.005 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.09 ( 9872) covalent geometry : angle 0.51070 / 0.26 (13400) SS BOND : bond 0.00199 / 0.14 ( 50) SS BOND : angle 0.86960 / 0.71 ( 100) hydrogen bonds : bond 0.02869 / 2.06 ( 195) hydrogen bonds : angle 5.61335 / 4.07 ( 375) link_ALPHA1-3 : bond 0.00575 / 0.30 ( 1) link_ALPHA1-3 : angle 1.25523 / 0.64 ( 3) link_BETA1-4 : bond 0.00417 / 0.20 ( 4) link_BETA1-4 : angle 1.01132 / 0.58 ( 12) link_NAG-ASN : bond 0.00441 / 0.21 ( 8) link_NAG-ASN : angle 1.86383 / 1.22 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.404 Fit side-chains REVERT: A 550 PHE cc_start: 0.7965 (m-80) cc_final: 0.7644 (m-80) REVERT: H 187 LYS cc_start: 0.8537 (tptp) cc_final: 0.8117 (mttm) outliers start: 5 outliers final: 2 residues processed: 38 average time/residue: 0.0818 time to fit residues: 5.0644 Evaluate side-chains 32 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 158 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 97 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 114 optimal weight: 8.9990 chunk 110 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 52 optimal weight: 0.0770 chunk 58 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 118 optimal weight: 0.4980 chunk 102 optimal weight: 2.9990 overall best weight: 1.5144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 400 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.104936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.070986 restraints weight = 20042.861| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.16 r_work: 0.3142 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9935 Z= 0.191 Angle : 0.587 8.965 13539 Z= 0.297 Chirality : 0.047 0.242 1492 Planarity : 0.004 0.048 1764 Dihedral : 4.776 25.886 1318 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.80 % Favored : 96.12 % Rotamer: Outliers : 0.94 % Allowed : 7.14 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.25), residues: 1211 helix: -0.93 (0.61), residues: 75 sheet: -0.40 (0.42), residues: 166 loop : 0.03 (0.21), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 453 TYR 0.011 0.001 TYR A 265 PHE 0.018 0.001 PHE A 443 TRP 0.010 0.001 TRP A 510 HIS 0.006 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.19 ( 9872) covalent geometry : angle 0.57226 / 0.29 (13400) SS BOND : bond 0.00382 / 0.29 ( 50) SS BOND : angle 1.30850 / 1.06 ( 100) hydrogen bonds : bond 0.03617 / 2.65 ( 195) hydrogen bonds : angle 5.68558 / 4.12 ( 375) link_ALPHA1-3 : bond 0.00485 / 0.26 ( 1) link_ALPHA1-3 : angle 1.26544 / 0.63 ( 3) link_BETA1-4 : bond 0.00381 / 0.19 ( 4) link_BETA1-4 : angle 1.29978 / 0.71 ( 12) link_NAG-ASN : bond 0.00247 / 0.10 ( 8) link_NAG-ASN : angle 1.85813 / 1.28 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.393 Fit side-chains REVERT: A 484 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8831 (mm) REVERT: A 550 PHE cc_start: 0.7921 (m-80) cc_final: 0.7606 (m-80) REVERT: B 198 MET cc_start: 0.8683 (mmm) cc_final: 0.8481 (tpp) outliers start: 10 outliers final: 7 residues processed: 39 average time/residue: 0.0789 time to fit residues: 5.1171 Evaluate side-chains 34 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 282 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 118 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 0.0570 chunk 107 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 78 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.108652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.073358 restraints weight = 20769.104| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.30 r_work: 0.3171 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9935 Z= 0.097 Angle : 0.519 7.270 13539 Z= 0.261 Chirality : 0.045 0.245 1492 Planarity : 0.004 0.045 1764 Dihedral : 4.511 24.260 1318 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.39 % Favored : 96.53 % Rotamer: Outliers : 0.94 % Allowed : 7.52 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.25), residues: 1211 helix: 0.23 (0.69), residues: 61 sheet: -0.40 (0.43), residues: 161 loop : 0.16 (0.21), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 135 TYR 0.008 0.001 TYR B 590 PHE 0.027 0.001 PHE B 534 TRP 0.005 0.001 TRP A 510 HIS 0.006 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 ( 9872) covalent geometry : angle 0.50796 / 0.26 (13400) SS BOND : bond 0.00231 / 0.17 ( 50) SS BOND : angle 0.93340 / 0.75 ( 100) hydrogen bonds : bond 0.02903 / 2.08 ( 195) hydrogen bonds : angle 5.52436 / 4.01 ( 375) link_ALPHA1-3 : bond 0.00536 / 0.28 ( 1) link_ALPHA1-3 : angle 1.25542 / 0.64 ( 3) link_BETA1-4 : bond 0.00401 / 0.19 ( 4) link_BETA1-4 : angle 1.04407 / 0.60 ( 12) link_NAG-ASN : bond 0.00374 / 0.17 ( 8) link_NAG-ASN : angle 1.80126 / 1.19 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 484 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8840 (mm) REVERT: A 550 PHE cc_start: 0.7991 (m-80) cc_final: 0.7702 (m-80) REVERT: A 559 MET cc_start: 0.6358 (mmm) cc_final: 0.5927 (mmt) REVERT: H 187 LYS cc_start: 0.8589 (tptp) cc_final: 0.8158 (mttm) outliers start: 10 outliers final: 5 residues processed: 37 average time/residue: 0.0775 time to fit residues: 4.9348 Evaluate side-chains 35 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 282 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 88 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 4 optimal weight: 0.0980 chunk 111 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 24 optimal weight: 0.2980 chunk 94 optimal weight: 0.4980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.106807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.073742 restraints weight = 20044.248| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.14 r_work: 0.3173 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9935 Z= 0.113 Angle : 0.522 7.383 13539 Z= 0.262 Chirality : 0.045 0.237 1492 Planarity : 0.004 0.044 1764 Dihedral : 4.441 20.097 1318 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.05 % Favored : 95.87 % Rotamer: Outliers : 0.85 % Allowed : 7.33 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.25), residues: 1211 helix: 0.18 (0.69), residues: 61 sheet: -0.38 (0.44), residues: 158 loop : 0.18 (0.21), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 135 TYR 0.008 0.001 TYR B 590 PHE 0.026 0.001 PHE B 534 TRP 0.006 0.001 TRP A 510 HIS 0.005 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.11 ( 9872) covalent geometry : angle 0.51104 / 0.26 (13400) SS BOND : bond 0.00249 / 0.19 ( 50) SS BOND : angle 0.97847 / 0.82 ( 100) hydrogen bonds : bond 0.03043 / 2.21 ( 195) hydrogen bonds : angle 5.49327 / 3.97 ( 375) link_ALPHA1-3 : bond 0.00468 / 0.25 ( 1) link_ALPHA1-3 : angle 1.24235 / 0.63 ( 3) link_BETA1-4 : bond 0.00391 / 0.19 ( 4) link_BETA1-4 : angle 1.15010 / 0.64 ( 12) link_NAG-ASN : bond 0.00312 / 0.14 ( 8) link_NAG-ASN : angle 1.75901 / 1.18 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 484 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8829 (mm) REVERT: A 550 PHE cc_start: 0.7989 (m-80) cc_final: 0.7719 (m-80) REVERT: H 187 LYS cc_start: 0.8600 (tptp) cc_final: 0.8163 (mttm) outliers start: 9 outliers final: 6 residues processed: 36 average time/residue: 0.0771 time to fit residues: 4.7570 Evaluate side-chains 36 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 282 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 104 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.105775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.072626 restraints weight = 19892.970| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 3.15 r_work: 0.3154 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9935 Z= 0.138 Angle : 0.542 7.373 13539 Z= 0.273 Chirality : 0.046 0.228 1492 Planarity : 0.004 0.044 1764 Dihedral : 4.545 22.095 1318 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.80 % Favored : 96.12 % Rotamer: Outliers : 0.85 % Allowed : 7.33 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.25), residues: 1211 helix: -0.46 (0.66), residues: 68 sheet: -0.43 (0.44), residues: 158 loop : 0.10 (0.21), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 193 TYR 0.008 0.001 TYR A 265 PHE 0.027 0.001 PHE B 534 TRP 0.007 0.001 TRP B 482 HIS 0.006 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 9872) covalent geometry : angle 0.52995 / 0.27 (13400) SS BOND : bond 0.00284 / 0.21 ( 50) SS BOND : angle 1.06302 / 0.89 ( 100) hydrogen bonds : bond 0.03212 / 2.32 ( 195) hydrogen bonds : angle 5.55289 / 4.03 ( 375) link_ALPHA1-3 : bond 0.00466 / 0.25 ( 1) link_ALPHA1-3 : angle 1.25788 / 0.63 ( 3) link_BETA1-4 : bond 0.00371 / 0.18 ( 4) link_BETA1-4 : angle 1.16966 / 0.64 ( 12) link_NAG-ASN : bond 0.00292 / 0.14 ( 8) link_NAG-ASN : angle 1.79069 / 1.22 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 484 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8825 (mm) REVERT: A 550 PHE cc_start: 0.8009 (m-80) cc_final: 0.7740 (m-80) REVERT: A 559 MET cc_start: 0.6215 (mmm) cc_final: 0.5801 (mmt) outliers start: 9 outliers final: 6 residues processed: 37 average time/residue: 0.0851 time to fit residues: 5.1922 Evaluate side-chains 37 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 282 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.4980 chunk 44 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.106446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.073448 restraints weight = 19950.560| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 3.13 r_work: 0.3172 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9935 Z= 0.108 Angle : 0.516 7.652 13539 Z= 0.259 Chirality : 0.045 0.231 1492 Planarity : 0.004 0.043 1764 Dihedral : 4.408 19.299 1318 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.88 % Favored : 96.04 % Rotamer: Outliers : 0.66 % Allowed : 7.42 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.25), residues: 1211 helix: 0.17 (0.70), residues: 61 sheet: -0.22 (0.48), residues: 138 loop : 0.19 (0.21), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 135 TYR 0.008 0.001 TYR B 590 PHE 0.036 0.001 PHE B 534 TRP 0.005 0.001 TRP B 482 HIS 0.005 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 9872) covalent geometry : angle 0.50713 / 0.26 (13400) SS BOND : bond 0.00248 / 0.18 ( 50) SS BOND : angle 0.81911 / 0.68 ( 100) hydrogen bonds : bond 0.02948 / 2.13 ( 195) hydrogen bonds : angle 5.48741 / 3.98 ( 375) link_ALPHA1-3 : bond 0.00478 / 0.25 ( 1) link_ALPHA1-3 : angle 1.25319 / 0.63 ( 3) link_BETA1-4 : bond 0.00408 / 0.20 ( 4) link_BETA1-4 : angle 1.10240 / 0.63 ( 12) link_NAG-ASN : bond 0.00331 / 0.16 ( 8) link_NAG-ASN : angle 1.73135 / 1.14 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.390 Fit side-chains REVERT: A 484 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8840 (mm) REVERT: A 550 PHE cc_start: 0.8093 (m-80) cc_final: 0.7847 (m-80) REVERT: H 187 LYS cc_start: 0.8534 (tptp) cc_final: 0.8149 (ttmt) outliers start: 7 outliers final: 4 residues processed: 38 average time/residue: 0.0793 time to fit residues: 5.1361 Evaluate side-chains 37 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 282 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 43 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS A 405 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.105219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.072141 restraints weight = 20014.037| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.14 r_work: 0.3142 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9935 Z= 0.155 Angle : 0.551 7.511 13539 Z= 0.278 Chirality : 0.046 0.222 1492 Planarity : 0.004 0.044 1764 Dihedral : 4.547 21.443 1318 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.13 % Favored : 95.79 % Rotamer: Outliers : 0.75 % Allowed : 7.42 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.25), residues: 1211 helix: -0.53 (0.65), residues: 68 sheet: -0.28 (0.46), residues: 148 loop : 0.09 (0.21), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 190 TYR 0.009 0.001 TYR A 265 PHE 0.032 0.001 PHE B 534 TRP 0.008 0.001 TRP B 482 HIS 0.006 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 ( 9872) covalent geometry : angle 0.54082 / 0.27 (13400) SS BOND : bond 0.00320 / 0.24 ( 50) SS BOND : angle 0.97290 / 0.80 ( 100) hydrogen bonds : bond 0.03277 / 2.39 ( 195) hydrogen bonds : angle 5.55284 / 4.03 ( 375) link_ALPHA1-3 : bond 0.00423 / 0.22 ( 1) link_ALPHA1-3 : angle 1.24438 / 0.62 ( 3) link_BETA1-4 : bond 0.00373 / 0.18 ( 4) link_BETA1-4 : angle 1.21843 / 0.67 ( 12) link_NAG-ASN : bond 0.00213 / 0.11 ( 8) link_NAG-ASN : angle 1.79158 / 1.25 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2420.07 seconds wall clock time: 42 minutes 8.19 seconds (2528.19 seconds total)