Starting phenix.real_space_refine on Wed Mar 4 01:35:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mn6_23917/03_2026/7mn6_23917.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mn6_23917/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7mn6_23917/03_2026/7mn6_23917.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mn6_23917/03_2026/7mn6_23917.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mn6_23917/03_2026/7mn6_23917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mn6_23917/03_2026/7mn6_23917.map" } 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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.32, per 1000 atoms: 0.24 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: 0.82 Conformation dependent library (CDL) restraints added in 571.4 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: 1.86 Time building geometry restraints manager: 1.13 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 - 19.34: 5951 19.34 - 38.68: 194 38.68 - 58.01: 59 58.01 - 77.35: 26 77.35 - 96.69: 11 Dihedral angle restraints: 6241 sinusoidal: 2738 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 6238 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: 6.750 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.710 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 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 : 11.930 96.688 3841 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 covalent geometry : bond 0.01266 ( 9872) covalent geometry : angle 1.51118 (13400) SS BOND : bond 0.02224 ( 50) SS BOND : angle 3.71627 ( 100) hydrogen bonds : bond 0.21963 ( 195) hydrogen bonds : angle 8.29895 ( 375) link_ALPHA1-3 : bond 0.02699 ( 1) link_ALPHA1-3 : angle 2.11481 ( 3) link_BETA1-4 : bond 0.02653 ( 4) link_BETA1-4 : angle 6.01590 ( 12) link_NAG-ASN : bond 0.01046 ( 8) link_NAG-ASN : angle 5.66630 ( 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 : 0.364 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: 0.1360 time to fit residues: 20.4620 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 : 0.361 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 GLN A 545 HIS B 260 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.114919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.082113 restraints weight = 19484.048| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.99 r_work: 0.3308 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9935 Z= 0.149 Angle : 0.684 8.509 13539 Z= 0.352 Chirality : 0.048 0.233 1492 Planarity : 0.005 0.044 1764 Dihedral : 7.707 65.427 1587 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.56 % Allowed : 5.17 % Favored : 94.27 % 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 (0.24), residues: 1211 helix: -1.24 (0.55), residues: 74 sheet: -0.48 (0.40), residues: 171 loop : 0.20 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 354 TYR 0.016 0.002 TYR B 554 PHE 0.017 0.001 PHE A 219 TRP 0.008 0.001 TRP B 415 HIS 0.012 0.001 HIS B 318 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9872) covalent geometry : angle 0.66226 (13400) SS BOND : bond 0.00330 ( 50) SS BOND : angle 1.28083 ( 100) hydrogen bonds : bond 0.04502 ( 195) hydrogen bonds : angle 6.36193 ( 375) link_ALPHA1-3 : bond 0.01265 ( 1) link_ALPHA1-3 : angle 1.68077 ( 3) link_BETA1-4 : bond 0.00545 ( 4) link_BETA1-4 : angle 2.67099 ( 12) link_NAG-ASN : bond 0.00451 ( 8) link_NAG-ASN : angle 2.93943 ( 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: 6 poor density : 47 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 550 PHE cc_start: 0.7816 (m-80) cc_final: 0.7325 (m-80) REVERT: A 559 MET cc_start: 0.6873 (mmm) cc_final: 0.6315 (mmt) REVERT: H 187 LYS cc_start: 0.8386 (tptm) cc_final: 0.8160 (mttm) outliers start: 6 outliers final: 5 residues processed: 52 average time/residue: 0.0898 time to fit residues: 7.0717 Evaluate side-chains 39 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 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 509 CYS Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 277 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 116 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 114 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 32 optimal weight: 0.0010 chunk 27 optimal weight: 0.9980 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 GLN A 435 ASN B 193 HIS B 302 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.113510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.079885 restraints weight = 20513.932| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.93 r_work: 0.3207 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 9935 Z= 0.190 Angle : 0.631 9.424 13539 Z= 0.323 Chirality : 0.049 0.220 1492 Planarity : 0.005 0.050 1764 Dihedral : 6.480 55.556 1587 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.94 % Allowed : 5.73 % 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: -0.15 (0.24), residues: 1211 helix: -1.23 (0.58), residues: 75 sheet: -0.37 (0.40), residues: 172 loop : 0.11 (0.21), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 340 TYR 0.014 0.002 TYR A 265 PHE 0.021 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 covalent geometry : bond 0.00465 ( 9872) covalent geometry : angle 0.61887 (13400) SS BOND : bond 0.00478 ( 50) SS BOND : angle 1.13419 ( 100) hydrogen bonds : bond 0.04034 ( 195) hydrogen bonds : angle 6.05088 ( 375) link_ALPHA1-3 : bond 0.00857 ( 1) link_ALPHA1-3 : angle 1.31658 ( 3) link_BETA1-4 : bond 0.00599 ( 4) link_BETA1-4 : angle 1.51153 ( 12) link_NAG-ASN : bond 0.00236 ( 8) link_NAG-ASN : angle 2.01401 ( 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: 10 poor density : 39 time to evaluate : 0.373 Fit side-chains REVERT: A 550 PHE cc_start: 0.7899 (m-80) cc_final: 0.7490 (m-80) REVERT: A 559 MET cc_start: 0.6899 (mmm) cc_final: 0.6283 (mmt) REVERT: B 302 ASN cc_start: 0.9236 (OUTLIER) cc_final: 0.9031 (t0) outliers start: 10 outliers final: 7 residues processed: 46 average time/residue: 0.0703 time to fit residues: 5.4885 Evaluate side-chains 38 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 302 ASN 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: 4.9990 chunk 45 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 49 optimal weight: 0.0570 chunk 11 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 298 GLN B 302 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.107007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.073626 restraints weight = 20113.601| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 3.19 r_work: 0.3164 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3259 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= 0.161 Angle : 0.581 8.267 13539 Z= 0.295 Chirality : 0.047 0.233 1492 Planarity : 0.005 0.050 1764 Dihedral : 5.949 54.972 1587 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.85 % Allowed : 6.48 % 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: -0.20 (0.24), residues: 1211 helix: -1.30 (0.57), residues: 75 sheet: -0.39 (0.40), residues: 176 loop : 0.08 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 340 TYR 0.012 0.001 TYR B 301 PHE 0.015 0.001 PHE A 443 TRP 0.010 0.001 TRP A 510 HIS 0.006 0.001 HIS B 318 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 9872) covalent geometry : angle 0.57131 (13400) SS BOND : bond 0.00362 ( 50) SS BOND : angle 0.90023 ( 100) hydrogen bonds : bond 0.03547 ( 195) hydrogen bonds : angle 5.96075 ( 375) link_ALPHA1-3 : bond 0.00876 ( 1) link_ALPHA1-3 : angle 1.30180 ( 3) link_BETA1-4 : bond 0.00424 ( 4) link_BETA1-4 : angle 1.27818 ( 12) link_NAG-ASN : bond 0.00284 ( 8) link_NAG-ASN : angle 1.95552 ( 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 43 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.361 Fit side-chains REVERT: A 550 PHE cc_start: 0.7850 (m-80) cc_final: 0.7449 (m-80) REVERT: B 463 SER cc_start: 0.9132 (t) cc_final: 0.8925 (m) outliers start: 9 outliers final: 6 residues processed: 40 average time/residue: 0.0702 time to fit residues: 4.6828 Evaluate side-chains 38 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.0570 chunk 48 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 113 optimal weight: 30.0000 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.107820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.074578 restraints weight = 19964.000| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 3.18 r_work: 0.3192 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9935 Z= 0.106 Angle : 0.539 9.839 13539 Z= 0.271 Chirality : 0.045 0.239 1492 Planarity : 0.004 0.047 1764 Dihedral : 5.606 54.132 1587 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.47 % Favored : 96.45 % Rotamer: Outliers : 0.75 % Allowed : 6.77 % Favored : 92.48 % 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: -0.62 (0.63), residues: 68 sheet: -0.43 (0.41), residues: 176 loop : 0.16 (0.21), residues: 967 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 0.010 0.001 PHE A 219 TRP 0.006 0.001 TRP A 510 HIS 0.005 0.001 HIS B 318 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9872) covalent geometry : angle 0.53142 (13400) SS BOND : bond 0.00270 ( 50) SS BOND : angle 0.73345 ( 100) hydrogen bonds : bond 0.03156 ( 195) hydrogen bonds : angle 5.63601 ( 375) link_ALPHA1-3 : bond 0.00912 ( 1) link_ALPHA1-3 : angle 1.20000 ( 3) link_BETA1-4 : bond 0.00448 ( 4) link_BETA1-4 : angle 1.12340 ( 12) link_NAG-ASN : bond 0.00348 ( 8) link_NAG-ASN : angle 1.84133 ( 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 43 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.379 Fit side-chains REVERT: A 550 PHE cc_start: 0.7871 (m-80) cc_final: 0.7503 (m-80) REVERT: A 559 MET cc_start: 0.6479 (mmm) cc_final: 0.5975 (mmt) REVERT: H 187 LYS cc_start: 0.8530 (tptm) cc_final: 0.8317 (mttm) outliers start: 8 outliers final: 5 residues processed: 41 average time/residue: 0.0737 time to fit residues: 5.1675 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 : 0.330 ------------------------------------------------------------------------------- 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 282 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 97 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 114 optimal weight: 8.9990 chunk 110 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 58 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 118 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.105627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.072308 restraints weight = 19940.043| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.15 r_work: 0.3146 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9935 Z= 0.174 Angle : 0.580 8.632 13539 Z= 0.294 Chirality : 0.047 0.236 1492 Planarity : 0.004 0.048 1764 Dihedral : 5.800 54.909 1587 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.80 % Favored : 96.12 % Rotamer: Outliers : 1.03 % Allowed : 6.86 % Favored : 92.11 % 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: -0.19 (0.25), residues: 1211 helix: -1.02 (0.60), residues: 75 sheet: -0.40 (0.42), residues: 166 loop : 0.06 (0.21), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 203 TYR 0.011 0.001 TYR A 265 PHE 0.018 0.001 PHE B 534 TRP 0.009 0.001 TRP B 482 HIS 0.006 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 9872) covalent geometry : angle 0.56835 (13400) SS BOND : bond 0.00356 ( 50) SS BOND : angle 1.11366 ( 100) hydrogen bonds : bond 0.03592 ( 195) hydrogen bonds : angle 5.66411 ( 375) link_ALPHA1-3 : bond 0.00768 ( 1) link_ALPHA1-3 : angle 1.26730 ( 3) link_BETA1-4 : bond 0.00387 ( 4) link_BETA1-4 : angle 1.28327 ( 12) link_NAG-ASN : bond 0.00238 ( 8) link_NAG-ASN : angle 1.83638 ( 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 43 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.430 Fit side-chains REVERT: A 550 PHE cc_start: 0.7836 (m-80) cc_final: 0.7471 (m-80) REVERT: H 187 LYS cc_start: 0.8573 (tptm) cc_final: 0.8323 (mttm) outliers start: 11 outliers final: 6 residues processed: 39 average time/residue: 0.0750 time to fit residues: 5.0442 Evaluate side-chains 34 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 118 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 78 optimal weight: 0.0010 chunk 18 optimal weight: 3.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 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 = 0.3911 r_free = 0.3911 target = 0.106889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.073754 restraints weight = 20006.731| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.16 r_work: 0.3177 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9935 Z= 0.110 Angle : 0.534 8.438 13539 Z= 0.269 Chirality : 0.045 0.237 1492 Planarity : 0.004 0.046 1764 Dihedral : 5.584 53.845 1587 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.47 % Favored : 96.45 % Rotamer: Outliers : 0.85 % Allowed : 7.42 % Favored : 91.73 % 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: -0.03 (0.25), residues: 1211 helix: -0.41 (0.65), residues: 68 sheet: -0.37 (0.43), residues: 166 loop : 0.13 (0.21), residues: 977 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 0.018 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 covalent geometry : bond 0.00263 ( 9872) covalent geometry : angle 0.52154 (13400) SS BOND : bond 0.00274 ( 50) SS BOND : angle 1.13918 ( 100) hydrogen bonds : bond 0.03054 ( 195) hydrogen bonds : angle 5.53191 ( 375) link_ALPHA1-3 : bond 0.00743 ( 1) link_ALPHA1-3 : angle 1.19873 ( 3) link_BETA1-4 : bond 0.00425 ( 4) link_BETA1-4 : angle 1.07763 ( 12) link_NAG-ASN : bond 0.00352 ( 8) link_NAG-ASN : angle 1.76593 ( 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 43 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.360 Fit side-chains REVERT: A 484 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8837 (mm) REVERT: A 550 PHE cc_start: 0.7936 (m-80) cc_final: 0.7624 (m-80) REVERT: A 559 MET cc_start: 0.6383 (mmm) cc_final: 0.5949 (mmt) REVERT: H 187 LYS cc_start: 0.8510 (tptm) cc_final: 0.8251 (mttm) outliers start: 9 outliers final: 6 residues processed: 39 average time/residue: 0.0750 time to fit residues: 4.9181 Evaluate side-chains 34 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 88 optimal weight: 20.0000 chunk 20 optimal weight: 0.5980 chunk 60 optimal weight: 0.0040 chunk 110 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 24 optimal weight: 0.0870 chunk 94 optimal weight: 0.0270 overall best weight: 0.3228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 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 = 0.3907 r_free = 0.3907 target = 0.110542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.075293 restraints weight = 20986.541| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 3.35 r_work: 0.3187 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9935 Z= 0.082 Angle : 0.501 8.421 13539 Z= 0.252 Chirality : 0.044 0.236 1492 Planarity : 0.004 0.044 1764 Dihedral : 5.335 52.900 1587 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.39 % Favored : 96.53 % Rotamer: Outliers : 0.66 % Allowed : 7.61 % Favored : 91.73 % 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: 0.16 (0.25), residues: 1211 helix: 0.46 (0.72), residues: 61 sheet: -0.39 (0.45), residues: 146 loop : 0.23 (0.21), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 135 TYR 0.009 0.001 TYR B 590 PHE 0.029 0.001 PHE B 534 TRP 0.006 0.001 TRP B 205 HIS 0.005 0.000 HIS B 318 Details of bonding type rmsd covalent geometry : bond 0.00188 ( 9872) covalent geometry : angle 0.49106 (13400) SS BOND : bond 0.00188 ( 50) SS BOND : angle 0.93327 ( 100) hydrogen bonds : bond 0.02708 ( 195) hydrogen bonds : angle 5.35839 ( 375) link_ALPHA1-3 : bond 0.00644 ( 1) link_ALPHA1-3 : angle 1.20645 ( 3) link_BETA1-4 : bond 0.00426 ( 4) link_BETA1-4 : angle 1.06517 ( 12) link_NAG-ASN : bond 0.00409 ( 8) link_NAG-ASN : angle 1.66983 ( 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 40 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.480 Fit side-chains REVERT: A 484 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8833 (mm) REVERT: A 550 PHE cc_start: 0.7971 (m-80) cc_final: 0.7700 (m-80) REVERT: B 31 MET cc_start: 0.7656 (mtp) cc_final: 0.7422 (ttm) REVERT: H 187 LYS cc_start: 0.8465 (tptm) cc_final: 0.8230 (mttm) outliers start: 7 outliers final: 3 residues processed: 38 average time/residue: 0.0874 time to fit residues: 5.4360 Evaluate side-chains 34 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 A residue 484 ILE 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: 10.0000 chunk 17 optimal weight: 0.0060 chunk 73 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 87 optimal weight: 0.0000 chunk 107 optimal weight: 4.9990 chunk 92 optimal weight: 0.2980 chunk 103 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 overall best weight: 0.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.110743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.075637 restraints weight = 20851.362| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 3.34 r_work: 0.3194 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9935 Z= 0.081 Angle : 0.499 8.430 13539 Z= 0.249 Chirality : 0.044 0.228 1492 Planarity : 0.004 0.044 1764 Dihedral : 5.227 53.065 1587 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.22 % Favored : 96.70 % Rotamer: Outliers : 0.38 % Allowed : 8.08 % 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: 0.25 (0.25), residues: 1211 helix: 0.62 (0.73), residues: 61 sheet: -0.24 (0.45), residues: 158 loop : 0.28 (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 0.038 0.001 PHE B 534 TRP 0.005 0.001 TRP A 402 HIS 0.005 0.000 HIS B 318 Details of bonding type rmsd covalent geometry : bond 0.00181 ( 9872) covalent geometry : angle 0.49085 (13400) SS BOND : bond 0.00190 ( 50) SS BOND : angle 0.76275 ( 100) hydrogen bonds : bond 0.02617 ( 195) hydrogen bonds : angle 5.31938 ( 375) link_ALPHA1-3 : bond 0.00634 ( 1) link_ALPHA1-3 : angle 1.26826 ( 3) link_BETA1-4 : bond 0.00428 ( 4) link_BETA1-4 : angle 1.08941 ( 12) link_NAG-ASN : bond 0.00382 ( 8) link_NAG-ASN : angle 1.60027 ( 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 38 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.379 Fit side-chains REVERT: A 484 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8827 (mm) REVERT: A 550 PHE cc_start: 0.7976 (m-80) cc_final: 0.7727 (m-80) REVERT: A 559 MET cc_start: 0.6321 (mmm) cc_final: 0.5900 (mmt) REVERT: B 354 ARG cc_start: 0.7618 (ttp-110) cc_final: 0.7361 (ttp-110) REVERT: H 187 LYS cc_start: 0.8432 (tptm) cc_final: 0.8133 (mttm) outliers start: 4 outliers final: 3 residues processed: 37 average time/residue: 0.0828 time to fit residues: 4.8793 Evaluate side-chains 34 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 A residue 484 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.1980 chunk 44 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 115 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.109333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.073991 restraints weight = 20940.721| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 3.35 r_work: 0.3173 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9935 Z= 0.109 Angle : 0.516 8.221 13539 Z= 0.258 Chirality : 0.045 0.217 1492 Planarity : 0.004 0.045 1764 Dihedral : 5.308 53.733 1587 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.55 % Favored : 96.37 % Rotamer: Outliers : 0.47 % Allowed : 8.18 % Favored : 91.35 % 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: 0.23 (0.25), residues: 1211 helix: 0.53 (0.72), residues: 61 sheet: -0.36 (0.46), residues: 143 loop : 0.28 (0.21), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 354 TYR 0.008 0.001 TYR B 590 PHE 0.034 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 covalent geometry : bond 0.00265 ( 9872) covalent geometry : angle 0.50730 (13400) SS BOND : bond 0.00239 ( 50) SS BOND : angle 0.88339 ( 100) hydrogen bonds : bond 0.02924 ( 195) hydrogen bonds : angle 5.33779 ( 375) link_ALPHA1-3 : bond 0.00545 ( 1) link_ALPHA1-3 : angle 1.31360 ( 3) link_BETA1-4 : bond 0.00414 ( 4) link_BETA1-4 : angle 1.16345 ( 12) link_NAG-ASN : bond 0.00302 ( 8) link_NAG-ASN : angle 1.59194 ( 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 36 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.301 Fit side-chains REVERT: A 484 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8813 (mm) REVERT: A 550 PHE cc_start: 0.7990 (m-80) cc_final: 0.7739 (m-80) REVERT: H 187 LYS cc_start: 0.8448 (tptm) cc_final: 0.8171 (mttm) outliers start: 5 outliers final: 3 residues processed: 34 average time/residue: 0.0910 time to fit residues: 4.7448 Evaluate side-chains 34 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 105 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 34 optimal weight: 0.0470 chunk 67 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.109461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.074182 restraints weight = 20972.991| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 3.36 r_work: 0.3159 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9935 Z= 0.101 Angle : 0.510 8.245 13539 Z= 0.255 Chirality : 0.045 0.216 1492 Planarity : 0.004 0.044 1764 Dihedral : 5.288 53.581 1587 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.55 % Favored : 96.37 % Rotamer: Outliers : 0.38 % Allowed : 8.46 % Favored : 91.17 % 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 (0.25), residues: 1211 helix: 0.55 (0.72), residues: 61 sheet: -0.15 (0.46), residues: 153 loop : 0.28 (0.21), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 354 TYR 0.008 0.001 TYR B 590 PHE 0.030 0.001 PHE B 534 TRP 0.004 0.001 TRP B 482 HIS 0.005 0.001 HIS B 318 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 9872) covalent geometry : angle 0.50219 (13400) SS BOND : bond 0.00227 ( 50) SS BOND : angle 0.80806 ( 100) hydrogen bonds : bond 0.02804 ( 195) hydrogen bonds : angle 5.34144 ( 375) link_ALPHA1-3 : bond 0.00543 ( 1) link_ALPHA1-3 : angle 1.31246 ( 3) link_BETA1-4 : bond 0.00395 ( 4) link_BETA1-4 : angle 1.11615 ( 12) link_NAG-ASN : bond 0.00327 ( 8) link_NAG-ASN : angle 1.57259 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2467.35 seconds wall clock time: 42 minutes 46.53 seconds (2566.53 seconds total)