Starting phenix.real_space_refine on Mon Jul 28 01:16:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mn6_23917/07_2025/7mn6_23917.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mn6_23917/07_2025/7mn6_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_2025/7mn6_23917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mn6_23917/07_2025/7mn6_23917.map" model { file = "/net/cci-nas-00/data/ceres_data/7mn6_23917/07_2025/7mn6_23917.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mn6_23917/07_2025/7mn6_23917.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.045 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.67, per 1000 atoms: 0.69 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: 2.47 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.24 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: 3.07 Time building geometry restraints manager: 2.93 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: 6.860 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: 0.430 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.450 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.950 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.23), 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 TRP 0.076 0.004 TRP B 415 HIS 0.001 0.000 HIS B 349 PHE 0.045 0.003 PHE B 400 TYR 0.119 0.005 TYR A 50 ARG 0.007 0.001 ARG A 164 Details of bonding type rmsd link_NAG-ASN : bond 0.01046 ( 8) link_NAG-ASN : angle 5.66630 ( 24) link_BETA1-4 : bond 0.02653 ( 4) link_BETA1-4 : angle 6.01590 ( 12) link_ALPHA1-3 : bond 0.02699 ( 1) link_ALPHA1-3 : angle 2.11481 ( 3) hydrogen bonds : bond 0.21963 ( 195) hydrogen bonds : angle 8.29895 ( 375) SS BOND : bond 0.02224 ( 50) SS BOND : angle 3.71627 ( 100) covalent geometry : bond 0.01266 ( 9872) covalent geometry : angle 1.51118 (13400) *********************** 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 : 1.146 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: 0.3146 time to fit residues: 47.7838 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 : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 400 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.112648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.079545 restraints weight = 19349.939| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.97 r_work: 0.3261 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9935 Z= 0.191 Angle : 0.703 8.919 13539 Z= 0.361 Chirality : 0.050 0.251 1492 Planarity : 0.005 0.044 1764 Dihedral : 7.585 59.129 1587 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.56 % Allowed : 4.89 % Favored : 94.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.24), residues: 1211 helix: -1.36 (0.55), residues: 74 sheet: -0.50 (0.38), residues: 181 loop : 0.19 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 482 HIS 0.010 0.001 HIS B 318 PHE 0.016 0.002 PHE A 219 TYR 0.017 0.002 TYR B 554 ARG 0.004 0.001 ARG A 475 Details of bonding type rmsd link_NAG-ASN : bond 0.00368 ( 8) link_NAG-ASN : angle 2.55828 ( 24) link_BETA1-4 : bond 0.00389 ( 4) link_BETA1-4 : angle 2.33340 ( 12) link_ALPHA1-3 : bond 0.01308 ( 1) link_ALPHA1-3 : angle 2.27183 ( 3) hydrogen bonds : bond 0.04390 ( 195) hydrogen bonds : angle 6.26320 ( 375) SS BOND : bond 0.00529 ( 50) SS BOND : angle 1.36685 ( 100) covalent geometry : bond 0.00465 ( 9872) covalent geometry : angle 0.68421 (13400) *********************** 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 54 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 1.343 Fit side-chains REVERT: A 550 PHE cc_start: 0.7814 (m-80) cc_final: 0.7418 (m-80) REVERT: A 559 MET cc_start: 0.6925 (mmm) cc_final: 0.6208 (mmt) REVERT: H 187 LYS cc_start: 0.8483 (tptm) cc_final: 0.8265 (mttm) REVERT: H 208 TYR cc_start: 0.7664 (m-80) cc_final: 0.7448 (m-80) outliers start: 6 outliers final: 4 residues processed: 53 average time/residue: 0.2797 time to fit residues: 23.4495 Evaluate side-chains 39 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 431 LEU 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 95 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 0.4980 chunk 21 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 133 GLN A 435 ASN A 545 HIS 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 = 0.3924 r_free = 0.3924 target = 0.112733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.079146 restraints weight = 20518.313| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.91 r_work: 0.3185 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9935 Z= 0.189 Angle : 0.630 10.365 13539 Z= 0.323 Chirality : 0.048 0.221 1492 Planarity : 0.005 0.051 1764 Dihedral : 6.313 55.672 1587 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.13 % Allowed : 5.45 % Favored : 93.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.24), residues: 1211 helix: -1.34 (0.57), residues: 75 sheet: -0.50 (0.38), residues: 182 loop : 0.09 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 510 HIS 0.009 0.001 HIS B 193 PHE 0.020 0.002 PHE A 443 TYR 0.013 0.001 TYR A 265 ARG 0.003 0.000 ARG A 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 8) link_NAG-ASN : angle 2.02503 ( 24) link_BETA1-4 : bond 0.00598 ( 4) link_BETA1-4 : angle 1.48826 ( 12) link_ALPHA1-3 : bond 0.01043 ( 1) link_ALPHA1-3 : angle 1.09085 ( 3) hydrogen bonds : bond 0.04199 ( 195) hydrogen bonds : angle 6.05044 ( 375) SS BOND : bond 0.00488 ( 50) SS BOND : angle 1.13404 ( 100) covalent geometry : bond 0.00465 ( 9872) covalent geometry : angle 0.61785 (13400) *********************** 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 48 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 1.003 Fit side-chains REVERT: A 550 PHE cc_start: 0.7933 (m-80) cc_final: 0.7568 (m-80) REVERT: H 209 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7589 (mp) outliers start: 12 outliers final: 6 residues processed: 43 average time/residue: 0.1700 time to fit residues: 12.5446 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 : 1.150 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain H residue 209 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 31 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 53 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 chunk 109 optimal weight: 0.0370 chunk 51 optimal weight: 7.9990 chunk 4 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- 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 = 0.3919 r_free = 0.3919 target = 0.107146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.074017 restraints weight = 19793.813| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 3.15 r_work: 0.3181 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9935 Z= 0.131 Angle : 0.561 8.140 13539 Z= 0.283 Chirality : 0.046 0.238 1492 Planarity : 0.004 0.047 1764 Dihedral : 5.793 54.361 1587 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.89 % Favored : 97.03 % Rotamer: Outliers : 0.94 % Allowed : 6.02 % Favored : 93.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.25), residues: 1211 helix: -1.25 (0.57), residues: 75 sheet: -0.42 (0.40), residues: 176 loop : 0.11 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 482 HIS 0.006 0.001 HIS B 318 PHE 0.017 0.001 PHE B 534 TYR 0.015 0.001 TYR H 224 ARG 0.002 0.000 ARG B 340 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 8) link_NAG-ASN : angle 1.90457 ( 24) link_BETA1-4 : bond 0.00423 ( 4) link_BETA1-4 : angle 1.16017 ( 12) link_ALPHA1-3 : bond 0.00946 ( 1) link_ALPHA1-3 : angle 1.37537 ( 3) hydrogen bonds : bond 0.03260 ( 195) hydrogen bonds : angle 5.88264 ( 375) SS BOND : bond 0.00321 ( 50) SS BOND : angle 0.92608 ( 100) covalent geometry : bond 0.00318 ( 9872) covalent geometry : angle 0.55102 (13400) *********************** 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 44 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 1.081 Fit side-chains REVERT: A 550 PHE cc_start: 0.7841 (m-80) cc_final: 0.7499 (m-80) REVERT: B 463 SER cc_start: 0.9146 (t) cc_final: 0.8940 (m) REVERT: H 187 LYS cc_start: 0.8496 (tptp) cc_final: 0.8172 (mttm) REVERT: H 208 TYR cc_start: 0.7925 (m-80) cc_final: 0.7390 (m-80) outliers start: 10 outliers final: 5 residues processed: 41 average time/residue: 0.1632 time to fit residues: 11.5322 Evaluate side-chains 35 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET 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 89 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 113 optimal weight: 20.0000 chunk 40 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 = 0.3866 r_free = 0.3866 target = 0.105964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.072230 restraints weight = 19951.343| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 3.15 r_work: 0.3158 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3586 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= 0.133 Angle : 0.551 7.309 13539 Z= 0.277 Chirality : 0.046 0.242 1492 Planarity : 0.004 0.048 1764 Dihedral : 5.681 54.214 1587 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.72 % Favored : 96.20 % Rotamer: Outliers : 0.75 % Allowed : 6.86 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.25), residues: 1211 helix: -0.62 (0.63), residues: 68 sheet: -0.36 (0.42), residues: 166 loop : 0.14 (0.21), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 205 HIS 0.005 0.001 HIS B 318 PHE 0.016 0.001 PHE B 534 TYR 0.009 0.001 TYR A 265 ARG 0.003 0.000 ARG B 203 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 8) link_NAG-ASN : angle 1.82922 ( 24) link_BETA1-4 : bond 0.00444 ( 4) link_BETA1-4 : angle 1.18345 ( 12) link_ALPHA1-3 : bond 0.00864 ( 1) link_ALPHA1-3 : angle 1.12072 ( 3) hydrogen bonds : bond 0.03218 ( 195) hydrogen bonds : angle 5.68202 ( 375) SS BOND : bond 0.00285 ( 50) SS BOND : angle 1.05168 ( 100) covalent geometry : bond 0.00325 ( 9872) covalent geometry : angle 0.53953 (13400) *********************** 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 41 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 1.072 Fit side-chains REVERT: A 550 PHE cc_start: 0.7901 (m-80) cc_final: 0.7593 (m-80) REVERT: H 208 TYR cc_start: 0.7998 (m-80) cc_final: 0.7442 (m-80) outliers start: 8 outliers final: 6 residues processed: 38 average time/residue: 0.1692 time to fit residues: 11.0428 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 : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 158 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 112 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 111 optimal weight: 8.9990 chunk 46 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 98 optimal weight: 0.1980 chunk 24 optimal weight: 0.0010 chunk 110 optimal weight: 5.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- 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 = 0.3874 r_free = 0.3874 target = 0.108388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.073213 restraints weight = 20549.957| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 3.27 r_work: 0.3170 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9935 Z= 0.115 Angle : 0.531 8.075 13539 Z= 0.268 Chirality : 0.045 0.240 1492 Planarity : 0.004 0.047 1764 Dihedral : 5.588 53.568 1587 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.14 % Favored : 96.78 % Rotamer: Outliers : 0.85 % Allowed : 6.86 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.25), residues: 1211 helix: 0.19 (0.68), residues: 61 sheet: -0.38 (0.43), residues: 161 loop : 0.20 (0.21), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 510 HIS 0.005 0.001 HIS B 318 PHE 0.018 0.001 PHE B 534 TYR 0.009 0.001 TYR B 590 ARG 0.002 0.000 ARG A 193 Details of bonding type rmsd link_NAG-ASN : bond 0.00326 ( 8) link_NAG-ASN : angle 1.74815 ( 24) link_BETA1-4 : bond 0.00391 ( 4) link_BETA1-4 : angle 1.08299 ( 12) link_ALPHA1-3 : bond 0.00846 ( 1) link_ALPHA1-3 : angle 1.29577 ( 3) hydrogen bonds : bond 0.02988 ( 195) hydrogen bonds : angle 5.58364 ( 375) SS BOND : bond 0.00256 ( 50) SS BOND : angle 1.17997 ( 100) covalent geometry : bond 0.00280 ( 9872) covalent geometry : angle 0.51725 (13400) *********************** 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 44 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 1.155 Fit side-chains revert: symmetry clash REVERT: A 484 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8820 (mm) REVERT: A 550 PHE cc_start: 0.7966 (m-80) cc_final: 0.7671 (m-80) REVERT: H 208 TYR cc_start: 0.7817 (m-80) cc_final: 0.7597 (m-80) outliers start: 9 outliers final: 7 residues processed: 41 average time/residue: 0.2113 time to fit residues: 14.4944 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 : 1.332 ------------------------------------------------------------------------------- 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 500 CYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 58 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.105439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.072313 restraints weight = 20134.449| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.13 r_work: 0.3138 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9935 Z= 0.168 Angle : 0.564 7.554 13539 Z= 0.284 Chirality : 0.046 0.230 1492 Planarity : 0.004 0.048 1764 Dihedral : 5.733 54.503 1587 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.13 % Favored : 95.79 % Rotamer: Outliers : 1.13 % Allowed : 7.24 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.25), residues: 1211 helix: -0.42 (0.65), residues: 68 sheet: -0.39 (0.43), residues: 166 loop : 0.13 (0.21), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 482 HIS 0.006 0.001 HIS B 318 PHE 0.018 0.001 PHE B 534 TYR 0.010 0.001 TYR A 265 ARG 0.002 0.000 ARG B 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00241 ( 8) link_NAG-ASN : angle 1.77671 ( 24) link_BETA1-4 : bond 0.00399 ( 4) link_BETA1-4 : angle 1.24945 ( 12) link_ALPHA1-3 : bond 0.00601 ( 1) link_ALPHA1-3 : angle 1.27188 ( 3) hydrogen bonds : bond 0.03377 ( 195) hydrogen bonds : angle 5.61323 ( 375) SS BOND : bond 0.00340 ( 50) SS BOND : angle 1.12223 ( 100) covalent geometry : bond 0.00419 ( 9872) covalent geometry : angle 0.55179 (13400) *********************** 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: 12 poor density : 31 time to evaluate : 1.096 Fit side-chains revert: symmetry clash REVERT: A 484 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8838 (mm) REVERT: A 550 PHE cc_start: 0.7921 (m-80) cc_final: 0.7608 (m-80) REVERT: H 187 LYS cc_start: 0.8617 (tptp) cc_final: 0.8178 (mttm) REVERT: H 208 TYR cc_start: 0.7953 (m-80) cc_final: 0.7697 (m-80) outliers start: 12 outliers final: 8 residues processed: 40 average time/residue: 0.1696 time to fit residues: 11.8988 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 : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 500 CYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 16 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 24 optimal weight: 0.0570 chunk 45 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 60 optimal weight: 0.0000 chunk 39 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.106876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.072924 restraints weight = 20474.509| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.24 r_work: 0.3166 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9935 Z= 0.100 Angle : 0.523 7.585 13539 Z= 0.263 Chirality : 0.045 0.233 1492 Planarity : 0.004 0.045 1764 Dihedral : 5.517 53.465 1587 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.30 % Favored : 96.61 % Rotamer: Outliers : 0.75 % Allowed : 7.80 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.25), residues: 1211 helix: 0.09 (0.67), residues: 61 sheet: -0.45 (0.43), residues: 158 loop : 0.19 (0.21), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 482 HIS 0.005 0.001 HIS B 318 PHE 0.028 0.001 PHE B 534 TYR 0.008 0.001 TYR B 590 ARG 0.002 0.000 ARG B 340 Details of bonding type rmsd link_NAG-ASN : bond 0.00350 ( 8) link_NAG-ASN : angle 1.71678 ( 24) link_BETA1-4 : bond 0.00413 ( 4) link_BETA1-4 : angle 1.09124 ( 12) link_ALPHA1-3 : bond 0.00636 ( 1) link_ALPHA1-3 : angle 1.22253 ( 3) hydrogen bonds : bond 0.02924 ( 195) hydrogen bonds : angle 5.47703 ( 375) SS BOND : bond 0.00245 ( 50) SS BOND : angle 0.97208 ( 100) covalent geometry : bond 0.00238 ( 9872) covalent geometry : angle 0.51235 (13400) *********************** 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: 8 poor density : 31 time to evaluate : 1.464 Fit side-chains revert: symmetry clash REVERT: A 484 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8831 (mm) REVERT: A 550 PHE cc_start: 0.7984 (m-80) cc_final: 0.7702 (m-80) outliers start: 8 outliers final: 6 residues processed: 37 average time/residue: 0.1874 time to fit residues: 11.7641 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 : 1.049 ------------------------------------------------------------------------------- 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 500 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 105 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 50 optimal weight: 0.0980 chunk 83 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 GLN A 405 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.107854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.075431 restraints weight = 20689.185| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 3.01 r_work: 0.3210 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 9935 Z= 0.269 Angle : 0.655 9.261 13539 Z= 0.332 Chirality : 0.050 0.208 1492 Planarity : 0.005 0.047 1764 Dihedral : 6.103 56.063 1587 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.79 % Favored : 95.13 % Rotamer: Outliers : 1.03 % Allowed : 7.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.25), residues: 1211 helix: -1.21 (0.60), residues: 75 sheet: -0.42 (0.45), residues: 150 loop : -0.10 (0.21), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 482 HIS 0.008 0.001 HIS B 249 PHE 0.036 0.002 PHE B 534 TYR 0.013 0.002 TYR A 265 ARG 0.003 0.001 ARG B 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 8) link_NAG-ASN : angle 1.90034 ( 24) link_BETA1-4 : bond 0.00347 ( 4) link_BETA1-4 : angle 1.47344 ( 12) link_ALPHA1-3 : bond 0.00483 ( 1) link_ALPHA1-3 : angle 1.45305 ( 3) hydrogen bonds : bond 0.04129 ( 195) hydrogen bonds : angle 5.79157 ( 375) SS BOND : bond 0.00485 ( 50) SS BOND : angle 1.40282 ( 100) covalent geometry : bond 0.00664 ( 9872) covalent geometry : angle 0.64028 (13400) *********************** 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 42 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 1.071 Fit side-chains revert: symmetry clash REVERT: A 484 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.8947 (mm) REVERT: A 550 PHE cc_start: 0.8003 (m-80) cc_final: 0.7701 (m-80) outliers start: 11 outliers final: 8 residues processed: 39 average time/residue: 0.1704 time to fit residues: 11.3298 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 : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 500 CYS 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 55 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 63 optimal weight: 0.2980 chunk 95 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 57 optimal weight: 0.0570 chunk 2 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 24 optimal weight: 0.0070 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.105984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.073041 restraints weight = 20114.198| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 3.15 r_work: 0.3154 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9935 Z= 0.097 Angle : 0.531 7.801 13539 Z= 0.267 Chirality : 0.045 0.229 1492 Planarity : 0.004 0.044 1764 Dihedral : 5.616 53.401 1587 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.55 % Favored : 96.37 % Rotamer: Outliers : 0.75 % Allowed : 7.61 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.25), residues: 1211 helix: -0.03 (0.69), residues: 61 sheet: -0.55 (0.44), residues: 158 loop : 0.11 (0.21), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 415 HIS 0.006 0.001 HIS B 318 PHE 0.035 0.001 PHE B 534 TYR 0.009 0.001 TYR H 224 ARG 0.002 0.000 ARG B 340 Details of bonding type rmsd link_NAG-ASN : bond 0.00356 ( 8) link_NAG-ASN : angle 1.74415 ( 24) link_BETA1-4 : bond 0.00429 ( 4) link_BETA1-4 : angle 1.11558 ( 12) link_ALPHA1-3 : bond 0.00622 ( 1) link_ALPHA1-3 : angle 1.26061 ( 3) hydrogen bonds : bond 0.02974 ( 195) hydrogen bonds : angle 5.55277 ( 375) SS BOND : bond 0.00240 ( 50) SS BOND : angle 0.88056 ( 100) covalent geometry : bond 0.00227 ( 9872) covalent geometry : angle 0.52151 (13400) ********************** 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: 8 poor density : 33 time to evaluate : 1.325 Fit side-chains revert: symmetry clash REVERT: A 484 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8834 (mm) REVERT: A 550 PHE cc_start: 0.8017 (m-80) cc_final: 0.7769 (m-80) REVERT: A 559 MET cc_start: 0.6173 (mmm) cc_final: 0.5742 (mmt) REVERT: H 187 LYS cc_start: 0.8590 (tptp) cc_final: 0.8165 (tppt) outliers start: 8 outliers final: 7 residues processed: 38 average time/residue: 0.1951 time to fit residues: 13.0629 Evaluate side-chains 39 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 2.357 ------------------------------------------------------------------------------- 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 500 CYS 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 8 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 90 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3891 r_free = 0.3891 target = 0.105704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.072732 restraints weight = 20083.854| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 3.13 r_work: 0.3157 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9935 Z= 0.117 Angle : 0.529 7.730 13539 Z= 0.265 Chirality : 0.045 0.221 1492 Planarity : 0.004 0.043 1764 Dihedral : 5.536 53.456 1587 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.96 % Favored : 95.95 % Rotamer: Outliers : 0.75 % Allowed : 7.80 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.25), residues: 1211 helix: 0.05 (0.69), residues: 61 sheet: -0.50 (0.44), residues: 158 loop : 0.16 (0.21), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 510 HIS 0.005 0.001 HIS B 318 PHE 0.032 0.001 PHE B 534 TYR 0.008 0.001 TYR B 590 ARG 0.001 0.000 ARG A 193 Details of bonding type rmsd link_NAG-ASN : bond 0.00292 ( 8) link_NAG-ASN : angle 1.66741 ( 24) link_BETA1-4 : bond 0.00392 ( 4) link_BETA1-4 : angle 1.20863 ( 12) link_ALPHA1-3 : bond 0.00526 ( 1) link_ALPHA1-3 : angle 1.30999 ( 3) hydrogen bonds : bond 0.03084 ( 195) hydrogen bonds : angle 5.48247 ( 375) SS BOND : bond 0.00265 ( 50) SS BOND : angle 0.90997 ( 100) covalent geometry : bond 0.00284 ( 9872) covalent geometry : angle 0.51984 (13400) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5601.42 seconds wall clock time: 101 minutes 8.28 seconds (6068.28 seconds total)