Starting phenix.real_space_refine on Sun Jul 27 21:58:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mn5_23916/07_2025/7mn5_23916.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mn5_23916/07_2025/7mn5_23916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mn5_23916/07_2025/7mn5_23916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mn5_23916/07_2025/7mn5_23916.map" model { file = "/net/cci-nas-00/data/ceres_data/7mn5_23916/07_2025/7mn5_23916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mn5_23916/07_2025/7mn5_23916.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.054 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 5896 2.51 5 N 1695 2.21 5 O 1817 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9526 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4496 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 37, 'TRANS': 547} Chain breaks: 2 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: "B" Number of atoms: 4471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4471 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 38, 'TRANS': 540} Chain breaks: 3 Chain: "C" 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: "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: 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: "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: 6.71, per 1000 atoms: 0.70 Number of scatterers: 9526 At special positions: 0 Unit cell: (80.995, 141.115, 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 1817 8.00 N 1695 7.00 C 5896 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=2.02 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=2.04 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=1.71 Simple disulfide: pdb=" SG CYS A 246 " - pdb=" SG CYS A 255 " distance=2.04 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=2.04 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 529 " distance=2.02 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=2.03 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=2.05 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 629 " distance=2.05 Simple disulfide: pdb=" SG CYS H 182 " - pdb=" SG CYS H 196 " distance=2.11 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=2.02 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 53 " distance=2.05 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 195 " - pdb=" SG CYS B 204 " distance=2.07 Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 212 " distance=2.04 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS B 227 " distance=2.03 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 235 " distance=2.04 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 244 " distance=2.03 Simple disulfide: pdb=" SG CYS B 240 " - pdb=" SG CYS B 252 " distance=2.03 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=2.04 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=2.12 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=2.03 Simple disulfide: pdb=" SG CYS B 531 " - pdb=" SG CYS B 540 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 584 " distance=2.03 Simple disulfide: pdb=" SG CYS B 587 " - pdb=" SG CYS B 596 " distance=2.06 Simple disulfide: pdb=" SG CYS B 600 " - pdb=" SG CYS B 623 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM 9524 O5 NAG B1502 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " 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 B 259 " " NAG D 1 " - " ASN A 469 " " NAG E 1 " - " ASN A 250 " Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 1.2 seconds 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2222 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 26 sheets defined 15.7% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 41 through 54 Processing helix chain 'A' and resid 74 through 80 removed outlier: 4.181A 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 167 removed outlier: 3.920A pdb=" N ILE A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 198 through 202 Processing helix chain 'A' and resid 347 through 352 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 380 through 390 removed outlier: 4.123A 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: 3.591A pdb=" N HIS A 466 " --> pdb=" O CYS A 463 " (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 'H' and resid 186 through 190 removed outlier: 3.802A pdb=" N CYS H 190 " --> pdb=" O LYS H 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 51 Processing helix chain 'B' and resid 71 through 75 Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 199 through 203 removed outlier: 4.197A pdb=" N ARG B 203 " --> pdb=" O LYS B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 212 removed outlier: 3.888A pdb=" N CYS B 212 " --> pdb=" O SER B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 347 through 351 Processing helix chain 'B' and resid 360 through 365 Processing helix chain 'B' and resid 377 through 381 removed outlier: 3.575A pdb=" N PHE B 381 " --> pdb=" O PRO B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 398 removed outlier: 3.995A pdb=" N GLN B 398 " --> pdb=" O PRO B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 401 No H-bonds generated for 'chain 'B' and resid 399 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 507 Processing helix chain 'B' and resid 515 through 519 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 7.288A 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: 6.965A 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: 5.372A pdb=" N GLY A 146 " --> pdb=" O PHE A 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 231 through 235 removed outlier: 7.732A pdb=" N GLY A 234 " --> pdb=" O CYS A 243 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N CYS A 243 " --> pdb=" O GLY A 234 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 249 through 251 Processing sheet with id=AA6, first strand: chain 'A' and resid 280 through 282 Processing sheet with id=AA7, first strand: chain 'A' and resid 300 through 302 removed outlier: 7.190A pdb=" N VAL A 296 " --> pdb=" O CYS A 320 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 356 through 357 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 363 removed outlier: 6.376A pdb=" N LEU A 397 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N MET A 433 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE A 399 " --> pdb=" O MET A 433 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N PHE A 428 " --> pdb=" O ARG A 453 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N TYR A 455 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU A 430 " --> pdb=" O TYR A 455 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N SER A 457 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE A 432 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N LYS A 485 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE A 456 " --> pdb=" O LYS A 485 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 523 through 525 removed outlier: 3.535A pdb=" N TYR A 523 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 528 " --> pdb=" O ARG A 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 542 through 545 Processing sheet with id=AB3, first strand: chain 'A' and resid 579 through 581 Processing sheet with id=AB4, first strand: chain 'A' and resid 593 through 595 Processing sheet with id=AB5, first strand: chain 'A' and resid 602 through 604 Processing sheet with id=AB6, first strand: chain 'H' and resid 216 through 217 Processing sheet with id=AB7, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AB8, first strand: chain 'B' and resid 60 through 63 removed outlier: 7.319A pdb=" N LEU B 154 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA B 115 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N GLN B 156 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU B 117 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL B 153 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 258 through 260 Processing sheet with id=AC1, first strand: chain 'B' and resid 272 through 275 removed outlier: 3.622A pdb=" N GLU B 280 " --> pdb=" O ASN B 275 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 289 through 291 Processing sheet with id=AC3, first strand: chain 'B' and resid 319 through 322 Processing sheet with id=AC4, first strand: chain 'B' and resid 342 through 343 removed outlier: 6.889A pdb=" N CYS B 342 " --> pdb=" O PHE B 371 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 374 through 376 removed outlier: 6.621A pdb=" N LEU B 374 " --> pdb=" O TYR B 411 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LEU B 465 " --> pdb=" O TYR B 441 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 443 " --> pdb=" O LEU B 465 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA B 466 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N THR B 496 " --> pdb=" O ALA B 466 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE B 468 " --> pdb=" O THR B 496 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 553 through 556 Processing sheet with id=AC7, first strand: chain 'B' and resid 590 through 592 Processing sheet with id=AC8, first strand: chain 'B' and resid 615 through 617 187 hydrogen bonds defined for protein. 333 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: 3.18 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2062 1.33 - 1.45: 2147 1.45 - 1.57: 5398 1.57 - 1.69: 2 1.69 - 1.81: 134 Bond restraints: 9743 Sorted by residual: bond pdb=" CA HIS A 578 " pdb=" C HIS A 578 " ideal model delta sigma weight residual 1.520 1.549 -0.029 4.80e-03 4.34e+04 3.77e+01 bond pdb=" N PRO A 512 " pdb=" CD PRO A 512 " ideal model delta sigma weight residual 1.473 1.399 0.074 1.40e-02 5.10e+03 2.79e+01 bond pdb=" CA PRO A 403 " pdb=" C PRO A 403 " ideal model delta sigma weight residual 1.514 1.542 -0.028 5.50e-03 3.31e+04 2.62e+01 bond pdb=" N PRO B 316 " pdb=" CD PRO B 316 " ideal model delta sigma weight residual 1.473 1.410 0.063 1.40e-02 5.10e+03 2.02e+01 bond pdb=" CA SER A 401 " pdb=" C SER A 401 " ideal model delta sigma weight residual 1.521 1.576 -0.055 1.26e-02 6.30e+03 1.89e+01 ... (remaining 9738 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 10558 1.74 - 3.49: 2248 3.49 - 5.23: 359 5.23 - 6.98: 51 6.98 - 8.72: 5 Bond angle restraints: 13221 Sorted by residual: angle pdb=" C GLU B 348 " pdb=" CA GLU B 348 " pdb=" CB GLU B 348 " ideal model delta sigma weight residual 116.54 109.39 7.15 1.15e+00 7.56e-01 3.87e+01 angle pdb=" CA LYS B 336 " pdb=" C LYS B 336 " pdb=" N PRO B 337 " ideal model delta sigma weight residual 117.68 121.52 -3.84 7.10e-01 1.98e+00 2.93e+01 angle pdb=" N ALA B 87 " pdb=" CA ALA B 87 " pdb=" C ALA B 87 " ideal model delta sigma weight residual 108.99 117.42 -8.43 1.57e+00 4.06e-01 2.88e+01 angle pdb=" C SER B 335 " pdb=" N LYS B 336 " pdb=" CA LYS B 336 " ideal model delta sigma weight residual 122.07 128.95 -6.88 1.44e+00 4.82e-01 2.28e+01 angle pdb=" CA ASP B 421 " pdb=" CB ASP B 421 " pdb=" CG ASP B 421 " ideal model delta sigma weight residual 112.60 117.36 -4.76 1.00e+00 1.00e+00 2.27e+01 ... (remaining 13216 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.86: 5921 21.86 - 43.72: 170 43.72 - 65.59: 49 65.59 - 87.45: 19 87.45 - 109.31: 5 Dihedral angle restraints: 6164 sinusoidal: 2705 harmonic: 3459 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 -177.93 -89.07 1 1.00e+01 1.00e-02 9.44e+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 93.00 166.55 -73.55 1 1.00e+01 1.00e-02 6.88e+01 dihedral pdb=" CB CYS B 199 " pdb=" SG CYS B 199 " pdb=" SG CYS B 212 " pdb=" CB CYS B 212 " ideal model delta sinusoidal sigma weight residual -86.00 -157.79 71.79 1 1.00e+01 1.00e-02 6.60e+01 ... (remaining 6161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1266 0.101 - 0.203: 174 0.203 - 0.304: 20 0.304 - 0.405: 12 0.405 - 0.507: 1 Chirality restraints: 1473 Sorted by residual: chirality pdb=" C1 MAN C 4 " pdb=" O3 BMA C 3 " pdb=" C2 MAN C 4 " pdb=" O5 MAN C 4 " both_signs ideal model delta sigma weight residual False 2.40 2.47 -0.07 2.00e-02 2.50e+03 1.26e+01 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 -2.47 0.07 2.00e-02 2.50e+03 1.13e+01 chirality pdb=" C1 NAG B1502 " pdb=" ND2 ASN B 187 " pdb=" C2 NAG B1502 " pdb=" O5 NAG B1502 " both_signs ideal model delta sigma weight residual False -2.40 -2.91 0.51 2.00e-01 2.50e+01 6.42e+00 ... (remaining 1470 not shown) Planarity restraints: 1748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 187 " 0.058 2.00e-02 2.50e+03 1.19e-01 1.77e+02 pdb=" CG ASN B 187 " -0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN B 187 " 0.064 2.00e-02 2.50e+03 pdb=" ND2 ASN B 187 " -0.215 2.00e-02 2.50e+03 pdb=" C1 NAG B1502 " 0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 469 " -0.101 2.00e-02 2.50e+03 1.16e-01 1.70e+02 pdb=" CG ASN A 469 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN A 469 " 0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN A 469 " 0.192 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 408 " 0.064 2.00e-02 2.50e+03 8.78e-02 9.64e+01 pdb=" CG ASN A 408 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN A 408 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 408 " -0.155 2.00e-02 2.50e+03 pdb=" C1 NAG A1101 " 0.100 2.00e-02 2.50e+03 ... (remaining 1745 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2314 2.83 - 3.35: 8451 3.35 - 3.86: 15566 3.86 - 4.38: 18729 4.38 - 4.90: 30639 Nonbonded interactions: 75699 Sorted by model distance: nonbonded pdb=" OG1 THR A 334 " pdb=" O PHE A 340 " model vdw 2.311 3.040 nonbonded pdb=" OD1 ASP A 581 " pdb=" NZ LYS A 602 " model vdw 2.389 3.120 nonbonded pdb=" O GLN A 298 " pdb=" OG1 THR A 299 " model vdw 2.434 3.040 nonbonded pdb=" CG ASN B 187 " pdb=" O5 NAG B1502 " model vdw 2.443 2.616 nonbonded pdb=" O4 BMA C 3 " pdb=" O6 BMA C 3 " model vdw 2.456 3.040 ... (remaining 75694 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 'D' selection = chain 'E' } 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: 3.370 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: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.620 Find NCS groups from input model: 0.200 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: 0.010 Load rotamer database and sin/cos tables:13.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 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 0.324 9806 Z= 0.827 Angle : 1.637 45.300 13360 Z= 1.038 Chirality : 0.080 0.507 1473 Planarity : 0.008 0.115 1740 Dihedral : 11.949 109.309 3792 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 0.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.24), residues: 1195 helix: -2.59 (0.50), residues: 69 sheet: -1.10 (0.39), residues: 153 loop : 0.45 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.006 TRP B 415 HIS 0.001 0.000 HIS A 545 PHE 0.041 0.002 PHE A 535 TYR 0.051 0.003 TYR B 163 ARG 0.010 0.001 ARG B 487 Details of bonding type rmsd link_NAG-ASN : bond 0.07113 ( 8) link_NAG-ASN : angle 15.69677 ( 24) link_BETA1-4 : bond 0.04047 ( 4) link_BETA1-4 : angle 3.41923 ( 12) link_ALPHA1-3 : bond 0.05225 ( 1) link_ALPHA1-3 : angle 1.86259 ( 3) hydrogen bonds : bond 0.22484 ( 187) hydrogen bonds : angle 8.06506 ( 333) SS BOND : bond 0.04995 ( 50) SS BOND : angle 3.67442 ( 100) covalent geometry : bond 0.01255 ( 9743) covalent geometry : angle 1.46496 (13221) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 PHE cc_start: 0.4206 (p90) cc_final: 0.3542 (p90) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 1.2984 time to fit residues: 202.2031 Evaluate side-chains 55 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 50 optimal weight: 20.0000 chunk 30 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 56 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 chunk 108 optimal weight: 8.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 GLN ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 HIS B 470 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.128744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.088840 restraints weight = 16495.191| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 3.22 r_work: 0.3316 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9806 Z= 0.167 Angle : 0.682 14.275 13360 Z= 0.355 Chirality : 0.048 0.153 1473 Planarity : 0.005 0.039 1740 Dihedral : 7.651 65.326 1571 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.10 % Allowed : 7.14 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.24), residues: 1195 helix: -2.39 (0.47), residues: 95 sheet: -0.79 (0.42), residues: 138 loop : 0.20 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 205 HIS 0.014 0.001 HIS B 564 PHE 0.014 0.002 PHE B 279 TYR 0.014 0.001 TYR B 343 ARG 0.005 0.001 ARG B 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00346 ( 8) link_NAG-ASN : angle 2.54744 ( 24) link_BETA1-4 : bond 0.00225 ( 4) link_BETA1-4 : angle 2.17905 ( 12) link_ALPHA1-3 : bond 0.01004 ( 1) link_ALPHA1-3 : angle 2.69035 ( 3) hydrogen bonds : bond 0.04713 ( 187) hydrogen bonds : angle 6.13094 ( 333) SS BOND : bond 0.00389 ( 50) SS BOND : angle 1.32801 ( 100) covalent geometry : bond 0.00387 ( 9743) covalent geometry : angle 0.66239 (13221) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 53 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASN cc_start: 0.7954 (t0) cc_final: 0.7720 (t0) REVERT: A 158 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7822 (mmp) REVERT: H 181 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8130 (tmtt) REVERT: B 538 GLN cc_start: 0.7774 (pt0) cc_final: 0.6970 (pp30) outliers start: 22 outliers final: 6 residues processed: 69 average time/residue: 1.2464 time to fit residues: 93.0627 Evaluate side-chains 51 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain B residue 272 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 90 optimal weight: 3.9990 chunk 61 optimal weight: 0.3980 chunk 70 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 GLN ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.127595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.087407 restraints weight = 16791.721| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 3.23 r_work: 0.3270 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9806 Z= 0.121 Angle : 0.579 15.198 13360 Z= 0.293 Chirality : 0.046 0.186 1473 Planarity : 0.005 0.041 1740 Dihedral : 6.554 57.384 1571 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.52 % Allowed : 7.62 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.24), residues: 1195 helix: -1.78 (0.55), residues: 82 sheet: -0.70 (0.44), residues: 136 loop : 0.10 (0.20), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 510 HIS 0.005 0.001 HIS B 249 PHE 0.015 0.001 PHE A 543 TYR 0.009 0.001 TYR B 274 ARG 0.005 0.000 ARG B 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 8) link_NAG-ASN : angle 2.10048 ( 24) link_BETA1-4 : bond 0.00626 ( 4) link_BETA1-4 : angle 1.80892 ( 12) link_ALPHA1-3 : bond 0.01128 ( 1) link_ALPHA1-3 : angle 1.62140 ( 3) hydrogen bonds : bond 0.03509 ( 187) hydrogen bonds : angle 5.62082 ( 333) SS BOND : bond 0.00316 ( 50) SS BOND : angle 0.95970 ( 100) covalent geometry : bond 0.00285 ( 9743) covalent geometry : angle 0.56574 (13221) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 1.106 Fit side-chains revert: symmetry clash REVERT: A 490 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7866 (tpp-160) REVERT: H 181 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8239 (tmtt) REVERT: B 238 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8152 (pt0) REVERT: B 538 GLN cc_start: 0.7786 (pt0) cc_final: 0.6991 (pp30) outliers start: 16 outliers final: 6 residues processed: 55 average time/residue: 1.3846 time to fit residues: 82.2514 Evaluate side-chains 49 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 307 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 116 optimal weight: 10.0000 chunk 112 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 35 optimal weight: 0.4980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 HIS B 362 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.124064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.083743 restraints weight = 16580.028| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 3.20 r_work: 0.3210 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9806 Z= 0.162 Angle : 0.608 17.259 13360 Z= 0.299 Chirality : 0.047 0.169 1473 Planarity : 0.005 0.039 1740 Dihedral : 6.069 56.309 1571 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.29 % Allowed : 7.05 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.24), residues: 1195 helix: -1.73 (0.56), residues: 76 sheet: -0.78 (0.44), residues: 138 loop : 0.01 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 521 HIS 0.006 0.001 HIS B 249 PHE 0.015 0.002 PHE A 94 TYR 0.014 0.001 TYR B 274 ARG 0.005 0.000 ARG B 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00349 ( 8) link_NAG-ASN : angle 3.13804 ( 24) link_BETA1-4 : bond 0.00318 ( 4) link_BETA1-4 : angle 1.80635 ( 12) link_ALPHA1-3 : bond 0.01051 ( 1) link_ALPHA1-3 : angle 2.16518 ( 3) hydrogen bonds : bond 0.03675 ( 187) hydrogen bonds : angle 5.56725 ( 333) SS BOND : bond 0.00367 ( 50) SS BOND : angle 0.84136 ( 100) covalent geometry : bond 0.00393 ( 9743) covalent geometry : angle 0.58865 (13221) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 45 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 ASN cc_start: 0.8108 (t0) cc_final: 0.7649 (t0) REVERT: A 490 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7827 (tpp-160) REVERT: H 181 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8268 (tmtt) REVERT: H 186 GLU cc_start: 0.7380 (pm20) cc_final: 0.7014 (pm20) REVERT: B 238 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8178 (pt0) REVERT: B 538 GLN cc_start: 0.7820 (pt0) cc_final: 0.7000 (pp30) outliers start: 24 outliers final: 10 residues processed: 65 average time/residue: 1.2585 time to fit residues: 89.3658 Evaluate side-chains 51 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 198 MET Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 531 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 71 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 33 optimal weight: 0.0770 chunk 43 optimal weight: 0.0370 chunk 76 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 249 HIS B 318 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.124953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.084759 restraints weight = 16539.357| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 3.18 r_work: 0.3227 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9806 Z= 0.112 Angle : 0.550 16.223 13360 Z= 0.272 Chirality : 0.045 0.176 1473 Planarity : 0.004 0.038 1740 Dihedral : 5.582 54.989 1571 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.19 % Allowed : 7.81 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.24), residues: 1195 helix: -1.89 (0.54), residues: 82 sheet: -0.77 (0.45), residues: 138 loop : -0.02 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 205 HIS 0.003 0.001 HIS B 174 PHE 0.010 0.001 PHE A 244 TYR 0.010 0.001 TYR B 274 ARG 0.006 0.000 ARG B 330 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 8) link_NAG-ASN : angle 2.86847 ( 24) link_BETA1-4 : bond 0.00412 ( 4) link_BETA1-4 : angle 1.63981 ( 12) link_ALPHA1-3 : bond 0.01027 ( 1) link_ALPHA1-3 : angle 1.80499 ( 3) hydrogen bonds : bond 0.03255 ( 187) hydrogen bonds : angle 5.41040 ( 333) SS BOND : bond 0.00278 ( 50) SS BOND : angle 1.00607 ( 100) covalent geometry : bond 0.00268 ( 9743) covalent geometry : angle 0.52948 (13221) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 41 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 ASN cc_start: 0.8126 (t0) cc_final: 0.7679 (t0) REVERT: A 490 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7833 (tpp-160) REVERT: H 181 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8277 (tmtt) REVERT: H 186 GLU cc_start: 0.7333 (pm20) cc_final: 0.6990 (pm20) REVERT: B 238 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8162 (pt0) REVERT: B 538 GLN cc_start: 0.7764 (pt0) cc_final: 0.6975 (pp30) outliers start: 23 outliers final: 9 residues processed: 59 average time/residue: 1.1025 time to fit residues: 71.2474 Evaluate side-chains 50 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 531 CYS Chi-restraints excluded: chain B residue 564 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 56 optimal weight: 0.4980 chunk 89 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.2980 chunk 84 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 99 optimal weight: 0.5980 chunk 61 optimal weight: 0.0980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS B 90 GLN B 249 HIS B 318 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.124165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.083873 restraints weight = 16665.602| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 3.16 r_work: 0.3225 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 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 : 0.003 0.034 9806 Z= 0.125 Angle : 0.546 16.201 13360 Z= 0.271 Chirality : 0.045 0.173 1473 Planarity : 0.004 0.038 1740 Dihedral : 5.353 55.549 1571 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.29 % Allowed : 7.71 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.24), residues: 1195 helix: -1.80 (0.55), residues: 82 sheet: -0.87 (0.45), residues: 138 loop : -0.06 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 510 HIS 0.003 0.001 HIS B 174 PHE 0.014 0.001 PHE A 543 TYR 0.016 0.001 TYR A 523 ARG 0.005 0.000 ARG B 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00290 ( 8) link_NAG-ASN : angle 2.64891 ( 24) link_BETA1-4 : bond 0.00363 ( 4) link_BETA1-4 : angle 1.60448 ( 12) link_ALPHA1-3 : bond 0.01001 ( 1) link_ALPHA1-3 : angle 1.66632 ( 3) hydrogen bonds : bond 0.03172 ( 187) hydrogen bonds : angle 5.28053 ( 333) SS BOND : bond 0.00324 ( 50) SS BOND : angle 0.79405 ( 100) covalent geometry : bond 0.00301 ( 9743) covalent geometry : angle 0.53021 (13221) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 45 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: A 124 ASN cc_start: 0.8183 (t0) cc_final: 0.7716 (t0) REVERT: A 490 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7762 (tpp-160) REVERT: A 534 ASN cc_start: 0.7212 (m-40) cc_final: 0.6995 (m-40) REVERT: H 181 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8418 (tmtt) REVERT: H 186 GLU cc_start: 0.7414 (pm20) cc_final: 0.6821 (pm20) REVERT: H 215 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7677 (pm20) REVERT: B 238 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8191 (pt0) REVERT: B 538 GLN cc_start: 0.7771 (pt0) cc_final: 0.6993 (pp30) outliers start: 24 outliers final: 10 residues processed: 64 average time/residue: 1.1872 time to fit residues: 82.5863 Evaluate side-chains 53 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 531 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 41 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 85 optimal weight: 0.4980 chunk 44 optimal weight: 0.0060 chunk 105 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS B 318 HIS ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.124791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.084599 restraints weight = 16684.539| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 3.21 r_work: 0.3226 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9806 Z= 0.096 Angle : 0.530 15.253 13360 Z= 0.263 Chirality : 0.044 0.180 1473 Planarity : 0.004 0.040 1740 Dihedral : 5.154 54.297 1571 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.00 % Allowed : 8.76 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.25), residues: 1195 helix: -1.30 (0.60), residues: 74 sheet: -0.72 (0.47), residues: 133 loop : 0.02 (0.21), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 205 HIS 0.003 0.000 HIS B 249 PHE 0.009 0.001 PHE A 244 TYR 0.012 0.001 TYR A 523 ARG 0.007 0.000 ARG B 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00338 ( 8) link_NAG-ASN : angle 2.41076 ( 24) link_BETA1-4 : bond 0.00404 ( 4) link_BETA1-4 : angle 1.53411 ( 12) link_ALPHA1-3 : bond 0.00891 ( 1) link_ALPHA1-3 : angle 1.55803 ( 3) hydrogen bonds : bond 0.02840 ( 187) hydrogen bonds : angle 5.19523 ( 333) SS BOND : bond 0.00226 ( 50) SS BOND : angle 0.76217 ( 100) covalent geometry : bond 0.00226 ( 9743) covalent geometry : angle 0.51645 (13221) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 45 time to evaluate : 1.152 Fit side-chains revert: symmetry clash REVERT: A 124 ASN cc_start: 0.8149 (t0) cc_final: 0.7678 (t0) REVERT: A 158 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8245 (mmp) REVERT: A 534 ASN cc_start: 0.7301 (m-40) cc_final: 0.7101 (m-40) REVERT: H 181 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8351 (tmtt) REVERT: H 186 GLU cc_start: 0.7657 (pm20) cc_final: 0.7091 (pm20) REVERT: H 209 LEU cc_start: 0.8374 (mp) cc_final: 0.8113 (tp) REVERT: H 215 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7649 (pm20) REVERT: B 538 GLN cc_start: 0.7736 (pt0) cc_final: 0.7037 (pp30) outliers start: 21 outliers final: 10 residues processed: 62 average time/residue: 1.1260 time to fit residues: 76.3614 Evaluate side-chains 53 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 531 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 24 optimal weight: 0.7980 chunk 118 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 0.1980 chunk 92 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS B 318 HIS B 320 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.124467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.084202 restraints weight = 16719.682| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 3.22 r_work: 0.3234 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9806 Z= 0.105 Angle : 0.536 15.675 13360 Z= 0.267 Chirality : 0.045 0.176 1473 Planarity : 0.004 0.039 1740 Dihedral : 5.106 55.046 1571 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.00 % Allowed : 9.05 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.25), residues: 1195 helix: -1.26 (0.60), residues: 74 sheet: -0.68 (0.47), residues: 133 loop : 0.04 (0.21), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 205 HIS 0.003 0.000 HIS B 249 PHE 0.013 0.001 PHE A 543 TYR 0.012 0.001 TYR A 523 ARG 0.005 0.000 ARG B 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00306 ( 8) link_NAG-ASN : angle 2.36785 ( 24) link_BETA1-4 : bond 0.00396 ( 4) link_BETA1-4 : angle 1.52738 ( 12) link_ALPHA1-3 : bond 0.00771 ( 1) link_ALPHA1-3 : angle 1.46297 ( 3) hydrogen bonds : bond 0.02892 ( 187) hydrogen bonds : angle 5.16142 ( 333) SS BOND : bond 0.00251 ( 50) SS BOND : angle 0.89789 ( 100) covalent geometry : bond 0.00254 ( 9743) covalent geometry : angle 0.52130 (13221) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 43 time to evaluate : 1.156 Fit side-chains revert: symmetry clash REVERT: A 124 ASN cc_start: 0.8143 (t0) cc_final: 0.7683 (t0) REVERT: A 158 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8267 (mmp) REVERT: A 319 MET cc_start: 0.7930 (mpt) cc_final: 0.7123 (mpt) REVERT: A 475 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.6512 (mmt-90) REVERT: A 490 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7790 (tpp-160) REVERT: H 181 LYS cc_start: 0.8666 (mmpt) cc_final: 0.8399 (tmtt) REVERT: H 186 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7118 (pm20) REVERT: H 215 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7650 (pm20) REVERT: B 538 GLN cc_start: 0.7733 (pt0) cc_final: 0.7036 (pp30) outliers start: 21 outliers final: 12 residues processed: 61 average time/residue: 1.1926 time to fit residues: 79.2288 Evaluate side-chains 58 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 41 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain H residue 186 GLU Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 531 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 111 optimal weight: 0.2980 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 45 optimal weight: 0.0870 chunk 80 optimal weight: 0.4980 chunk 77 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.125180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.085318 restraints weight = 16536.231| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 3.17 r_work: 0.3241 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9806 Z= 0.088 Angle : 0.518 14.675 13360 Z= 0.258 Chirality : 0.044 0.182 1473 Planarity : 0.004 0.040 1740 Dihedral : 4.907 54.072 1571 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.62 % Allowed : 9.52 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.25), residues: 1195 helix: -1.27 (0.60), residues: 74 sheet: -0.64 (0.48), residues: 133 loop : 0.10 (0.21), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 205 HIS 0.004 0.000 HIS B 249 PHE 0.008 0.001 PHE A 244 TYR 0.012 0.001 TYR A 523 ARG 0.006 0.000 ARG B 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00369 ( 8) link_NAG-ASN : angle 2.21390 ( 24) link_BETA1-4 : bond 0.00411 ( 4) link_BETA1-4 : angle 1.47623 ( 12) link_ALPHA1-3 : bond 0.00704 ( 1) link_ALPHA1-3 : angle 1.42317 ( 3) hydrogen bonds : bond 0.02658 ( 187) hydrogen bonds : angle 5.02395 ( 333) SS BOND : bond 0.00202 ( 50) SS BOND : angle 0.85556 ( 100) covalent geometry : bond 0.00203 ( 9743) covalent geometry : angle 0.50397 (13221) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 2.099 Fit side-chains revert: symmetry clash REVERT: A 124 ASN cc_start: 0.8096 (t0) cc_final: 0.7614 (t0) REVERT: A 158 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8223 (mmp) REVERT: A 475 ARG cc_start: 0.7173 (OUTLIER) cc_final: 0.6526 (mmt-90) REVERT: A 490 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7805 (tpp-160) REVERT: H 181 LYS cc_start: 0.8620 (mmpt) cc_final: 0.8368 (tmtt) REVERT: H 186 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7079 (pm20) REVERT: H 209 LEU cc_start: 0.8454 (mp) cc_final: 0.8137 (tt) REVERT: H 215 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7619 (pm20) REVERT: B 538 GLN cc_start: 0.7711 (pt0) cc_final: 0.7048 (pp30) outliers start: 17 outliers final: 9 residues processed: 58 average time/residue: 1.5943 time to fit residues: 101.1566 Evaluate side-chains 55 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain H residue 186 GLU Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 531 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 70 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 6 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 118 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 249 HIS B 318 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.122922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.082668 restraints weight = 16916.102| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 3.22 r_work: 0.3204 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9806 Z= 0.146 Angle : 0.587 16.872 13360 Z= 0.288 Chirality : 0.046 0.166 1473 Planarity : 0.004 0.037 1740 Dihedral : 5.171 56.277 1571 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.81 % Allowed : 9.81 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.25), residues: 1195 helix: -0.99 (0.63), residues: 68 sheet: -0.66 (0.48), residues: 133 loop : 0.04 (0.21), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 452 HIS 0.005 0.001 HIS B 174 PHE 0.013 0.002 PHE A 543 TYR 0.012 0.001 TYR A 523 ARG 0.014 0.001 ARG A 339 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 8) link_NAG-ASN : angle 2.47893 ( 24) link_BETA1-4 : bond 0.00360 ( 4) link_BETA1-4 : angle 1.55109 ( 12) link_ALPHA1-3 : bond 0.00652 ( 1) link_ALPHA1-3 : angle 1.43616 ( 3) hydrogen bonds : bond 0.03243 ( 187) hydrogen bonds : angle 5.15462 ( 333) SS BOND : bond 0.00335 ( 50) SS BOND : angle 0.92744 ( 100) covalent geometry : bond 0.00359 ( 9743) covalent geometry : angle 0.57262 (13221) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 1.412 Fit side-chains revert: symmetry clash REVERT: A 124 ASN cc_start: 0.8124 (t0) cc_final: 0.7656 (t0) REVERT: A 475 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6484 (mmt-90) REVERT: A 490 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7744 (tpp-160) REVERT: H 181 LYS cc_start: 0.8674 (mmpt) cc_final: 0.8354 (tmtt) REVERT: H 186 GLU cc_start: 0.7622 (pm20) cc_final: 0.7075 (pm20) REVERT: H 215 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7651 (pm20) REVERT: B 538 GLN cc_start: 0.7756 (pt0) cc_final: 0.6954 (pp30) outliers start: 19 outliers final: 12 residues processed: 58 average time/residue: 1.7061 time to fit residues: 108.0031 Evaluate side-chains 55 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 531 CYS Chi-restraints excluded: chain B residue 564 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 48 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS B 318 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.123093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.082898 restraints weight = 16705.711| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 3.21 r_work: 0.3209 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9806 Z= 0.132 Angle : 0.574 16.277 13360 Z= 0.282 Chirality : 0.046 0.169 1473 Planarity : 0.004 0.056 1740 Dihedral : 5.124 55.204 1571 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.90 % Allowed : 9.81 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.25), residues: 1195 helix: -1.07 (0.63), residues: 68 sheet: -0.57 (0.47), residues: 138 loop : 0.03 (0.21), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 205 HIS 0.004 0.001 HIS B 174 PHE 0.010 0.001 PHE A 94 TYR 0.012 0.001 TYR A 523 ARG 0.012 0.000 ARG A 339 Details of bonding type rmsd link_NAG-ASN : bond 0.00294 ( 8) link_NAG-ASN : angle 2.39531 ( 24) link_BETA1-4 : bond 0.00353 ( 4) link_BETA1-4 : angle 1.52815 ( 12) link_ALPHA1-3 : bond 0.00608 ( 1) link_ALPHA1-3 : angle 1.43931 ( 3) hydrogen bonds : bond 0.03109 ( 187) hydrogen bonds : angle 5.14066 ( 333) SS BOND : bond 0.00308 ( 50) SS BOND : angle 0.87720 ( 100) covalent geometry : bond 0.00324 ( 9743) covalent geometry : angle 0.56004 (13221) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7076.47 seconds wall clock time: 125 minutes 18.43 seconds (7518.43 seconds total)